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mahmoodn

vmd-install1

mahmoodn
Mar 5th, 2018
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  1. mahmood@cluster:namd$ ls
  2. plugins tar vmd-1.9.3
  3. mahmood@cluster:namd$ cd plugins/
  4. mahmood@cluster:plugins$ vim Make-arch
  5. mahmood@cluster:plugins$ grep -A 14 LINUXAMD64: Make-arch
  6. LINUXAMD64:
  7. $(MAKE) dynlibs staticlibs bins \
  8. "ARCH = LINUXAMD64" \
  9. "COPTO = -fPIC -m64 -o " \
  10. "LOPTO = -fPIC -m64 -lstdc++ -o " \
  11. "CC = gcc" \
  12. "CXX = g++" \
  13. "DEF = -D" \
  14. "CCFLAGS = -m64 -O2 -fPIC -Wall" \
  15. "CXXFLAGS = -m64 -O2 -fPIC -Wall" \
  16. "AR = ar" \
  17. "NM = nm -p" \
  18. "RANLIB = touch" \
  19. "SHLD = gcc -shared"
  20.  
  21. mahmood@cluster:plugins$ make LINUXAMD64
  22. Building Molecule File Reader plugins
  23. src/periodic_table.h:160: warning: 'get_pte_idx_from_string' defined but not used
  24. src/readpdb.h:187: warning: 'get_pdb_header' defined but not used
  25. src/readpdb.h:207: warning: 'get_pdb_conect' defined but not used
  26. src/readpdb.h:348: warning: 'write_raw_pdb_record' defined but not used
  27. src/vmddir.h:145: warning: 'vmd_file_is_executable' defined but not used
  28. src/periodic_table.h:95: warning: 'get_pte_label' defined but not used
  29. src/periodic_table.h:133: warning: 'get_pte_idx' defined but not used
  30. src/babelplugin.c:319: warning: 'openbabel11type_from_name' defined but not used
  31. src/qmplugin.h:711: warning: 'symmetry_expand' defined but not used
  32. src/qmplugin.h:835: warning: 'eatline' defined but not used
  33. src/qmplugin.h:846: warning: 'eatwhitelines' defined but not used
  34. src/qmplugin.h:895: warning: 'iswhiteline' defined but not used
  35. src/qmplugin.h:901: warning: 'strtoupper' defined but not used
  36. src/qmplugin.h:962: warning: 'goto_keyline' defined but not used
  37. src/qmplugin.h:1006: warning: 'have_keyline' defined but not used
  38. src/qmplugin.h:1077: warning: 'thisline' defined but not used
  39. src/qmplugin.h:1097: warning: 'whereami' defined but not used
  40. src/qmplugin.h:437: warning: 'init_qmdata' defined but not used
  41. src/qmplugin.h:471: warning: 'add_wavefunction' defined but not used
  42. src/qmplugin.h:490: warning: 'replace_wavefunction' defined but not used
  43. src/qmplugin.h:507: warning: 'del_wavefunction' defined but not used
  44. src/qmplugin.h:540: warning: 'angular_momentum_expon' defined but not used
  45. src/qmplugin.h:585: warning: 'print_matrix4' defined but not used
  46. src/qmplugin.h:1028: warning: 'fpexpftoc' defined but not used
  47. src/ccp4plugin.C: In function 'int read_ccp4_data(void*, int, float*, float*)':
  48. src/ccp4plugin.C:490: warning: comparison between signed and unsigned integer expressions
  49. src/ccp4plugin.C:520: warning: comparison between signed and unsigned integer expressions
  50. src/ccp4plugin.C:551: warning: comparison between signed and unsigned integer expressions
  51. src/ccp4plugin.C:583: warning: comparison between signed and unsigned integer expressions
  52. src/ccp4plugin.C:618: warning: comparison between signed and unsigned integer expressions
  53. src/ccp4plugin.C:650: warning: comparison between signed and unsigned integer expressions
  54. src/ccp4plugin.C: In function 'void* open_ccp4_read(const char*, const char*, int*)':
  55. src/ccp4plugin.C:84: warning: 'dataOffset' may be used uninitialized in this function
  56. src/endianswap.h: At global scope:
  57. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  58. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  59. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  60. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  61. src/cpmdplugin.c:84: warning: 'read_cpmd_structure' defined but not used
  62. src/periodic_table.h:133: warning: 'int get_pte_idx(const char*)' defined but not used
  63. src/periodic_table.h:160: warning: 'int get_pte_idx_from_string(const char*)' defined but not used
  64. src/dcdplugin.c: In function 'read_dcdheader':
  65. src/dcdplugin.c:256: warning: dereferencing type-punned pointer will break strict-aliasing rules
  66. src/dcdplugin.c: At top level:
  67. src/fastio.h:459: warning: 'fio_readv' defined but not used
  68. src/fastio.h:605: warning: 'fio_read_int32' defined but not used
  69. src/fastio.h:609: warning: 'fio_write_str' defined but not used
  70. src/endianswap.h:32: warning: 'swap2_unaligned' defined but not used
  71. src/endianswap.h:96: warning: 'swap2_aligned' defined but not used
  72. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  73. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  74. src/endianswap.h:110: warning: 'void swap4_aligned(void*, long int)' defined but not used
  75. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  76. src/fs4plugin.C: In function 'void* open_fs4_read(const char*, const char*, int*)':
  77. src/fs4plugin.C:147: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
  78. src/fs4plugin.C:147: note: initialized from here
  79. src/endianswap.h: At global scope:
  80. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  81. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  82. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  83. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  84. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  85. src/fortread.h:36: warning: 'int fort_eat_recmark(FILE*, int)' defined but not used
  86. src/fortread.h:55: warning: 'int fort_get_endian_reclen(int, int, int, int*, int*)' defined but not used
  87. src/fortread.h:133: warning: 'void strnwscpy(char*, const char*, int)' defined but not used
  88. src/qmplugin.h:895: warning: 'iswhiteline' defined but not used
  89. src/qmplugin.h:901: warning: 'strtoupper' defined but not used
  90. src/qmplugin.h:1077: warning: 'thisline' defined but not used
  91. src/qmplugin.h:1097: warning: 'whereami' defined but not used
  92. src/qmplugin.h:585: warning: 'print_matrix4' defined but not used
  93. src/qmplugin.h:1028: warning: 'fpexpftoc' defined but not used
  94. src/periodic_table.h:95: warning: 'get_pte_label' defined but not used
  95. src/periodic_table.h:102: warning: 'get_pte_mass' defined but not used
  96. src/periodic_table.h:109: warning: 'get_pte_vdw_radius' defined but not used
  97. src/periodic_table.h:133: warning: 'get_pte_idx' defined but not used
  98. src/gamessplugin.c:997: warning: 'print_input_data' defined but not used
  99. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  100. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  101. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  102. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  103. src/endianswap.h: In function 'void* open_grd_read(const char*, const char*, int*)':
  104. src/endianswap.h:117: warning: dereferencing pointer 'N' does break strict-aliasing rules
  105. src/endianswap.h:115: note: initialized from here
  106. src/endianswap.h:117: warning: dereferencing pointer 'N' does break strict-aliasing rules
  107. src/endianswap.h:115: note: initialized from here
  108. src/endianswap.h:117: warning: dereferencing pointer 'N' does break strict-aliasing rules
  109. src/endianswap.h:115: note: initialized from here
  110. src/endianswap.h:117: warning: dereferencing pointer 'N' does break strict-aliasing rules
  111. src/endianswap.h:115: note: initialized from here
  112. src/endianswap.h: At global scope:
  113. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  114. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  115. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  116. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  117. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  118. src/gridplugin.C: In function 'void* open_grid_read(const char*, const char*, int*)':
  119. src/gridplugin.C:104: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
  120. src/gridplugin.C:104: note: initialized from here
  121. src/gridplugin.C:105: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
  122. src/gridplugin.C:105: note: initialized from here
  123. src/gridplugin.C:106: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
  124. src/gridplugin.C:106: note: initialized from here
  125. src/endianswap.h: At global scope:
  126. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  127. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  128. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  129. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  130. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  131. src/fortread.h:36: warning: 'int fort_eat_recmark(FILE*, int)' defined but not used
  132. src/fortread.h:55: warning: 'int fort_get_endian_reclen(int, int, int, int*, int*)' defined but not used
  133. src/fortread.h:133: warning: 'void strnwscpy(char*, const char*, int)' defined but not used
  134. In file included from src/gromacsplugin.C:25:
  135. src/endianswap.h: In function 'int put_trx_real(md_file*, float)':
  136. src/endianswap.h:117: warning: dereferencing pointer 'N' does break strict-aliasing rules
  137. src/endianswap.h:115: note: initialized from here
  138. src/endianswap.h: In function 'int trx_real(md_file*, float*)':
  139. src/endianswap.h:143: warning: dereferencing pointer 'N' does break strict-aliasing rules
  140. src/endianswap.h:135: warning: dereferencing pointer 'N' does break strict-aliasing rules
  141. src/endianswap.h:128: note: initialized from here
  142. src/endianswap.h:144: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
  143. src/endianswap.h:139: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
  144. src/endianswap.h:139: note: initialized from here
  145. src/endianswap.h: At global scope:
  146. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  147. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  148. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  149. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  150. src/jsplugin.c: In function 'js_blockio_check_and_set':
  151. src/jsplugin.c:223: warning: no return statement in function returning non-void
  152. src/jsplugin.c: At top level:
  153. src/fastio.h:459: warning: 'fio_readv' defined but not used
  154. src/hash.c:183: warning: 'hash_delete' defined but not used
  155. src/hash.c:280: warning: 'hash_stats' defined but not used
  156. src/endianswap.h:32: warning: 'swap2_unaligned' defined but not used
  157. src/endianswap.h:46: warning: 'swap4_unaligned' defined but not used
  158. src/endianswap.h:65: warning: 'swap8_unaligned' defined but not used
  159. src/periodic_table.h:95: warning: 'get_pte_label' defined but not used
  160. src/periodic_table.h:160: warning: 'get_pte_idx_from_string' defined but not used
  161. src/hash.c:183: warning: 'hash_delete' defined but not used
  162. src/hash.c:223: warning: 'hash_entries' defined but not used
  163. src/hash.c:280: warning: 'hash_stats' defined but not used
  164. src/inthash.c:182: warning: 'inthash_delete' defined but not used
  165. src/inthash.c:277: warning: 'inthash_stats' defined but not used
  166. src/hash.c:183: warning: 'int hash_delete(hash_t*, const char*)' defined but not used
  167. src/hash.c:223: warning: 'int hash_entries(hash_t*)' defined but not used
  168. src/hash.c:280: warning: 'char* hash_stats(hash_t*)' defined but not used
  169. src/moldenplugin.c: In function 'read_wave_coeffs':
  170. src/moldenplugin.c:1278: warning: format '%s' expects type 'char *', but argument 3 has type 'char (*)[10]'
  171. src/moldenplugin.c: At top level:
  172. src/periodic_table.h:95: warning: 'get_pte_label' defined but not used
  173. src/periodic_table.h:102: warning: 'get_pte_mass' defined but not used
  174. src/periodic_table.h:109: warning: 'get_pte_vdw_radius' defined but not used
  175. src/periodic_table.h:133: warning: 'get_pte_idx' defined but not used
  176. src/qmplugin.h:711: warning: 'symmetry_expand' defined but not used
  177. src/qmplugin.h:1006: warning: 'have_keyline' defined but not used
  178. src/qmplugin.h:1077: warning: 'thisline' defined but not used
  179. src/qmplugin.h:1097: warning: 'whereami' defined but not used
  180. src/qmplugin.h:490: warning: 'replace_wavefunction' defined but not used
  181. src/qmplugin.h:507: warning: 'del_wavefunction' defined but not used
  182. src/qmplugin.h:585: warning: 'print_matrix4' defined but not used
  183. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  184. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  185. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  186. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  187. src/periodic_table.h:133: warning: 'get_pte_idx' defined but not used
  188. src/pdbxplugin.C: In function 'int getUniqueResID(char*, int)':
  189. src/pdbxplugin.C:439: warning: unused variable 'i'
  190. src/pdbxplugin.C: In function 'int parseStructureFaster(molfile_atom_t*, int*, pdbxParser*)':
  191. src/pdbxplugin.C:480: warning: unused variable 'j'
  192. src/pdbxplugin.C:499: warning: unused variable 'oldChain'
  193. src/pdbxplugin.C: In function 'bool readAngleBonds(molfile_atom_t*, pdbxParser*)':
  194. src/pdbxplugin.C:799: warning: unused variable 'bondTable'
  195. src/pdbxplugin.C:803: warning: unused variable 'j'
  196. src/pdbxplugin.C:807: warning: unused variable 'modelNum'
  197. src/pdbxplugin.C:818: warning: unused variable 'atom'
  198. src/pdbxplugin.C:880: warning: unused variable 'test'
  199. src/pdbxplugin.C: In function 'bool readRMSDBonds(molfile_atom_t*, pdbxParser*)':
  200. src/pdbxplugin.C:980: warning: unused variable 'bondTable'
  201. src/pdbxplugin.C:984: warning: unused variable 'j'
  202. src/pdbxplugin.C:987: warning: unused variable 'modelNum'
  203. src/pdbxplugin.C:998: warning: unused variable 'atom'
  204. src/pdbxplugin.C: In function 'void* open_file_write(const char*, const char*, int)':
  205. src/pdbxplugin.C:1405: warning: unused variable 'fd'
  206. src/periodic_table.h: At global scope:
  207. src/periodic_table.h:95: warning: 'const char* get_pte_label(int)' defined but not used
  208. src/periodic_table.h:133: warning: 'int get_pte_idx(const char*)' defined but not used
  209. src/inthash.c:182: warning: 'int inthash_delete(inthash_t*, int)' defined but not used
  210. src/inthash.c:222: warning: 'int inthash_entries(inthash_t*)' defined but not used
  211. src/inthash.c:277: warning: 'char* inthash_stats(inthash_t*)' defined but not used
  212. src/pdbxplugin.C:309: warning: 'float stringToFloat(char*)' defined but not used
  213. src/pltplugin.C: In function 'int read_plt_data(void*, int, float*, float*)':
  214. src/pltplugin.C:138: warning: comparison between signed and unsigned integer expressions
  215. src/endianswap.h: At global scope:
  216. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  217. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  218. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  219. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  220. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  221. In file included from src/plyplugin.C:25:
  222. src/ply.c:43: warning: deprecated conversion from string constant to 'char*'
  223. src/ply.c:43: warning: deprecated conversion from string constant to 'char*'
  224. src/ply.c:43: warning: deprecated conversion from string constant to 'char*'
  225. src/ply.c:43: warning: deprecated conversion from string constant to 'char*'
  226. src/ply.c:43: warning: deprecated conversion from string constant to 'char*'
  227. src/ply.c:43: warning: deprecated conversion from string constant to 'char*'
  228. src/ply.c:43: warning: deprecated conversion from string constant to 'char*'
  229. src/ply.c:43: warning: deprecated conversion from string constant to 'char*'
  230. src/ply.c:43: warning: deprecated conversion from string constant to 'char*'
  231. src/ply.c:48: warning: deprecated conversion from string constant to 'char*'
  232. src/ply.c:48: warning: deprecated conversion from string constant to 'char*'
  233. src/ply.c:48: warning: deprecated conversion from string constant to 'char*'
  234. src/ply.c:48: warning: deprecated conversion from string constant to 'char*'
  235. src/ply.c:48: warning: deprecated conversion from string constant to 'char*'
  236. src/ply.c:48: warning: deprecated conversion from string constant to 'char*'
  237. src/ply.c:48: warning: deprecated conversion from string constant to 'char*'
  238. src/ply.c:48: warning: deprecated conversion from string constant to 'char*'
  239. src/ply.c:48: warning: deprecated conversion from string constant to 'char*'
  240. src/ply.c: In function 'PlyFile* ply_write(FILE*, int, char**, int)':
  241. src/ply.c:146: warning: deprecated conversion from string constant to 'char*'
  242. src/ply.c:157: warning: deprecated conversion from string constant to 'char*'
  243. src/ply.c:159: warning: deprecated conversion from string constant to 'char*'
  244. src/ply.c: In function 'PlyFile* open_for_writing_ply(char*, int, char**, int)':
  245. src/ply.c:199: warning: deprecated conversion from string constant to 'char*'
  246. src/ply.c:191: warning: unused variable 'i'
  247. src/ply.c:193: warning: unused variable 'elem'
  248. src/ply.c: In function 'void element_layout_ply(PlyFile*, char*, int, int, PlyProperty*)':
  249. src/ply.c:259: warning: deprecated conversion from string constant to 'char*'
  250. src/ply.c:260: warning: deprecated conversion from string constant to 'char*'
  251. src/ply.c:263: warning: deprecated conversion from string constant to 'char*'
  252. src/ply.c: In function 'void ply_describe_property(PlyFile*, char*, PlyProperty*)':
  253. src/ply.c:300: warning: deprecated conversion from string constant to 'char*'
  254. src/ply.c:301: warning: deprecated conversion from string constant to 'char*'
  255. src/ply.c:314: warning: deprecated conversion from string constant to 'char*'
  256. src/ply.c: In function 'void element_count_ply(PlyFile*, char*, int)':
  257. src/ply.c:336: warning: unused variable 'i'
  258. src/ply.c:338: warning: unused variable 'prop'
  259. src/ply.c: In function 'void put_element_ply(PlyFile*, void*)':
  260. src/ply.c:462: warning: unused variable 'i'
  261. src/ply.c: In function 'PlyFile* ply_read(FILE*, int*, char***)':
  262. src/ply.c:627: warning: deprecated conversion from string constant to 'char*'
  263. src/ply.c:640: warning: deprecated conversion from string constant to 'char*'
  264. src/ply.c:647: warning: deprecated conversion from string constant to 'char*'
  265. src/ply.c:650: warning: deprecated conversion from string constant to 'char*'
  266. src/ply.c:652: warning: deprecated conversion from string constant to 'char*'
  267. src/ply.c:654: warning: deprecated conversion from string constant to 'char*'
  268. src/ply.c:661: warning: deprecated conversion from string constant to 'char*'
  269. src/ply.c:663: warning: deprecated conversion from string constant to 'char*'
  270. src/ply.c:665: warning: deprecated conversion from string constant to 'char*'
  271. src/ply.c:667: warning: deprecated conversion from string constant to 'char*'
  272. src/ply.c:669: warning: deprecated conversion from string constant to 'char*'
  273. src/ply.c:683: warning: deprecated conversion from string constant to 'char*'
  274. src/ply.c:691: warning: deprecated conversion from string constant to 'char*'
  275. src/ply.c: In function 'PlyFile* ply_open_for_reading(char*, int*, char***, int*, float*)':
  276. src/ply.c:732: warning: deprecated conversion from string constant to 'char*'
  277. src/ply.c: In function 'PlyProperty** get_element_description_ply(PlyFile*, char*, int*, int*)':
  278. src/ply.c:793: warning: deprecated conversion from string constant to 'char*'
  279. src/ply.c:795: warning: deprecated conversion from string constant to 'char*'
  280. src/ply.c: In function 'PlyOtherProp* get_other_properties(PlyFile*, PlyElement*, int)':
  281. src/ply.c:1065: warning: deprecated conversion from string constant to 'char*'
  282. src/ply.c:1076: warning: deprecated conversion from string constant to 'char*'
  283. src/ply.c:1083: warning: deprecated conversion from string constant to 'char*'
  284. src/ply.c: In function 'PlyOtherElems* get_other_element_ply(PlyFile*)':
  285. src/ply.c:1174: warning: deprecated conversion from string constant to 'char*'
  286. src/ply.c:1176: warning: deprecated conversion from string constant to 'char*'
  287. src/ply.c: In function 'int equal_strings(char*, char*)':
  288. src/ply.c:1307: warning: unused variable 'i'
  289. src/ply.c: In function 'void ascii_get_element(PlyFile*, char*)':
  290. src/ply.c:1442: warning: deprecated conversion from string constant to 'char*'
  291. src/ply.c:1492: warning: deprecated conversion from string constant to 'char*'
  292. src/ply.c:1413: warning: unused variable 'i'
  293. src/ply.c:1419: warning: unused variable 'fp'
  294. src/ply.c: In function 'void binary_get_element(PlyFile*, char*)':
  295. src/ply.c:1574: warning: deprecated conversion from string constant to 'char*'
  296. src/ply.c:1615: warning: deprecated conversion from string constant to 'char*'
  297. src/ply.c:1637: warning: deprecated conversion from string constant to 'char*'
  298. src/ply.c:1548: warning: unused variable 'i'
  299. src/ply.c: In function 'char** get_words(FILE*, int*, char**)':
  300. src/ply.c:1709: warning: deprecated conversion from string constant to 'char*'
  301. src/ply.c:1700: warning: unused variable 'i'
  302. src/ply.c:1700: warning: unused variable 'j'
  303. src/ply.c: In function 'void add_element(PlyFile*, char**, int)':
  304. src/ply.c:2255: warning: deprecated conversion from string constant to 'char*'
  305. src/ply.c:2262: warning: deprecated conversion from string constant to 'char*'
  306. src/ply.c: In function 'void add_property(PlyFile*, char**, int)':
  307. src/ply.c:2320: warning: deprecated conversion from string constant to 'char*'
  308. src/ply.c:2322: warning: deprecated conversion from string constant to 'char*'
  309. src/ply.c:2328: warning: deprecated conversion from string constant to 'char*'
  310. src/ply.c:2345: warning: deprecated conversion from string constant to 'char*'
  311. src/ply.c:2313: warning: unused variable 'prop_type'
  312. src/ply.c:2314: warning: unused variable 'count_type'
  313. src/ply.c: In function 'char** get_element_list_ply(PlyFile*, int*)':
  314. src/ply.c:2515: warning: deprecated conversion from string constant to 'char*'
  315. src/ply.c: In function 'void append_comment_ply(PlyFile*, char*)':
  316. src/ply.c:2537: warning: deprecated conversion from string constant to 'char*'
  317. src/ply.c: In function 'void append_obj_info_ply(PlyFile*, char*)':
  318. src/ply.c:2577: warning: deprecated conversion from string constant to 'char*'
  319. src/ply.c: In function 'void describe_element_ply(PlyFile*, char*, int)':
  320. src/ply.c:2762: warning: unused variable 'i'
  321. src/ply.c:2764: warning: unused variable 'prop'
  322. src/ply.c: In function 'void describe_property_ply(PlyFile*, PlyProperty*)':
  323. src/ply.c:2801: warning: deprecated conversion from string constant to 'char*'
  324. src/ply.c:2802: warning: deprecated conversion from string constant to 'char*'
  325. src/ply.c:2815: warning: deprecated conversion from string constant to 'char*'
  326. src/ply.c: In function 'void describe_other_properties_ply(PlyFile*, PlyOtherProp*, int)':
  327. src/ply.c:2849: warning: deprecated conversion from string constant to 'char*'
  328. src/ply.c:2850: warning: deprecated conversion from string constant to 'char*'
  329. src/ply.c:2865: warning: deprecated conversion from string constant to 'char*'
  330. src/ply.c: At global scope:
  331. src/ply.c:2930: warning: missing braces around initializer for 'RuleName'
  332. src/ply.c:2930: warning: missing braces around initializer for 'RuleName'
  333. src/ply.c:2930: warning: missing braces around initializer for 'RuleName'
  334. src/ply.c:2930: warning: missing braces around initializer for 'RuleName'
  335. src/ply.c:2930: warning: missing braces around initializer for 'RuleName'
  336. src/ply.c:2930: warning: missing braces around initializer for 'RuleName'
  337. src/ply.c:2930: warning: missing braces around initializer for 'RuleName'
  338. src/ply.c:2930: warning: deprecated conversion from string constant to 'char*'
  339. src/ply.c:2930: warning: deprecated conversion from string constant to 'char*'
  340. src/ply.c:2930: warning: deprecated conversion from string constant to 'char*'
  341. src/ply.c:2930: warning: deprecated conversion from string constant to 'char*'
  342. src/ply.c:2930: warning: deprecated conversion from string constant to 'char*'
  343. src/ply.c:2930: warning: deprecated conversion from string constant to 'char*'
  344. src/ply.c:2930: warning: deprecated conversion from string constant to 'char*'
  345. src/ply.c: In function 'PlyPropRules* init_rule_ply(PlyFile*, char*)':
  346. src/ply.c:2960: warning: deprecated conversion from string constant to 'char*'
  347. src/ply.c:2962: warning: deprecated conversion from string constant to 'char*'
  348. src/ply.c: In function 'void start_props_ply(PlyFile*, PlyPropRules*)':
  349. src/ply.c:3046: warning: unused variable 'i'
  350. src/ply.c:3047: warning: unused variable 'count'
  351. src/ply.c:3048: warning: unused variable 'elem'
  352. src/ply.c: In function 'void weight_props_ply(PlyFile*, float, void*)':
  353. src/ply.c:3074: warning: deprecated conversion from string constant to 'char*'
  354. src/ply.c:3075: warning: deprecated conversion from string constant to 'char*'
  355. src/ply.c: In function 'void* get_new_props_ply(PlyFile*)':
  356. src/ply.c:3126: warning: deprecated conversion from string constant to 'char*'
  357. src/ply.c:3132: warning: deprecated conversion from string constant to 'char*'
  358. src/plyplugin.C: At global scope:
  359. src/plyplugin.C:44: warning: deprecated conversion from string constant to 'char*'
  360. src/plyplugin.C:44: warning: deprecated conversion from string constant to 'char*'
  361. src/plyplugin.C:56: warning: deprecated conversion from string constant to 'char*'
  362. src/plyplugin.C:56: warning: deprecated conversion from string constant to 'char*'
  363. src/plyplugin.C:56: warning: deprecated conversion from string constant to 'char*'
  364. src/plyplugin.C:56: warning: deprecated conversion from string constant to 'char*'
  365. src/plyplugin.C:56: warning: deprecated conversion from string constant to 'char*'
  366. src/plyplugin.C:56: warning: deprecated conversion from string constant to 'char*'
  367. src/plyplugin.C:56: warning: deprecated conversion from string constant to 'char*'
  368. src/plyplugin.C:56: warning: deprecated conversion from string constant to 'char*'
  369. src/plyplugin.C:56: warning: deprecated conversion from string constant to 'char*'
  370. src/plyplugin.C:63: warning: deprecated conversion from string constant to 'char*'
  371. src/plyplugin.C:63: warning: deprecated conversion from string constant to 'char*'
  372. src/plyplugin.C: In function 'int read_rawgraphics(void*, int*, const molfile_graphics_t**)':
  373. src/plyplugin.C:121: warning: deprecated conversion from string constant to 'char*'
  374. src/plyplugin.C:137: warning: deprecated conversion from string constant to 'char*'
  375. src/plyplugin.C:141: warning: deprecated conversion from string constant to 'char*'
  376. src/plyplugin.C:145: warning: deprecated conversion from string constant to 'char*'
  377. src/plyplugin.C:149: warning: deprecated conversion from string constant to 'char*'
  378. src/plyplugin.C:153: warning: deprecated conversion from string constant to 'char*'
  379. src/plyplugin.C:157: warning: deprecated conversion from string constant to 'char*'
  380. src/plyplugin.C:175: warning: deprecated conversion from string constant to 'char*'
  381. src/plyplugin.C:187: warning: deprecated conversion from string constant to 'char*'
  382. src/plyplugin.C:190: warning: deprecated conversion from string constant to 'char*'
  383. In file included from src/plyplugin.C:25:
  384. src/ply.c: In function 'void ascii_get_element(PlyFile*, char*)':
  385. src/ply.c:1430: warning: 'other_data' may be used uninitialized in this function
  386. src/ply.c:1420: warning: 'item' may be used uninitialized in this function
  387. src/ply.c: In function 'void binary_get_element(PlyFile*, char*)':
  388. src/ply.c:1562: warning: 'other_data' may be used uninitialized in this function
  389. src/ply.c:1553: warning: 'item' may be used uninitialized in this function
  390. src/endianswap.h: At global scope:
  391. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  392. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  393. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  394. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  395. src/endianswap.h:110: warning: 'void swap4_aligned(void*, long int)' defined but not used
  396. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  397. src/endianswap.h:32: warning: 'swap2_unaligned' defined but not used
  398. src/endianswap.h:46: warning: 'swap4_unaligned' defined but not used
  399. src/endianswap.h:65: warning: 'swap8_unaligned' defined but not used
  400. src/endianswap.h:96: warning: 'swap2_aligned' defined but not used
  401. src/endianswap.h:124: warning: 'swap8_aligned' defined but not used
  402. src/fortread.h:36: warning: 'fort_eat_recmark' defined but not used
  403. src/fortread.h:55: warning: 'fort_get_endian_reclen' defined but not used
  404. src/fortread.h:103: warning: 'fortread_4' defined but not used
  405. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  406. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  407. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  408. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  409. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  410. src/uhbdplugin.C: In function 'int read_uhbd_data(void*, int, float*, float*)':
  411. src/uhbdplugin.C:249: warning: comparison between signed and unsigned integer expressions
  412. src/endianswap.h: At global scope:
  413. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  414. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  415. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  416. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  417. src/vaspplugin.h:111: warning: 'vasp_timestep_unitcell' defined but not used
  418. src/periodic_table.h:160: warning: 'get_pte_idx_from_string' defined but not used
  419. src/vaspplugin.h:111: warning: 'vasp_timestep_unitcell' defined but not used
  420. src/periodic_table.h:160: warning: 'get_pte_idx_from_string' defined but not used
  421. src/periodic_table.h:160: warning: 'get_pte_idx_from_string' defined but not used
  422. src/periodic_table.h:160: warning: 'get_pte_idx_from_string' defined but not used
  423. src/periodic_table.h:160: warning: 'get_pte_idx_from_string' defined but not used
  424. ../include/vmdconio.h:56: warning: 'int vmdcon_printf(int, const char*, ...)' defined but not used
  425. src/periodic_table.h:160: warning: 'int get_pte_idx_from_string(const char*)' defined but not used
  426. src/periodic_table.h:160: warning: 'get_pte_idx_from_string' defined but not used
  427. src/vmddir.h:145: warning: 'int vmd_file_is_executable(const char*)' defined but not used
  428. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  429. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  430. src/endianswap.h:110: warning: 'void swap4_aligned(void*, long int)' defined but not used
  431. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  432. src/maeffplugin.cxx: In function 'int<unnamed>::write_structure(void*, int, const molfile_atom_t*)':
  433. src/maeffplugin.cxx:1881: warning: unused variable 'last_ctnumber'
  434. src/periodic_table.h:160: warning: 'get_pte_idx_from_string' defined but not used
  435. src/readpdb.h:187: warning: 'get_pdb_header' defined but not used
  436. src/readpdb.h:207: warning: 'get_pdb_conect' defined but not used
  437. src/readpdb.h:348: warning: 'write_raw_pdb_record' defined but not used
  438. src/vmddir.h:145: warning: 'vmd_file_is_executable' defined but not used
  439. src/periodic_table.h:95: warning: 'get_pte_label' defined but not used
  440. src/periodic_table.h:133: warning: 'get_pte_idx' defined but not used
  441. src/babelplugin.c:319: warning: 'openbabel11type_from_name' defined but not used
  442. src/qmplugin.h:711: warning: 'symmetry_expand' defined but not used
  443. src/qmplugin.h:835: warning: 'eatline' defined but not used
  444. src/qmplugin.h:846: warning: 'eatwhitelines' defined but not used
  445. src/qmplugin.h:895: warning: 'iswhiteline' defined but not used
  446. src/qmplugin.h:901: warning: 'strtoupper' defined but not used
  447. src/qmplugin.h:962: warning: 'goto_keyline' defined but not used
  448. src/qmplugin.h:1006: warning: 'have_keyline' defined but not used
  449. src/qmplugin.h:1077: warning: 'thisline' defined but not used
  450. src/qmplugin.h:1097: warning: 'whereami' defined but not used
  451. src/qmplugin.h:437: warning: 'init_qmdata' defined but not used
  452. src/qmplugin.h:471: warning: 'add_wavefunction' defined but not used
  453. src/qmplugin.h:490: warning: 'replace_wavefunction' defined but not used
  454. src/qmplugin.h:507: warning: 'del_wavefunction' defined but not used
  455. src/qmplugin.h:540: warning: 'angular_momentum_expon' defined but not used
  456. src/qmplugin.h:585: warning: 'print_matrix4' defined but not used
  457. src/qmplugin.h:1028: warning: 'fpexpftoc' defined but not used
  458. src/ccp4plugin.C: In function 'int read_ccp4_data(void*, int, float*, float*)':
  459. src/ccp4plugin.C:490: warning: comparison between signed and unsigned integer expressions
  460. src/ccp4plugin.C:520: warning: comparison between signed and unsigned integer expressions
  461. src/ccp4plugin.C:551: warning: comparison between signed and unsigned integer expressions
  462. src/ccp4plugin.C:583: warning: comparison between signed and unsigned integer expressions
  463. src/ccp4plugin.C:618: warning: comparison between signed and unsigned integer expressions
  464. src/ccp4plugin.C:650: warning: comparison between signed and unsigned integer expressions
  465. src/ccp4plugin.C: In function 'void* open_ccp4_read(const char*, const char*, int*)':
  466. src/ccp4plugin.C:84: warning: 'dataOffset' may be used uninitialized in this function
  467. src/endianswap.h: At global scope:
  468. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  469. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  470. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  471. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  472. src/cpmdplugin.c:84: warning: 'read_cpmd_structure' defined but not used
  473. src/periodic_table.h:133: warning: 'int get_pte_idx(const char*)' defined but not used
  474. src/periodic_table.h:160: warning: 'int get_pte_idx_from_string(const char*)' defined but not used
  475. src/dcdplugin.c: In function 'read_dcdheader':
  476. src/dcdplugin.c:256: warning: dereferencing type-punned pointer will break strict-aliasing rules
  477. src/dcdplugin.c: At top level:
  478. src/fastio.h:459: warning: 'fio_readv' defined but not used
  479. src/fastio.h:605: warning: 'fio_read_int32' defined but not used
  480. src/fastio.h:609: warning: 'fio_write_str' defined but not used
  481. src/endianswap.h:32: warning: 'swap2_unaligned' defined but not used
  482. src/endianswap.h:96: warning: 'swap2_aligned' defined but not used
  483. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  484. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  485. src/endianswap.h:110: warning: 'void swap4_aligned(void*, long int)' defined but not used
  486. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  487. src/fs4plugin.C: In function 'void* open_fs4_read(const char*, const char*, int*)':
  488. src/fs4plugin.C:147: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
  489. src/fs4plugin.C:147: note: initialized from here
  490. src/endianswap.h: At global scope:
  491. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  492. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  493. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  494. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  495. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  496. src/fortread.h:36: warning: 'int fort_eat_recmark(FILE*, int)' defined but not used
  497. src/fortread.h:55: warning: 'int fort_get_endian_reclen(int, int, int, int*, int*)' defined but not used
  498. src/fortread.h:133: warning: 'void strnwscpy(char*, const char*, int)' defined but not used
  499. src/qmplugin.h:895: warning: 'iswhiteline' defined but not used
  500. src/qmplugin.h:901: warning: 'strtoupper' defined but not used
  501. src/qmplugin.h:1077: warning: 'thisline' defined but not used
  502. src/qmplugin.h:1097: warning: 'whereami' defined but not used
  503. src/qmplugin.h:585: warning: 'print_matrix4' defined but not used
  504. src/qmplugin.h:1028: warning: 'fpexpftoc' defined but not used
  505. src/periodic_table.h:95: warning: 'get_pte_label' defined but not used
  506. src/periodic_table.h:102: warning: 'get_pte_mass' defined but not used
  507. src/periodic_table.h:109: warning: 'get_pte_vdw_radius' defined but not used
  508. src/periodic_table.h:133: warning: 'get_pte_idx' defined but not used
  509. src/gamessplugin.c:997: warning: 'print_input_data' defined but not used
  510. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  511. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  512. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  513. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  514. src/endianswap.h: In function 'void* open_grd_read(const char*, const char*, int*)':
  515. src/endianswap.h:117: warning: dereferencing pointer 'N' does break strict-aliasing rules
  516. src/endianswap.h:115: note: initialized from here
  517. src/endianswap.h:117: warning: dereferencing pointer 'N' does break strict-aliasing rules
  518. src/endianswap.h:115: note: initialized from here
  519. src/endianswap.h:117: warning: dereferencing pointer 'N' does break strict-aliasing rules
  520. src/endianswap.h:115: note: initialized from here
  521. src/endianswap.h:117: warning: dereferencing pointer 'N' does break strict-aliasing rules
  522. src/endianswap.h:115: note: initialized from here
  523. src/endianswap.h: At global scope:
  524. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  525. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  526. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  527. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  528. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  529. src/gridplugin.C: In function 'void* open_grid_read(const char*, const char*, int*)':
  530. src/gridplugin.C:104: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
  531. src/gridplugin.C:104: note: initialized from here
  532. src/gridplugin.C:105: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
  533. src/gridplugin.C:105: note: initialized from here
  534. src/gridplugin.C:106: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
  535. src/gridplugin.C:106: note: initialized from here
  536. src/endianswap.h: At global scope:
  537. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  538. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  539. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  540. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  541. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  542. src/fortread.h:36: warning: 'int fort_eat_recmark(FILE*, int)' defined but not used
  543. src/fortread.h:55: warning: 'int fort_get_endian_reclen(int, int, int, int*, int*)' defined but not used
  544. src/fortread.h:133: warning: 'void strnwscpy(char*, const char*, int)' defined but not used
  545. In file included from src/gromacsplugin.C:25:
  546. src/endianswap.h: In function 'int put_trx_real(md_file*, float)':
  547. src/endianswap.h:117: warning: dereferencing pointer 'N' does break strict-aliasing rules
  548. src/endianswap.h:115: note: initialized from here
  549. src/endianswap.h: In function 'int trx_real(md_file*, float*)':
  550. src/endianswap.h:143: warning: dereferencing pointer 'N' does break strict-aliasing rules
  551. src/endianswap.h:135: warning: dereferencing pointer 'N' does break strict-aliasing rules
  552. src/endianswap.h:128: note: initialized from here
  553. src/endianswap.h:144: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
  554. src/endianswap.h:139: warning: dereferencing pointer '<anonymous>' does break strict-aliasing rules
  555. src/endianswap.h:139: note: initialized from here
  556. src/endianswap.h: At global scope:
  557. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  558. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  559. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  560. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  561. src/jsplugin.c: In function 'js_blockio_check_and_set':
  562. src/jsplugin.c:223: warning: no return statement in function returning non-void
  563. src/jsplugin.c: At top level:
  564. src/fastio.h:459: warning: 'fio_readv' defined but not used
  565. src/hash.c:183: warning: 'hash_delete' defined but not used
  566. src/hash.c:280: warning: 'hash_stats' defined but not used
  567. src/endianswap.h:32: warning: 'swap2_unaligned' defined but not used
  568. src/endianswap.h:46: warning: 'swap4_unaligned' defined but not used
  569. src/endianswap.h:65: warning: 'swap8_unaligned' defined but not used
  570. src/periodic_table.h:95: warning: 'get_pte_label' defined but not used
  571. src/periodic_table.h:160: warning: 'get_pte_idx_from_string' defined but not used
  572. src/hash.c:183: warning: 'hash_delete' defined but not used
  573. src/hash.c:223: warning: 'hash_entries' defined but not used
  574. src/hash.c:280: warning: 'hash_stats' defined but not used
  575. src/inthash.c:182: warning: 'inthash_delete' defined but not used
  576. src/inthash.c:277: warning: 'inthash_stats' defined but not used
  577. src/hash.c:183: warning: 'int hash_delete(hash_t*, const char*)' defined but not used
  578. src/hash.c:223: warning: 'int hash_entries(hash_t*)' defined but not used
  579. src/hash.c:280: warning: 'char* hash_stats(hash_t*)' defined but not used
  580. src/moldenplugin.c: In function 'read_wave_coeffs':
  581. src/moldenplugin.c:1278: warning: format '%s' expects type 'char *', but argument 3 has type 'char (*)[10]'
  582. src/moldenplugin.c: At top level:
  583. src/periodic_table.h:95: warning: 'get_pte_label' defined but not used
  584. src/periodic_table.h:102: warning: 'get_pte_mass' defined but not used
  585. src/periodic_table.h:109: warning: 'get_pte_vdw_radius' defined but not used
  586. src/periodic_table.h:133: warning: 'get_pte_idx' defined but not used
  587. src/qmplugin.h:711: warning: 'symmetry_expand' defined but not used
  588. src/qmplugin.h:1006: warning: 'have_keyline' defined but not used
  589. src/qmplugin.h:1077: warning: 'thisline' defined but not used
  590. src/qmplugin.h:1097: warning: 'whereami' defined but not used
  591. src/qmplugin.h:490: warning: 'replace_wavefunction' defined but not used
  592. src/qmplugin.h:507: warning: 'del_wavefunction' defined but not used
  593. src/qmplugin.h:585: warning: 'print_matrix4' defined but not used
  594. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  595. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  596. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  597. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  598. src/periodic_table.h:133: warning: 'get_pte_idx' defined but not used
  599. src/pdbxplugin.C: In function 'int getUniqueResID(char*, int)':
  600. src/pdbxplugin.C:439: warning: unused variable 'i'
  601. src/pdbxplugin.C: In function 'int parseStructureFaster(molfile_atom_t*, int*, pdbxParser*)':
  602. src/pdbxplugin.C:480: warning: unused variable 'j'
  603. src/pdbxplugin.C:499: warning: unused variable 'oldChain'
  604. src/pdbxplugin.C: In function 'bool readAngleBonds(molfile_atom_t*, pdbxParser*)':
  605. src/pdbxplugin.C:799: warning: unused variable 'bondTable'
  606. src/pdbxplugin.C:803: warning: unused variable 'j'
  607. src/pdbxplugin.C:807: warning: unused variable 'modelNum'
  608. src/pdbxplugin.C:818: warning: unused variable 'atom'
  609. src/pdbxplugin.C:880: warning: unused variable 'test'
  610. src/pdbxplugin.C: In function 'bool readRMSDBonds(molfile_atom_t*, pdbxParser*)':
  611. src/pdbxplugin.C:980: warning: unused variable 'bondTable'
  612. src/pdbxplugin.C:984: warning: unused variable 'j'
  613. src/pdbxplugin.C:987: warning: unused variable 'modelNum'
  614. src/pdbxplugin.C:998: warning: unused variable 'atom'
  615. src/pdbxplugin.C: In function 'void* open_file_write(const char*, const char*, int)':
  616. src/pdbxplugin.C:1405: warning: unused variable 'fd'
  617. src/periodic_table.h: At global scope:
  618. src/periodic_table.h:95: warning: 'const char* get_pte_label(int)' defined but not used
  619. src/periodic_table.h:133: warning: 'int get_pte_idx(const char*)' defined but not used
  620. src/inthash.c:182: warning: 'int inthash_delete(inthash_t*, int)' defined but not used
  621. src/inthash.c:222: warning: 'int inthash_entries(inthash_t*)' defined but not used
  622. src/inthash.c:277: warning: 'char* inthash_stats(inthash_t*)' defined but not used
  623. src/pdbxplugin.C:309: warning: 'float stringToFloat(char*)' defined but not used
  624. src/pltplugin.C: In function 'int read_plt_data(void*, int, float*, float*)':
  625. src/pltplugin.C:138: warning: comparison between signed and unsigned integer expressions
  626. src/endianswap.h: At global scope:
  627. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  628. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  629. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  630. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  631. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  632. In file included from src/plyplugin.C:25:
  633. src/ply.c:43: warning: deprecated conversion from string constant to 'char*'
  634. src/ply.c:43: warning: deprecated conversion from string constant to 'char*'
  635. src/ply.c:43: warning: deprecated conversion from string constant to 'char*'
  636. src/ply.c:43: warning: deprecated conversion from string constant to 'char*'
  637. src/ply.c:43: warning: deprecated conversion from string constant to 'char*'
  638. src/ply.c:43: warning: deprecated conversion from string constant to 'char*'
  639. src/ply.c:43: warning: deprecated conversion from string constant to 'char*'
  640. src/ply.c:43: warning: deprecated conversion from string constant to 'char*'
  641. src/ply.c:43: warning: deprecated conversion from string constant to 'char*'
  642. src/ply.c:48: warning: deprecated conversion from string constant to 'char*'
  643. src/ply.c:48: warning: deprecated conversion from string constant to 'char*'
  644. src/ply.c:48: warning: deprecated conversion from string constant to 'char*'
  645. src/ply.c:48: warning: deprecated conversion from string constant to 'char*'
  646. src/ply.c:48: warning: deprecated conversion from string constant to 'char*'
  647. src/ply.c:48: warning: deprecated conversion from string constant to 'char*'
  648. src/ply.c:48: warning: deprecated conversion from string constant to 'char*'
  649. src/ply.c:48: warning: deprecated conversion from string constant to 'char*'
  650. src/ply.c:48: warning: deprecated conversion from string constant to 'char*'
  651. src/ply.c: In function 'PlyFile* ply_write(FILE*, int, char**, int)':
  652. src/ply.c:146: warning: deprecated conversion from string constant to 'char*'
  653. src/ply.c:157: warning: deprecated conversion from string constant to 'char*'
  654. src/ply.c:159: warning: deprecated conversion from string constant to 'char*'
  655. src/ply.c: In function 'PlyFile* open_for_writing_ply(char*, int, char**, int)':
  656. src/ply.c:199: warning: deprecated conversion from string constant to 'char*'
  657. src/ply.c:191: warning: unused variable 'i'
  658. src/ply.c:193: warning: unused variable 'elem'
  659. src/ply.c: In function 'void element_layout_ply(PlyFile*, char*, int, int, PlyProperty*)':
  660. src/ply.c:259: warning: deprecated conversion from string constant to 'char*'
  661. src/ply.c:260: warning: deprecated conversion from string constant to 'char*'
  662. src/ply.c:263: warning: deprecated conversion from string constant to 'char*'
  663. src/ply.c: In function 'void ply_describe_property(PlyFile*, char*, PlyProperty*)':
  664. src/ply.c:300: warning: deprecated conversion from string constant to 'char*'
  665. src/ply.c:301: warning: deprecated conversion from string constant to 'char*'
  666. src/ply.c:314: warning: deprecated conversion from string constant to 'char*'
  667. src/ply.c: In function 'void element_count_ply(PlyFile*, char*, int)':
  668. src/ply.c:336: warning: unused variable 'i'
  669. src/ply.c:338: warning: unused variable 'prop'
  670. src/ply.c: In function 'void put_element_ply(PlyFile*, void*)':
  671. src/ply.c:462: warning: unused variable 'i'
  672. src/ply.c: In function 'PlyFile* ply_read(FILE*, int*, char***)':
  673. src/ply.c:627: warning: deprecated conversion from string constant to 'char*'
  674. src/ply.c:640: warning: deprecated conversion from string constant to 'char*'
  675. src/ply.c:647: warning: deprecated conversion from string constant to 'char*'
  676. src/ply.c:650: warning: deprecated conversion from string constant to 'char*'
  677. src/ply.c:652: warning: deprecated conversion from string constant to 'char*'
  678. src/ply.c:654: warning: deprecated conversion from string constant to 'char*'
  679. src/ply.c:661: warning: deprecated conversion from string constant to 'char*'
  680. src/ply.c:663: warning: deprecated conversion from string constant to 'char*'
  681. src/ply.c:665: warning: deprecated conversion from string constant to 'char*'
  682. src/ply.c:667: warning: deprecated conversion from string constant to 'char*'
  683. src/ply.c:669: warning: deprecated conversion from string constant to 'char*'
  684. src/ply.c:683: warning: deprecated conversion from string constant to 'char*'
  685. src/ply.c:691: warning: deprecated conversion from string constant to 'char*'
  686. src/ply.c: In function 'PlyFile* ply_open_for_reading(char*, int*, char***, int*, float*)':
  687. src/ply.c:732: warning: deprecated conversion from string constant to 'char*'
  688. src/ply.c: In function 'PlyProperty** get_element_description_ply(PlyFile*, char*, int*, int*)':
  689. src/ply.c:793: warning: deprecated conversion from string constant to 'char*'
  690. src/ply.c:795: warning: deprecated conversion from string constant to 'char*'
  691. src/ply.c: In function 'PlyOtherProp* get_other_properties(PlyFile*, PlyElement*, int)':
  692. src/ply.c:1065: warning: deprecated conversion from string constant to 'char*'
  693. src/ply.c:1076: warning: deprecated conversion from string constant to 'char*'
  694. src/ply.c:1083: warning: deprecated conversion from string constant to 'char*'
  695. src/ply.c: In function 'PlyOtherElems* get_other_element_ply(PlyFile*)':
  696. src/ply.c:1174: warning: deprecated conversion from string constant to 'char*'
  697. src/ply.c:1176: warning: deprecated conversion from string constant to 'char*'
  698. src/ply.c: In function 'int equal_strings(char*, char*)':
  699. src/ply.c:1307: warning: unused variable 'i'
  700. src/ply.c: In function 'void ascii_get_element(PlyFile*, char*)':
  701. src/ply.c:1442: warning: deprecated conversion from string constant to 'char*'
  702. src/ply.c:1492: warning: deprecated conversion from string constant to 'char*'
  703. src/ply.c:1413: warning: unused variable 'i'
  704. src/ply.c:1419: warning: unused variable 'fp'
  705. src/ply.c: In function 'void binary_get_element(PlyFile*, char*)':
  706. src/ply.c:1574: warning: deprecated conversion from string constant to 'char*'
  707. src/ply.c:1615: warning: deprecated conversion from string constant to 'char*'
  708. src/ply.c:1637: warning: deprecated conversion from string constant to 'char*'
  709. src/ply.c:1548: warning: unused variable 'i'
  710. src/ply.c: In function 'char** get_words(FILE*, int*, char**)':
  711. src/ply.c:1709: warning: deprecated conversion from string constant to 'char*'
  712. src/ply.c:1700: warning: unused variable 'i'
  713. src/ply.c:1700: warning: unused variable 'j'
  714. src/ply.c: In function 'void add_element(PlyFile*, char**, int)':
  715. src/ply.c:2255: warning: deprecated conversion from string constant to 'char*'
  716. src/ply.c:2262: warning: deprecated conversion from string constant to 'char*'
  717. src/ply.c: In function 'void add_property(PlyFile*, char**, int)':
  718. src/ply.c:2320: warning: deprecated conversion from string constant to 'char*'
  719. src/ply.c:2322: warning: deprecated conversion from string constant to 'char*'
  720. src/ply.c:2328: warning: deprecated conversion from string constant to 'char*'
  721. src/ply.c:2345: warning: deprecated conversion from string constant to 'char*'
  722. src/ply.c:2313: warning: unused variable 'prop_type'
  723. src/ply.c:2314: warning: unused variable 'count_type'
  724. src/ply.c: In function 'char** get_element_list_ply(PlyFile*, int*)':
  725. src/ply.c:2515: warning: deprecated conversion from string constant to 'char*'
  726. src/ply.c: In function 'void append_comment_ply(PlyFile*, char*)':
  727. src/ply.c:2537: warning: deprecated conversion from string constant to 'char*'
  728. src/ply.c: In function 'void append_obj_info_ply(PlyFile*, char*)':
  729. src/ply.c:2577: warning: deprecated conversion from string constant to 'char*'
  730. src/ply.c: In function 'void describe_element_ply(PlyFile*, char*, int)':
  731. src/ply.c:2762: warning: unused variable 'i'
  732. src/ply.c:2764: warning: unused variable 'prop'
  733. src/ply.c: In function 'void describe_property_ply(PlyFile*, PlyProperty*)':
  734. src/ply.c:2801: warning: deprecated conversion from string constant to 'char*'
  735. src/ply.c:2802: warning: deprecated conversion from string constant to 'char*'
  736. src/ply.c:2815: warning: deprecated conversion from string constant to 'char*'
  737. src/ply.c: In function 'void describe_other_properties_ply(PlyFile*, PlyOtherProp*, int)':
  738. src/ply.c:2849: warning: deprecated conversion from string constant to 'char*'
  739. src/ply.c:2850: warning: deprecated conversion from string constant to 'char*'
  740. src/ply.c:2865: warning: deprecated conversion from string constant to 'char*'
  741. src/ply.c: At global scope:
  742. src/ply.c:2930: warning: missing braces around initializer for 'RuleName'
  743. src/ply.c:2930: warning: missing braces around initializer for 'RuleName'
  744. src/ply.c:2930: warning: missing braces around initializer for 'RuleName'
  745. src/ply.c:2930: warning: missing braces around initializer for 'RuleName'
  746. src/ply.c:2930: warning: missing braces around initializer for 'RuleName'
  747. src/ply.c:2930: warning: missing braces around initializer for 'RuleName'
  748. src/ply.c:2930: warning: missing braces around initializer for 'RuleName'
  749. src/ply.c:2930: warning: deprecated conversion from string constant to 'char*'
  750. src/ply.c:2930: warning: deprecated conversion from string constant to 'char*'
  751. src/ply.c:2930: warning: deprecated conversion from string constant to 'char*'
  752. src/ply.c:2930: warning: deprecated conversion from string constant to 'char*'
  753. src/ply.c:2930: warning: deprecated conversion from string constant to 'char*'
  754. src/ply.c:2930: warning: deprecated conversion from string constant to 'char*'
  755. src/ply.c:2930: warning: deprecated conversion from string constant to 'char*'
  756. src/ply.c: In function 'PlyPropRules* init_rule_ply(PlyFile*, char*)':
  757. src/ply.c:2960: warning: deprecated conversion from string constant to 'char*'
  758. src/ply.c:2962: warning: deprecated conversion from string constant to 'char*'
  759. src/ply.c: In function 'void start_props_ply(PlyFile*, PlyPropRules*)':
  760. src/ply.c:3046: warning: unused variable 'i'
  761. src/ply.c:3047: warning: unused variable 'count'
  762. src/ply.c:3048: warning: unused variable 'elem'
  763. src/ply.c: In function 'void weight_props_ply(PlyFile*, float, void*)':
  764. src/ply.c:3074: warning: deprecated conversion from string constant to 'char*'
  765. src/ply.c:3075: warning: deprecated conversion from string constant to 'char*'
  766. src/ply.c: In function 'void* get_new_props_ply(PlyFile*)':
  767. src/ply.c:3126: warning: deprecated conversion from string constant to 'char*'
  768. src/ply.c:3132: warning: deprecated conversion from string constant to 'char*'
  769. src/plyplugin.C: At global scope:
  770. src/plyplugin.C:44: warning: deprecated conversion from string constant to 'char*'
  771. src/plyplugin.C:44: warning: deprecated conversion from string constant to 'char*'
  772. src/plyplugin.C:56: warning: deprecated conversion from string constant to 'char*'
  773. src/plyplugin.C:56: warning: deprecated conversion from string constant to 'char*'
  774. src/plyplugin.C:56: warning: deprecated conversion from string constant to 'char*'
  775. src/plyplugin.C:56: warning: deprecated conversion from string constant to 'char*'
  776. src/plyplugin.C:56: warning: deprecated conversion from string constant to 'char*'
  777. src/plyplugin.C:56: warning: deprecated conversion from string constant to 'char*'
  778. src/plyplugin.C:56: warning: deprecated conversion from string constant to 'char*'
  779. src/plyplugin.C:56: warning: deprecated conversion from string constant to 'char*'
  780. src/plyplugin.C:56: warning: deprecated conversion from string constant to 'char*'
  781. src/plyplugin.C:63: warning: deprecated conversion from string constant to 'char*'
  782. src/plyplugin.C:63: warning: deprecated conversion from string constant to 'char*'
  783. src/plyplugin.C: In function 'int read_rawgraphics(void*, int*, const molfile_graphics_t**)':
  784. src/plyplugin.C:121: warning: deprecated conversion from string constant to 'char*'
  785. src/plyplugin.C:137: warning: deprecated conversion from string constant to 'char*'
  786. src/plyplugin.C:141: warning: deprecated conversion from string constant to 'char*'
  787. src/plyplugin.C:145: warning: deprecated conversion from string constant to 'char*'
  788. src/plyplugin.C:149: warning: deprecated conversion from string constant to 'char*'
  789. src/plyplugin.C:153: warning: deprecated conversion from string constant to 'char*'
  790. src/plyplugin.C:157: warning: deprecated conversion from string constant to 'char*'
  791. src/plyplugin.C:175: warning: deprecated conversion from string constant to 'char*'
  792. src/plyplugin.C:187: warning: deprecated conversion from string constant to 'char*'
  793. src/plyplugin.C:190: warning: deprecated conversion from string constant to 'char*'
  794. In file included from src/plyplugin.C:25:
  795. src/ply.c: In function 'void ascii_get_element(PlyFile*, char*)':
  796. src/ply.c:1430: warning: 'other_data' may be used uninitialized in this function
  797. src/ply.c:1420: warning: 'item' may be used uninitialized in this function
  798. src/ply.c: In function 'void binary_get_element(PlyFile*, char*)':
  799. src/ply.c:1562: warning: 'other_data' may be used uninitialized in this function
  800. src/ply.c:1553: warning: 'item' may be used uninitialized in this function
  801. src/endianswap.h: At global scope:
  802. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  803. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  804. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  805. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  806. src/endianswap.h:110: warning: 'void swap4_aligned(void*, long int)' defined but not used
  807. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  808. src/endianswap.h:32: warning: 'swap2_unaligned' defined but not used
  809. src/endianswap.h:46: warning: 'swap4_unaligned' defined but not used
  810. src/endianswap.h:65: warning: 'swap8_unaligned' defined but not used
  811. src/endianswap.h:96: warning: 'swap2_aligned' defined but not used
  812. src/endianswap.h:124: warning: 'swap8_aligned' defined but not used
  813. src/fortread.h:36: warning: 'fort_eat_recmark' defined but not used
  814. src/fortread.h:55: warning: 'fort_get_endian_reclen' defined but not used
  815. src/fortread.h:103: warning: 'fortread_4' defined but not used
  816. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  817. src/endianswap.h:46: warning: 'void swap4_unaligned(void*, long int)' defined but not used
  818. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  819. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  820. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  821. src/uhbdplugin.C: In function 'int read_uhbd_data(void*, int, float*, float*)':
  822. src/uhbdplugin.C:249: warning: comparison between signed and unsigned integer expressions
  823. src/endianswap.h: At global scope:
  824. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  825. src/endianswap.h:65: warning: 'void swap8_unaligned(void*, long int)' defined but not used
  826. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  827. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  828. src/vaspplugin.h:111: warning: 'vasp_timestep_unitcell' defined but not used
  829. src/periodic_table.h:160: warning: 'get_pte_idx_from_string' defined but not used
  830. src/vaspplugin.h:111: warning: 'vasp_timestep_unitcell' defined but not used
  831. src/periodic_table.h:160: warning: 'get_pte_idx_from_string' defined but not used
  832. src/periodic_table.h:160: warning: 'get_pte_idx_from_string' defined but not used
  833. src/periodic_table.h:160: warning: 'get_pte_idx_from_string' defined but not used
  834. src/periodic_table.h:160: warning: 'get_pte_idx_from_string' defined but not used
  835. ../include/vmdconio.h:56: warning: 'int vmdcon_printf(int, const char*, ...)' defined but not used
  836. src/periodic_table.h:160: warning: 'int get_pte_idx_from_string(const char*)' defined but not used
  837. src/periodic_table.h:160: warning: 'get_pte_idx_from_string' defined but not used
  838. src/vmddir.h:145: warning: 'int vmd_file_is_executable(const char*)' defined but not used
  839. src/endianswap.h:32: warning: 'void swap2_unaligned(void*, long int)' defined but not used
  840. src/endianswap.h:96: warning: 'void swap2_aligned(void*, long int)' defined but not used
  841. src/endianswap.h:110: warning: 'void swap4_aligned(void*, long int)' defined but not used
  842. src/endianswap.h:124: warning: 'void swap8_aligned(void*, long int)' defined but not used
  843. src/maeffplugin.cxx: In function 'int<unnamed>::write_structure(void*, int, const molfile_atom_t*)':
  844. src/maeffplugin.cxx:1881: warning: unused variable 'last_ctnumber'
  845. ./mgpot_cubic.c: In function 'mgpot_longrng_cubic':
  846. ./mgpot_cubic.c:48: warning: unused variable 'bench_latcut_gpu'
  847. src/analyze.c: In function 'bp_analyze':
  848. src/analyze.c:117: warning: format '%4d' expects type 'int', but argument 2 has type 'long int'
  849. src/fpair.c: In function 'all_pairs':
  850. src/fpair.c:139: warning: format '%d' expects type 'int', but argument 3 has type 'long int'
  851. src/fpair.c:139: warning: format '%d' expects type 'int', but argument 4 has type 'long int'
  852. src/fpair.c:198: warning: format '%5d' expects type 'int', but argument 5 has type 'long int'
  853. src/fpair.c:198: warning: format '%5d' expects type 'int', but argument 8 has type 'long int'
  854. src/fpair.c:223: warning: format '%5d' expects type 'int', but argument 5 has type 'long int'
  855. src/fpair.c:223: warning: format '%5d' expects type 'int', but argument 8 has type 'long int'
  856. src/fpair.c:251: warning: format '%5d' expects type 'int', but argument 5 has type 'long int'
  857. src/fpair.c:251: warning: format '%5d' expects type 'int', but argument 8 has type 'long int'
  858. src/fpair.c:293: warning: format '%5d' expects type 'int', but argument 5 has type 'long int'
  859. src/fpair.c:293: warning: format '%5d' expects type 'int', but argument 8 has type 'long int'
  860. src/fpair.c:308: warning: format '%d' expects type 'int', but argument 2 has type 'long int'
  861. src/fpair.c:338: warning: format '%d' expects type 'int', but argument 3 has type 'long int'
  862. src/fpair.c:338: warning: format '%d' expects type 'int', but argument 4 has type 'long int'
  863. src/fpair.c:351: warning: format '%5d' expects type 'int', but argument 5 has type 'long int'
  864. src/fpair.c:351: warning: format '%5d' expects type 'int', but argument 8 has type 'long int'
  865. src/fpair.c:409: warning: format '%5d' expects type 'int', but argument 5 has type 'long int'
  866. src/fpair.c:409: warning: format '%5d' expects type 'int', but argument 8 has type 'long int'
  867. src/fpair.c:431: warning: format '%5d' expects type 'int', but argument 5 has type 'long int'
  868. src/fpair.c:431: warning: format '%5d' expects type 'int', but argument 8 has type 'long int'
  869. src/fpair.c:454: warning: format '%5d' expects type 'int', but argument 5 has type 'long int'
  870. src/fpair.c:454: warning: format '%5d' expects type 'int', but argument 8 has type 'long int'
  871. src/fpair.c: In function 'best_pair':
  872. src/fpair.c:1062: warning: unused variable 'criteria'
  873. src/fpair.c: In function 'write_best_pairs':
  874. src/fpair.c:1332: warning: format '%d' expects type 'int', but argument 6 has type 'long int'
  875. src/fpair.c: In function 'single_BB_Hbond':
  876. src/fpair.c:2203: warning: format '%5d' expects type 'int', but argument 2 has type 'long int'
  877. src/fpair.c:2203: warning: format '%5d' expects type 'int', but argument 3 has type 'long int'
  878. src/fpair.c: In function 'syn_or_anti':
  879. src/fpair.c:2226: warning: 'chi_angle' may be used uninitialized in this function
  880. src/fpair.c: In function 'ring_center':
  881. src/fpair.c:667: warning: 'natm' may be used uninitialized in this function
  882. src/fpair.c: In function 'single_BB_Hbond':
  883. src/fpair.c:2113: warning: 'dist' may be used uninitialized in this function
  884. src/fpair_sub.c: In function 'number_of_atoms':
  885. src/fpair_sub.c:197: warning: suggest parentheses around '&&' within '||'
  886. src/fpair_sub.c: In function 'read_pdb':
  887. src/fpair_sub.c:231: warning: suggest parentheses around '&&' within '||'
  888. src/fpair_sub.c: In function 'rot_2_lsplane':
  889. src/fpair_sub.c:2378: warning: unused variable 'inum'
  890. src/fpair_sub.c: In function 'rot_mol':
  891. src/fpair_sub.c:2455: warning: unused variable 'inum'
  892. src/fpair_sub.c: In function 'ref_idx':
  893. src/fpair_sub.c:70: warning: 'ii' may be used uninitialized in this function
  894. src/fpair_sub.c: In function 'identify_uncommon':
  895. src/fpair_sub.c:651: warning: 'c' may be used uninitialized in this function
  896. src/fpair_sub.c: In function 'base_info':
  897. src/fpair_sub.c:1977: warning: 'j' may be used uninitialized in this function
  898. src/multiple.c: In function 'write_multiplets':
  899. src/multiple.c:101: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  900. src/multiple.c:101: warning: format '%d' expects type 'int', but argument 4 has type 'long int'
  901. src/multiple.c:19: warning: 'npair' may be used uninitialized in this function
  902. src/pair_type.c: In function 'LW_pair_type':
  903. src/pair_type.c:21: warning: unused variable 'k'
  904. src/pair_type.c: In function 'get_pair_type':
  905. src/pair_type.c:120: warning: unused variable 'k'
  906. src/pair_type.c: In function 'NC_vector':
  907. src/pair_type.c:414: warning: 'natm' may be used uninitialized in this function
  908. src/pattern.c: In function 'motif':
  909. src/pattern.c:55: warning: format '%d' expects type 'int', but argument 2 has type 'long int'
  910. src/pattern.c:78: warning: format '%d' expects type 'int', but argument 2 has type 'long int'
  911. src/pattern.c: In function 'pattern_search':
  912. src/pattern.c:278: warning: unused variable 'yes'
  913. src/pattern.c: In function 'reorder_patt':
  914. src/pattern.c:551: warning: format '%d' expects type 'int', but argument 3 has type 'long int'
  915. src/pattern.c:562: warning: format '%d' expects type 'int', but argument 3 has type 'long int'
  916. src/pattern.c:470: warning: unused variable 'yes'
  917. src/pattern.c: In function 'further_classify':
  918. src/pattern.c:712: warning: unused variable 'nns'
  919. src/pattern.c:708: warning: unused variable 'yes'
  920. src/pattern.c: In function 'user_type_patt':
  921. src/pattern.c:820: warning: format '%4d' expects type 'int', but argument 4 has type 'long int'
  922. src/pattern.c:821: warning: format '%4d' expects type 'int', but argument 2 has type 'long int'
  923. src/pattern.c:821: warning: format '%4d' expects type 'int', but argument 4 has type 'long int'
  924. src/pattern.c:920: warning: format '%d' expects type 'int', but argument 3 has type 'long int'
  925. src/pattern.c: In function 'write_infor':
  926. src/pattern.c:932: warning: format '%d' expects type 'int', but argument 3 has type 'long int'
  927. src/pattern.c: In function 'cycling':
  928. src/pattern.c:965: warning: unused variable 'i'
  929. src/pattern.c: In function 'check_patt':
  930. src/pattern.c:997: warning: 'nm' may be used uninitialized in this function
  931. src/pattern.c: In function 'nline':
  932. src/pattern.c:240: warning: 'nl' may be used uninitialized in this function
  933. src/pattern.c: In function 'get_str':
  934. src/pattern.c:207: warning: 'nl' may be used uninitialized in this function
  935. src/ps-xy.c: In function 'process_2d_fig':
  936. src/ps-xy.c:307: warning: format '%4d' expects type 'int', but argument 2 has type 'long int'
  937. src/ps-xy.c:307: warning: format '%3d' expects type 'int', but argument 3 has type 'long int'
  938. src/ps-xy.c:35: warning: unused variable 'alfa'
  939. src/ps-xy.c: In function 'rot_2D_to_Yaxis':
  940. src/ps-xy.c:443: warning: unused variable 'atmnum'
  941. src/ps-xy.c:443: warning: unused variable 'j'
  942. src/ps-xy.c: In function 'xy4ps':
  943. src/ps-xy.c:492: warning: unused variable 'frame_box'
  944. src/ps-xy.c:488: warning: unused variable 'format'
  945. src/ps-xy-sub.c: In function 'head_to_tail':
  946. src/ps-xy-sub.c:59: warning: suggest parentheses around '&&' within '||'
  947. src/ps-xy-sub.c: In function 'rest_bases':
  948. src/ps-xy-sub.c:93: warning: 'ntest' may be used uninitialized in this function
  949. src/ps-xy-sub.c: In function 'rest_pairs':
  950. src/ps-xy-sub.c:120: warning: 'ntest' may be used uninitialized in this function
  951. src/ps-xy-sub.c: In function 'xy_base':
  952. src/ps-xy-sub.c:933: warning: 'x0' may be used uninitialized in this function
  953. src/ps-xy-sub.c:933: warning: 'y0' may be used uninitialized in this function
  954. src/rnaview.c: In function 'process_single_file':
  955. src/rnaview.c:135: warning: format '%d' expects type 'int', but argument 3 has type 'long int'
  956. src/rnaview.c: In function 'process_multiple_file':
  957. src/rnaview.c:252: warning: format '%d' expects type 'int', but argument 2 has type 'long int'
  958. src/rnaview.c:253: warning: format '%d' expects type 'int', but argument 3 has type 'long int'
  959. src/rnaview.c:254: warning: format '%d' expects type 'int', but argument 3 has type 'long int'
  960. src/rnaview.c: In function 'extract_nmr_coord':
  961. src/rnaview.c:448: warning: format '%d' expects type 'int', but argument 2 has type 'long int'
  962. src/rnaview.c:476: warning: format '%d' expects type 'int', but argument 3 has type 'long int'
  963. src/rnaview.c:420: warning: unused variable 'i'
  964. src/rnaview.c: In function 'rna':
  965. src/rnaview.c:706: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  966. src/rnaview.c:706: warning: format '%4d' expects type 'int', but argument 4 has type 'long int'
  967. src/rnaview.c:587: warning: unused variable 'prot_out'
  968. src/rnaview.c:583: warning: unused variable 'nprot_atom'
  969. src/rnaview.c:579: warning: unused variable 'str'
  970. src/rnaview.c: In function 'work_horse':
  971. src/rnaview.c:833: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  972. src/rnaview.c:833: warning: format '%4d' expects type 'int', but argument 4 has type 'long int'
  973. src/rnaview.c:835: warning: format '%4d' expects type 'int', but argument 2 has type 'long int'
  974. src/rnaview.c:835: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  975. src/rnaview.c: In function 'write_tmp_pdb':
  976. src/rnaview.c:1013: warning: format '%5d' expects type 'int', but argument 4 has type 'long int'
  977. src/rnaview.c:1013: warning: format '%4d' expects type 'int', but argument 8 has type 'long int'
  978. src/rnaview.c: In function 'print_sorted_pair':
  979. src/rnaview.c:1145: warning: suggest parentheses around '&&' within '||'
  980. src/rnaview.c:1151: warning: suggest parentheses around '&&' within '||'
  981. src/rnaview.c:1157: warning: suggest parentheses around '&&' within '||'
  982. src/rnaview.c:1162: warning: suggest parentheses around '&&' within '||'
  983. src/rnaview.c: In function 'process_multiple_file':
  984. src/rnaview.c:174: warning: 'resolution' may be used uninitialized in this function
  985. src/rnaxml-new.c: In function 'write_base_pair_int':
  986. src/rnaxml-new.c:252: warning: format '%d' expects type 'int', but argument 4 has type 'long int'
  987. src/rnaxml-new.c:260: warning: format '%d' expects type 'int', but argument 4 has type 'long int'
  988. src/rnaxml-new.c: In function 'xml_molecule':
  989. src/rnaxml-new.c:351: warning: format '%d' expects type 'int', but argument 4 has type 'long int'
  990. src/rnaxml-new.c:355: warning: format '%d' expects type 'int', but argument 4 has type 'long int'
  991. src/rnaxml-new.c:357: warning: format '%d' expects type 'int', but argument 4 has type 'long int'
  992. src/rnaxml-new.c:358: warning: format '%d' expects type 'int', but argument 4 has type 'long int'
  993. src/rnaxml-new.c:363: warning: format '%d' expects type 'int', but argument 4 has type 'long int'
  994. src/rnaxml-new.c:367: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  995. src/rnaxml-new.c: In function 'write_helix_mol':
  996. src/rnaxml-new.c:558: warning: format '%d' expects type 'int', but argument 4 has type 'long int'
  997. src/rnaxml-new.c:565: warning: format '%d' expects type 'int', but argument 4 has type 'long int'
  998. src/rnaxml-new.c:526: warning: 'helix_left' may be used uninitialized in this function
  999. src/rnaxml-new.c:526: warning: 'helix_right' may be used uninitialized in this function
  1000. src/statistics.c: In function 'print_edge_stat':
  1001. src/statistics.c:62: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  1002. src/statistics.c:62: warning: format '%4d' expects type 'int', but argument 5 has type 'long int'
  1003. src/statistics.c:62: warning: format '%4d' expects type 'int', but argument 7 has type 'long int'
  1004. src/statistics.c:64: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  1005. src/statistics.c:64: warning: format '%4d' expects type 'int', but argument 5 has type 'long int'
  1006. src/statistics.c:64: warning: format '%4d' expects type 'int', but argument 7 has type 'long int'
  1007. src/statistics.c:66: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  1008. src/statistics.c:66: warning: format '%4d' expects type 'int', but argument 5 has type 'long int'
  1009. src/statistics.c:66: warning: format '%4d' expects type 'int', but argument 7 has type 'long int'
  1010. src/statistics.c:68: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  1011. src/statistics.c:68: warning: format '%4d' expects type 'int', but argument 5 has type 'long int'
  1012. src/statistics.c:68: warning: format '%4d' expects type 'int', but argument 7 has type 'long int'
  1013. src/statistics.c:70: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  1014. src/statistics.c:70: warning: format '%4d' expects type 'int', but argument 5 has type 'long int'
  1015. src/statistics.c:70: warning: format '%4d' expects type 'int', but argument 7 has type 'long int'
  1016. src/statistics.c:72: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  1017. src/statistics.c:72: warning: format '%4d' expects type 'int', but argument 5 has type 'long int'
  1018. src/statistics.c:72: warning: format '%4d' expects type 'int', but argument 7 has type 'long int'
  1019. src/statistics.c:74: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  1020. src/statistics.c:74: warning: format '%4d' expects type 'int', but argument 5 has type 'long int'
  1021. src/statistics.c:74: warning: format '%4d' expects type 'int', but argument 7 has type 'long int'
  1022. src/statistics.c:79: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  1023. src/statistics.c:79: warning: format '%4d' expects type 'int', but argument 5 has type 'long int'
  1024. src/statistics.c:79: warning: format '%4d' expects type 'int', but argument 7 has type 'long int'
  1025. src/statistics.c:83: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  1026. src/statistics.c:83: warning: format '%4d' expects type 'int', but argument 5 has type 'long int'
  1027. src/statistics.c:83: warning: format '%4d' expects type 'int', but argument 7 has type 'long int'
  1028. src/statistics.c:92: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  1029. src/statistics.c:92: warning: format '%4d' expects type 'int', but argument 5 has type 'long int'
  1030. src/statistics.c:92: warning: format '%4d' expects type 'int', but argument 7 has type 'long int'
  1031. src/statistics.c:94: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  1032. src/statistics.c:94: warning: format '%4d' expects type 'int', but argument 5 has type 'long int'
  1033. src/statistics.c:94: warning: format '%4d' expects type 'int', but argument 7 has type 'long int'
  1034. src/statistics.c:97: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  1035. src/statistics.c:97: warning: format '%4d' expects type 'int', but argument 5 has type 'long int'
  1036. src/statistics.c:97: warning: format '%4d' expects type 'int', but argument 7 has type 'long int'
  1037. src/statistics.c:99: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  1038. src/statistics.c:99: warning: format '%4d' expects type 'int', but argument 5 has type 'long int'
  1039. src/statistics.c:99: warning: format '%4d' expects type 'int', but argument 7 has type 'long int'
  1040. src/statistics.c:105: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  1041. src/statistics.c:105: warning: format '%4d' expects type 'int', but argument 5 has type 'long int'
  1042. src/statistics.c:105: warning: format '%4d' expects type 'int', but argument 7 has type 'long int'
  1043. src/statistics.c:111: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  1044. src/statistics.c:111: warning: format '%4d' expects type 'int', but argument 5 has type 'long int'
  1045. src/statistics.c:111: warning: format '%4d' expects type 'int', but argument 7 has type 'long int'
  1046. src/statistics.c: In function 'print_statistic':
  1047. src/statistics.c:143: warning: format '%d' expects type 'int', but argument 3 has type 'long int'
  1048. src/statistics.c:146: warning: format '%5d' expects type 'int', but argument 3 has type 'long int'
  1049. src/statistics.c:151: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  1050. src/statistics.c:158: warning: format '%4d' expects type 'int', but argument 3 has type 'long int'
  1051. src/statistics.c:183: warning: format '%5d' expects type 'int', but argument 3 has type 'long int'
  1052. src/statistics.c:190: warning: format '%5d' expects type 'int', but argument 3 has type 'long int'
  1053. src/statistics.c:198: warning: format '%5d' expects type 'int', but argument 3 has type 'long int'
  1054. src/statistics.c:228: warning: format '%5d' expects type 'int', but argument 3 has type 'long int'
  1055. src/statistics.c:235: warning: format '%5d' expects type 'int', but argument 3 has type 'long int'
  1056. src/statistics.c:250: warning: format '%5d' expects type 'int', but argument 3 has type 'long int'
  1057. src/statistics.c: In function 'write_12_family_table':
  1058. src/statistics.c:438: warning: format '%5d' expects type 'int', but argument 3 has type 'long int'
  1059. src/statistics.c:438: warning: format '%5d' expects type 'int', but argument 5 has type 'long int'
  1060. src/statistics.c:438: warning: format '%5d' expects type 'int', but argument 7 has type 'long int'
  1061. src/statistics.c:438: warning: format '%5d' expects type 'int', but argument 9 has type 'long int'
  1062. src/statistics.c:440: warning: format '%5d' expects type 'int', but argument 3 has type 'long int'
  1063. src/statistics.c:440: warning: format '%5d' expects type 'int', but argument 5 has type 'long int'
  1064. src/statistics.c:440: warning: format '%5d' expects type 'int', but argument 7 has type 'long int'
  1065. src/statistics.c:440: warning: format '%5d' expects type 'int', but argument 9 has type 'long int'
  1066. src/statistics.c:442: warning: format '%5d' expects type 'int', but argument 3 has type 'long int'
  1067. src/statistics.c:442: warning: format '%5d' expects type 'int', but argument 5 has type 'long int'
  1068. src/statistics.c:442: warning: format '%5d' expects type 'int', but argument 7 has type 'long int'
  1069. src/statistics.c:442: warning: format '%5d' expects type 'int', but argument 9 has type 'long int'
  1070. src/statistics.c:444: warning: format '%5d' expects type 'int', but argument 3 has type 'long int'
  1071. src/statistics.c:444: warning: format '%5d' expects type 'int', but argument 5 has type 'long int'
  1072. src/statistics.c:444: warning: format '%5d' expects type 'int', but argument 7 has type 'long int'
  1073. src/statistics.c:444: warning: format '%5d' expects type 'int', but argument 9 has type 'long int'
  1074. src/statistics.c: In function 'pair_type_statistics':
  1075. src/statistics.c:801: warning: format '%9d' expects type 'int', but argument 3 has type 'long int'
  1076. src/statistics.c:805: warning: format '%9d' expects type 'int', but argument 3 has type 'long int'
  1077. src/statistics.c:809: warning: format '%9d' expects type 'int', but argument 3 has type 'long int'
  1078. src/statistics.c:809: warning: format '%9d' expects type 'int', but argument 4 has type 'long int'
  1079. src/statistics.c: In function 'write_single_Hbond_stat':
  1080. src/statistics.c:984: warning: format '%d' expects type 'int *', but argument 3 has type 'long int *'
  1081. src/statistics.c:984: warning: format '%d' expects type 'int *', but argument 4 has type 'long int *'
  1082. src/vrml.c: In function 'output_appearance':
  1083. src/vrml.c:596: warning: unused variable 'COLOR_BLACK'
  1084. src/vrml.c: At top level:
  1085. src/vrml.h:11: warning: 'vrml_def' declared 'static' but never defined
  1086. src/vrml.h:18: warning: 'vrml_invalid_def' declared 'static' but never defined
  1087. src/vrml.c: In function 'draw_interact':
  1088. src/vrml.c:119: warning: 'tr' may be used uninitialized in this function
  1089. src/xml2ps.c: In function 'xml2ps':
  1090. src/xml2ps.c:153: warning: format '%d' expects type 'int', but argument 2 has type 'long int'
  1091. src/xml2ps.c:153: warning: format '%d' expects type 'int', but argument 3 has type 'long int'
  1092. src/xml2ps.c:153: warning: format '%d' expects type 'int', but argument 4 has type 'long int'
  1093. src/xml2ps.c:185: warning: format '%d' expects type 'int', but argument 2 has type 'long int'
  1094. src/xml2ps.c:186: warning: format '%d' expects type 'int', but argument 2 has type 'long int'
  1095. src/xml2ps.c:187: warning: format '%d' expects type 'int', but argument 2 has type 'long int'
  1096. src/xml2ps.c:52: warning: unused variable 'key'
  1097. src/xml2ps.c:47: warning: unused variable 'parfile'
  1098. src/xml2ps.c: In function 'read_O3prime_P_xyz':
  1099. src/xml2ps.c:312: warning: unused variable 'model_id'
  1100. src/xml2ps.c: In function 'read_xy_coord':
  1101. src/xml2ps.c:849: warning: format '%d' expects type 'int', but argument 2 has type 'long int'
  1102. src/xml2ps.c:849: warning: format '%d' expects type 'int', but argument 3 has type 'long int'
  1103. src/xml2ps.c: In function 'read_sugar_syn':
  1104. src/xml2ps.c:888: warning: unused variable 'nposit'
  1105. src/xml2ps.c:888: warning: unused variable 'nxy'
  1106. src/xml2ps.c: In function 'get_sequence':
  1107. src/xml2ps.c:1025: warning: format '%d' expects type 'int', but argument 2 has type 'long int'
  1108. src/xml2ps.c:1025: warning: format '%d' expects type 'int', but argument 3 has type 'long int'
  1109. src/xml2ps.c: In function 'label_seq_number':
  1110. src/xml2ps.c:1617: warning: format '%d' expects type 'int', but argument 5 has type 'long int'
  1111. src/xml2ps.c:1621: warning: format '%d' expects type 'int', but argument 5 has type 'long int'
  1112. src/xml2ps.c: In function 'label_seq':
  1113. src/xml2ps.c:1654: warning: format '%d' expects type 'int', but argument 5 has type 'long int'
  1114. src/xml2ps.c:1658: warning: format '%d' expects type 'int', but argument 5 has type 'long int'
  1115. src/xml2ps.c:1662: warning: format '%d' expects type 'int', but argument 5 has type 'long int'
  1116. src/xml2ps.c:1666: warning: format '%d' expects type 'int', but argument 5 has type 'long int'
  1117. src/xml2ps.c:1674: warning: format '%d' expects type 'int', but argument 5 has type 'long int'
  1118. src/xml2ps.c:1678: warning: format '%d' expects type 'int', but argument 5 has type 'long int'
  1119. src/xml2ps.c:1682: warning: format '%d' expects type 'int', but argument 5 has type 'long int'
  1120. src/xml2ps.c:1686: warning: format '%d' expects type 'int', but argument 5 has type 'long int'
  1121. src/xml2ps.c: In function 'ps_head':
  1122. src/xml2ps.c:2270: warning: implicit declaration of function 'get_BDIR'
  1123. src/xml2ps.c: In function 'LW_shapes':
  1124. src/xml2ps.c:1746: warning: 'fill' may be used uninitialized in this function
  1125. src/xml2ps.c: In function 'get_xy_position':
  1126. src/xml2ps.c:1355: warning: 'm' may be used uninitialized in this function
  1127. src/xml2ps.c: In function 'get_xyz_coord':
  1128. src/xml2ps.c:395: warning: 'm' may be used uninitialized in this function
  1129. src/xml2ps.c: In function 'num_of_pair':
  1130. src/xml2ps.c:1191: warning: 'nlt' may be used uninitialized in this function
  1131. src/xml2ps.c: In function 'read_bs_pair':
  1132. src/xml2ps.c:1109: warning: 'n' may be used uninitialized in this function
  1133. src/ops.C: In member function 'virtual char* RegularOps::name()':
  1134. src/ops.C:58: warning: deprecated conversion from string constant to 'char*'
  1135. src/ops.C: In member function 'virtual char* PMFOps::name()':
  1136. src/ops.C:65: warning: deprecated conversion from string constant to 'char*'
  1137. src/interface.c: In function 'startFind':
  1138. src/interface.c:3455: warning: value computed is not used
  1139. src/ccprobcalc.c: In function 'ccprobcalc':
  1140. src/ccprobcalc.c:52: warning: unused variable 'uval'
  1141. src/ccprobcalc.c:51: warning: unused variable 'll'
  1142. src/ccprobcalc.c:51: warning: unused variable 'end'
  1143. src/ccprobcalc.c:51: warning: unused variable 'start'
  1144. src/ccprobcalc.c:50: warning: unused variable 'k'
  1145. src/ccprobcalc.c:52: warning: 'lstrt' may be used uninitialized in this function
  1146. src/display_align.c: In function 'display_align':
  1147. src/display_align.c:50: warning: unused variable 'k'
  1148. src/display_align.c:50: warning: unused variable 'j'
  1149. mahmood@cluster:plugins$ mkdir -p ../vmd-1.9.3/plugins
  1150. mahmood@cluster:plugins$ export PLUGINDIR=/home/mahmood/namd/vmd-1.9.3/plugins/
  1151. mahmood@cluster:plugins$ make distrib
  1152. Populating distribution directory with compiled plugins
  1153. Copying molfile plugins to /home/mahmood/namd/vmd-1.9.3/plugins/ destination area
  1154. abinitplugin.so ...
  1155. avsplugin.so ...
  1156. babelplugin.so ...
  1157. basissetplugin.so ...
  1158. bgfplugin.so ...
  1159. binposplugin.so ...
  1160. biomoccaplugin.so ...
  1161. brixplugin.so ...
  1162. carplugin.so ...
  1163. ccp4plugin.so ...
  1164. corplugin.so ...
  1165. cpmdplugin.so ...
  1166. crdplugin.so ...
  1167. cubeplugin.so ...
  1168. dcdplugin.so ...
  1169. dlpolyplugin.so ...
  1170. dsn6plugin.so ...
  1171. dxplugin.so ...
  1172. edmplugin.so ...
  1173. fs4plugin.so ...
  1174. gamessplugin.so ...
  1175. graspplugin.so ...
  1176. grdplugin.so ...
  1177. gridplugin.so ...
  1178. gromacsplugin.so ...
  1179. jsplugin.so ...
  1180. lammpsplugin.so ...
  1181. mapplugin.so ...
  1182. mdfplugin.so ...
  1183. mol2plugin.so ...
  1184. moldenplugin.so ...
  1185. molemeshplugin.so ...
  1186. msmsplugin.so ...
  1187. namdbinplugin.so ...
  1188. offplugin.so ...
  1189. parm7plugin.so ...
  1190. parmplugin.so ...
  1191. pbeqplugin.so ...
  1192. pdbplugin.so ...
  1193. pdbxplugin.so ...
  1194. phiplugin.so ...
  1195. pltplugin.so ...
  1196. plyplugin.so ...
  1197. pqrplugin.so ...
  1198. psfplugin.so ...
  1199. raster3dplugin.so ...
  1200. rst7plugin.so ...
  1201. situsplugin.so ...
  1202. spiderplugin.so ...
  1203. stlplugin.so ...
  1204. tinkerplugin.so ...
  1205. uhbdplugin.so ...
  1206. vaspchgcarplugin.so ...
  1207. vaspoutcarplugin.so ...
  1208. vaspparchgplugin.so ...
  1209. vaspposcarplugin.so ...
  1210. vasp5xdatcarplugin.so ...
  1211. vaspxdatcarplugin.so ...
  1212. vaspxmlplugin.so ...
  1213. vtkplugin.so ...
  1214. xbgfplugin.so ...
  1215. xsfplugin.so ...
  1216. xyzplugin.so ...
  1217. dtrplugin.so ...
  1218. maeffplugin.so ...
  1219. dmsplugin.so ...
  1220. hoomdplugin.so ...
  1221. netcdfplugin.so ...
  1222. tngplugin.so ...
  1223. vtfplugin.so ...
  1224. webpdbplugin.so ...
  1225. libmolfile_plugin.a ...
  1226. libmolfile_plugin.h ...
  1227. libmolfile_plugin.lib ...
  1228. libmolfile_plugin.h ...
  1229. Copying apbsrun 1.3 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/apbsrun1.3
  1230. Copying alascanfep 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/alascanfep1.0
  1231. Copying atomedit 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/atomedit1.0
  1232. Copying autoimd 1.7 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/autoimd1.7
  1233. Copying autoionize 1.4 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/autoionize1.4
  1234. Copying bdtk 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/bdtk1.0
  1235. Copying bendix 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/bendix1.1
  1236. Copying bignum 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/bignum1.0
  1237. Copying biocore 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/biocore1.1
  1238. Copying bossconvert 1.0 files to
  1239. /home/mahmood/namd/vmd-1.9.3/plugins//LINUXAMD64/tcl/bossconvert1.0
  1240. Copying cgtools 1.2 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/cgtools1.2
  1241. Copying chirality 1.2 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/chirality1.2
  1242. Copying cispeptide 1.3 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/cispeptide1.3
  1243. Copying cliptool 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/cliptool1.0
  1244. Copying clonerep 1.3 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/clonerep1.3
  1245. Copying colorscalebar 1.4 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/colorscalebar1.4
  1246. Copying contactmap 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/contactmap1.1
  1247. Copying dataimport 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/dataimport1.0
  1248. Copying demomaster 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/demomaster1.0
  1249. Copying dipwatch 1.2 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/dipwatch1.2
  1250. Copying dowser 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/dowser1.1
  1251. Copying exectool 1.2 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/exectool1.2
  1252. Copying extendedpdb 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/extendedpdb1.0
  1253. Copying fftk 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/fftk1.1
  1254. Copying gofrgui 1.3 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/gofrgui1.3
  1255. Copying heatmapper 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/heatmapper1.1
  1256. Copying hbonds 1.2 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/hbonds1.2
  1257. Copying idatm 0.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/idatm0.1
  1258. Copying ilstools 1.5 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/ilstools1.5
  1259. Copying imdmenu 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/imdmenu1.0
  1260. Copying inorganicbuilder 0.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/inorganicbuilder0.1
  1261. Copying irspecgui 1.3 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/irspecgui1.3
  1262. Copying mafft 1.1 files to
  1263. Copying mdff 0.5 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/mdff0.5
  1264. Copying membrane 1.2 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/membrane1.2
  1265. Copying mergestructs 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/mergestructs1.1
  1266. Copying molefacture 1.4 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/molefacture1.4
  1267. Copying moltoptools 0.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/moltoptools0.1
  1268. Copying multimolanim 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/multimolanim1.0
  1269. Copying multiplot 1.7 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/multiplot1.7
  1270. Copying multitext 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/multitext1.1
  1271. Copying namdenergy 1.4 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/namdenergy1.4
  1272. Copying namdgui 1.3 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/namdgui1.3
  1273. Copying namdplot 1.2 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/namdplot1.2
  1274. Copying namdserver 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/namdserver1.1
  1275. Copying nanotube 1.5 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/nanotube1.5
  1276. Copying navfly 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/navfly1.0
  1277. Copying navigate 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/navigate1.0
  1278. Copying networkview 1.41 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/networkview1.41
  1279. Copying nmwiz 1.2 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/nmwiz1.2
  1280. Copying optimization 1.3 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/optimization1.3
  1281. Copying palettetool 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/palettetool1.0
  1282. Copying paratool 1.5 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/paratool1.5
  1283. Copying parsefep 1.9 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/parsefep1.9
  1284. Copying pbctools 2.8 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/pbctools2.8
  1285. Copying pdbtool 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/pdbtool1.0
  1286. Copying plumed 2.5 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/plumed2.5
  1287. Copying propka 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/propka1.1
  1288. Copying psfgen 1.6 files to /home/mahmood/namd/vmd-1.9.3/plugins/ arch-specific dir
  1289. Copying qmtool 1.3 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/qmtool1.3
  1290. Copying qwikmd 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/qwikmd1.1
  1291. Copying ramaplot 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/ramaplot1.1
  1292. Copying readcharmmpar 1.3 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/readcharmmpar1.3
  1293. Copying readcharmmtop 1.2 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/readcharmmtop1.2
  1294. Copying remote 0.6 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/remote0.6
  1295. Copying resptool 1.2 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/resptool1.2
  1296. Copying rnaview 1.1 files to
  1297. /home/mahmood/namd/vmd-1.9.3/plugins//LINUXAMD64/tcl/rnaview1.1
  1298. Copying rmsd 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/rmsd1.0
  1299. Copying rmsdtt 3.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/rmsdtt3.0
  1300. Copying rmsdvt 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/rmsdvt1.0
  1301. Copying ruler 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/ruler1.0
  1302. Copying runante 0.2 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/runante0.2
  1303. Copying runsqm 0.2 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/runsqm0.2
  1304. Copying saltbr 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/saltbr1.1
  1305. Copying solvate 1.7 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/solvate1.7
  1306. Copying ssrestraints 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/ssrestraints1.1
  1307. Copying stingtool 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/stingtool1.0
  1308. Copying structurecheck 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/structurecheck1.1
  1309. Copying symmetrytool 1.3 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/symmetrytool1.3
  1310. Copying tablelist 5.13 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/tablelist5.13
  1311. Copying timeline 2.3 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/timeline2.3
  1312. Copying topotools 1.7 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/topotools1.7
  1313. Copying torsionplot 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/torsionplot1.1
  1314. Copying trunctraj 1.5 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/trunctraj1.5
  1315. Copying utilities 1.2 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/utilities1.2
  1316. Copying vdna 2.2 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/vdna2.2
  1317. Copying viewchangerender 1.8 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/viewchangerender1.8
  1318. Copying viewmaster 2.6 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/viewmaster2.6
  1319. Copying volmapgui 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/volmapgui1.1
  1320. Copying volutil 1.3 files to
  1321. /home/mahmood/namd/vmd-1.9.3/plugins//LINUXAMD64/tcl/volutil1.3
  1322. Copying vmddebug 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/vmddebug1.1
  1323. Copying vmdlite 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/vmdlite1.1
  1324. Copying vmdmovie 1.9 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/vmdmovie1.9
  1325. Copying vmdprefs 1.0 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/vmdprefs1.0
  1326. Copying vmdtkcon 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/vmdtkcon1.1
  1327. Copying zoomseq 1.2 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/zoomseq1.2
  1328. Copying blast 1.11 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/blast1.11
  1329. Copying clustalw 1.1 files to
  1330. /home/mahmood/namd/vmd-1.9.3/plugins//LINUXAMD64/tcl/clustalw1.1
  1331. Copying libbiokit 1.1 files.
  1332. ../compile/lib_LINUXAMD64/tcl/libbiokit1.1/qpair -> /home/mahmood/namd/vmd-1.9.3/plugins//LINUXAMD64/tcl/libbiokit1.1
  1333. ../compile/lib_LINUXAMD64/tcl/libbiokit1.1/seqqr -> /home/mahmood/namd/vmd-1.9.3/plugins//LINUXAMD64/tcl/libbiokit1.1
  1334. ../compile/lib_LINUXAMD64/tcl/libbiokit1.1/percid -> /home/mahmood/namd/vmd-1.9.3/plugins//LINUXAMD64/tcl/libbiokit1.1
  1335. ../compile/lib_LINUXAMD64/tcl/libbiokit1.1/rmsd -> /home/mahmood/namd/vmd-1.9.3/plugins//LINUXAMD64/tcl/libbiokit1.1
  1336. ../compile/lib_LINUXAMD64/tcl/libbiokit1.1/structqr -> /home/mahmood/namd/vmd-1.9.3/plugins//LINUXAMD64/tcl/libbiokit1.1
  1337. ../compile/lib_LINUXAMD64/tcl/libbiokit1.1/q -> /home/mahmood/namd/vmd-1.9.3/plugins//LINUXAMD64/tcl/libbiokit1.1
  1338. Copying multiseq 2.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/multiseq2.1
  1339. Copying multiseqdialog 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/multiseqdialog1.1
  1340. Copying phylotree 1.2 files to
  1341. /home/mahmood/namd/vmd-1.9.3/plugins//LINUXAMD64/tcl/phylotree1.2
  1342. Copying psipred 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/psipred1.1
  1343. Copying seqdata 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/seqdata1.1
  1344. Copying seqedit 1.1 files to /home/mahmood/namd/vmd-1.9.3/plugins//noarch/tcl/seqedit1.1
  1345. Copying stamp 1.2 files to
  1346. /home/mahmood/namd/vmd-1.9.3/plugins//LINUXAMD64/tcl/stamp1.2
  1347. mahmood@cluster:plugins$ cd ../vmd-1.9.3/
  1348. mahmood@cluster:vmd-1.9.3$ ./configure
  1349. using configure.options: LINUXAMD64 OPENGL OPENGLPBUFFER FLTK TK ACTC CUDA IMD LIBSBALL XINERAMA XINPUT LIBOPTIX LIBOSPRAY LIBTACHYON VRPN NETCDF COLVARS TCL PYTHON PTHREADS NUMPY SILENT ICC
  1350. mahmood@cluster:vmd-1.9.3$ grep install_bin_dir configure
  1351. $install_bin_dir="/home/mahmood/namd/vmd-1.9.3/install/bin";
  1352. $install_bin_dir = $ENV{VMDINSTALLBINDIR}
  1353. if [ ! -d "$install_bin_dir" ]; then \\
  1354. \$(MAKEDIR) "$install_bin_dir" ; \\
  1355. \$(COPY) run_vmd_tmp "$install_bin_dir"/$install_name ; \\
  1356. \$(ECHO) Make sure "$install_bin_dir"/$install_name is in your path.
  1357. mahmood@cluster:vmd-1.9.3$ grep install_library_dir configure
  1358. $install_library_dir="/home/mahmood/namd/vmd-1.9.3/install/lib/$install_name";
  1359. $install_library_dir = $ENV{VMDINSTALLLIBRARYDIR}
  1360. #define DEF_VMDENVVAR "$install_library_dir"
  1361. if [ ! -d "$install_library_dir" ]; then \\
  1362. \$(MAKEDIR) "$install_library_dir" ; \\
  1363. if [ ! -d "$install_library_dir"/doc ]; then \\
  1364. \$(MAKEDIR) "$install_library_dir"/doc; \\
  1365. -\$(COPY) ../Announcement "$install_library_dir"
  1366. -\$(COPY) ../README "$install_library_dir"
  1367. -\$(COPY) ../LICENSE "$install_library_dir"
  1368. -\$(COPY) $vmd_doc_dir/ug.pdf "$install_library_dir"/doc
  1369. if [ -f $install_library_dir/$config_progname ]; then \\
  1370. \$(MOVE) "$install_library_dir/$config_progname" "$install_library_dir/OLD_$config_progname" ; \$(DELETE) "$install_library_dir/OLD_$config_progname" ; fi
  1371. -\$(COPY) ../$config_arch/$config_progname "$install_library_dir"
  1372. (cd "$install_library_dir" ; \$(TAR) -xf -) \\
  1373. -\$(COPY) @vmd_other_exe "$install_library_dir"
  1374. (cd "$install_library_dir" ; \$(TAR) -xf -)
  1375. (cd "$install_library_dir" ; \$(TAR) -xf -)
  1376. (cd "$install_library_dir"/scripts ; \$(TAR) -xf -)
  1377. (cd "$install_library_dir" ; \$(TAR) -xf -)
  1378. (cd "$install_library_dir" ; \$(TAR) -xf -)
  1379. \$(COPY) ../$config_arch/OptiXShaders.ptx "$install_library_dir/shaders"; \\
  1380. -\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir"
  1381. \$(ECHO) 'defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\
  1382. \$(ECHO) 'set defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\
  1383. mahmood@cluster:vmd-1.9.3$ grep install_library_dir configure | head -n 1
  1384. $install_library_dir="/home/mahmood/namd/vmd-1.9.3/install/lib/$install_name";
  1385. mahmood@cluster:vmd-1.9.3$ grep install_bin_dir configure | head -n 1
  1386. $install_bin_dir="/home/mahmood/namd/vmd-1.9.3/install/bin";
  1387. mahmood@cluster:vmd-1.9.3$ ./configure
  1388. using configure.options: LINUXAMD64 OPENGL OPENGLPBUFFER FLTK TK ACTC CUDA IMD LIBSBALL XINERAMA XINPUT LIBOPTIX LIBOSPRAY LIBTACHYON VRPN NETCDF COLVARS TCL PYTHON PTHREADS NUMPY SILENT ICC
  1389. mahmood@cluster:vmd-1.9.3$ ./configure LINUXAMD64 OPENGL
  1390. mahmood@cluster:vmd-1.9.3$ cd src
  1391. mahmood@cluster:src$ make
  1392. echo "Compiling " OpenGLDisplayDevice.C " --> " OpenGLDisplayDevice.o " ..."; \
  1393. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c OpenGLDisplayDevice.C -o ../LINUXAMD64/OpenGLDisplayDevice.o
  1394. Compiling OpenGLDisplayDevice.C --> OpenGLDisplayDevice.o ...
  1395. echo "Compiling " OpenGLExtensions.C " --> " OpenGLExtensions.o " ..."; \
  1396. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c OpenGLExtensions.C -o ../LINUXAMD64/OpenGLExtensions.o
  1397. Compiling OpenGLExtensions.C --> OpenGLExtensions.o ...
  1398. echo "Compiling " OpenGLRenderer.C " --> " OpenGLRenderer.o " ..."; \
  1399. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c OpenGLRenderer.C -o ../LINUXAMD64/OpenGLRenderer.o
  1400. Compiling OpenGLRenderer.C --> OpenGLRenderer.o ...
  1401. echo "Compiling " OpenGLShader.C " --> " OpenGLShader.o " ..."; \
  1402. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c OpenGLShader.C -o ../LINUXAMD64/OpenGLShader.o
  1403. Compiling OpenGLShader.C --> OpenGLShader.o ...
  1404. echo "Compiling " OpenGLCache.C " --> " OpenGLCache.o " ..."; \
  1405. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c OpenGLCache.C -o ../LINUXAMD64/OpenGLCache.o
  1406. Compiling OpenGLCache.C --> OpenGLCache.o ...
  1407. echo "Compiling " androidvmdstart.C " --> " androidvmdstart.o " ..."; \
  1408. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c androidvmdstart.C -o ../LINUXAMD64/androidvmdstart.o
  1409. Compiling androidvmdstart.C --> androidvmdstart.o ...
  1410. echo "Compiling " Animation.C " --> " Animation.o " ..."; \
  1411. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Animation.C -o ../LINUXAMD64/Animation.o
  1412. Compiling Animation.C --> Animation.o ...
  1413. echo "Compiling " ArtDisplayDevice.C " --> " ArtDisplayDevice.o " ..."; \
  1414. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c ArtDisplayDevice.C -o ../LINUXAMD64/ArtDisplayDevice.o
  1415. Compiling ArtDisplayDevice.C --> ArtDisplayDevice.o ...
  1416. echo "Compiling " AtomColor.C " --> " AtomColor.o " ..."; \
  1417. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c AtomColor.C -o ../LINUXAMD64/AtomColor.o
  1418. Compiling AtomColor.C --> AtomColor.o ...
  1419. echo "Compiling " AtomParser.C " --> " AtomParser.o " ..."; \
  1420. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c AtomParser.C -o ../LINUXAMD64/AtomParser.o
  1421. Compiling AtomParser.C --> AtomParser.o ...
  1422. /usr/ccs/bin/yaccpar:5: warning: ignoring #pragma ident
  1423. echo "Compiling " AtomLexer.C " --> " AtomLexer.o " ..."; \
  1424. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c AtomLexer.C -o ../LINUXAMD64/AtomLexer.o
  1425. Compiling AtomLexer.C --> AtomLexer.o ...
  1426. lex.yy.c:1511: warning: 'void yyunput(int, char*)' defined but not used
  1427. echo "Compiling " AtomRep.C " --> " AtomRep.o " ..."; \
  1428. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c AtomRep.C -o ../LINUXAMD64/AtomRep.o
  1429. Compiling AtomRep.C --> AtomRep.o ...
  1430. echo "Compiling " AtomSel.C " --> " AtomSel.o " ..."; \
  1431. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c AtomSel.C -o ../LINUXAMD64/AtomSel.o
  1432. Compiling AtomSel.C --> AtomSel.o ...
  1433. echo "Compiling " Axes.C " --> " Axes.o " ..."; \
  1434. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Axes.C -o ../LINUXAMD64/Axes.o
  1435. Compiling Axes.C --> Axes.o ...
  1436. echo "Compiling " BaseMolecule.C " --> " BaseMolecule.o " ..."; \
  1437. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c BaseMolecule.C -o ../LINUXAMD64/BaseMolecule.o
  1438. Compiling BaseMolecule.C --> BaseMolecule.o ...
  1439. echo "Compiling " Benchmark.C " --> " Benchmark.o " ..."; \
  1440. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Benchmark.C -o ../LINUXAMD64/Benchmark.o
  1441. Compiling Benchmark.C --> Benchmark.o ...
  1442. echo "Compiling " BondSearch.C " --> " BondSearch.o " ..."; \
  1443. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c BondSearch.C -o ../LINUXAMD64/BondSearch.o
  1444. Compiling BondSearch.C --> BondSearch.o ...
  1445. echo "Compiling " CmdAnimate.C " --> " CmdAnimate.o " ..."; \
  1446. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c CmdAnimate.C -o ../LINUXAMD64/CmdAnimate.o
  1447. Compiling CmdAnimate.C --> CmdAnimate.o ...
  1448. echo "Compiling " CmdColor.C " --> " CmdColor.o " ..."; \
  1449. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c CmdColor.C -o ../LINUXAMD64/CmdColor.o
  1450. Compiling CmdColor.C --> CmdColor.o ...
  1451. echo "Compiling " CmdDisplay.C " --> " CmdDisplay.o " ..."; \
  1452. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c CmdDisplay.C -o ../LINUXAMD64/CmdDisplay.o
  1453. Compiling CmdDisplay.C --> CmdDisplay.o ...
  1454. echo "Compiling " CmdLabel.C " --> " CmdLabel.o " ..."; \
  1455. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c CmdLabel.C -o ../LINUXAMD64/CmdLabel.o
  1456. Compiling CmdLabel.C --> CmdLabel.o ...
  1457. echo "Compiling " CmdMaterial.C " --> " CmdMaterial.o " ..."; \
  1458. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c CmdMaterial.C -o ../LINUXAMD64/CmdMaterial.o
  1459. Compiling CmdMaterial.C --> CmdMaterial.o ...
  1460. echo "Compiling " CmdMenu.C " --> " CmdMenu.o " ..."; \
  1461. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c CmdMenu.C -o ../LINUXAMD64/CmdMenu.o
  1462. Compiling CmdMenu.C --> CmdMenu.o ...
  1463. echo "Compiling " CmdMol.C " --> " CmdMol.o " ..."; \
  1464. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c CmdMol.C -o ../LINUXAMD64/CmdMol.o
  1465. Compiling CmdMol.C --> CmdMol.o ...
  1466. echo "Compiling " CmdRender.C " --> " CmdRender.o " ..."; \
  1467. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c CmdRender.C -o ../LINUXAMD64/CmdRender.o
  1468. Compiling CmdRender.C --> CmdRender.o ...
  1469. echo "Compiling " CmdTrans.C " --> " CmdTrans.o " ..."; \
  1470. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c CmdTrans.C -o ../LINUXAMD64/CmdTrans.o
  1471. Compiling CmdTrans.C --> CmdTrans.o ...
  1472. echo "Compiling " CommandQueue.C " --> " CommandQueue.o " ..."; \
  1473. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c CommandQueue.C -o ../LINUXAMD64/CommandQueue.o
  1474. Compiling CommandQueue.C --> CommandQueue.o ...
  1475. echo "Compiling " CoorPluginData.C " --> " CoorPluginData.o " ..."; \
  1476. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c CoorPluginData.C -o ../LINUXAMD64/CoorPluginData.o
  1477. Compiling CoorPluginData.C --> CoorPluginData.o ...
  1478. echo "Compiling " CUDAAccel.C " --> " CUDAAccel.o " ..."; \
  1479. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c CUDAAccel.C -o ../LINUXAMD64/CUDAAccel.o
  1480. Compiling CUDAAccel.C --> CUDAAccel.o ...
  1481. CUDAAccel.C: In constructor 'CUDAAccel::CUDAAccel()':
  1482. CUDAAccel.C:33: warning: unused variable 'usabledevices'
  1483. echo "Compiling " DisplayDevice.C " --> " DisplayDevice.o " ..."; \
  1484. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c DisplayDevice.C -o ../LINUXAMD64/DisplayDevice.o
  1485. Compiling DisplayDevice.C --> DisplayDevice.o ...
  1486. echo "Compiling " Displayable.C " --> " Displayable.o " ..."; \
  1487. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Displayable.C -o ../LINUXAMD64/Displayable.o
  1488. Compiling Displayable.C --> Displayable.o ...
  1489. echo "Compiling " DisplayRocker.C " --> " DisplayRocker.o " ..."; \
  1490. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c DisplayRocker.C -o ../LINUXAMD64/DisplayRocker.o
  1491. Compiling DisplayRocker.C --> DisplayRocker.o ...
  1492. echo "Compiling " DispCmds.C " --> " DispCmds.o " ..."; \
  1493. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c DispCmds.C -o ../LINUXAMD64/DispCmds.o
  1494. Compiling DispCmds.C --> DispCmds.o ...
  1495. echo "Compiling " DrawMolecule.C " --> " DrawMolecule.o " ..."; \
  1496. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c DrawMolecule.C -o ../LINUXAMD64/DrawMolecule.o
  1497. Compiling DrawMolecule.C --> DrawMolecule.o ...
  1498. echo "Compiling " DrawMolItem.C " --> " DrawMolItem.o " ..."; \
  1499. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c DrawMolItem.C -o ../LINUXAMD64/DrawMolItem.o
  1500. Compiling DrawMolItem.C --> DrawMolItem.o ...
  1501. echo "Compiling " DrawMolItem2.C " --> " DrawMolItem2.o " ..."; \
  1502. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c DrawMolItem2.C -o ../LINUXAMD64/DrawMolItem2.o
  1503. Compiling DrawMolItem2.C --> DrawMolItem2.o ...
  1504. echo "Compiling " DrawMolItemRibbons.C " --> " DrawMolItemRibbons.o " ..."; \
  1505. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c DrawMolItemRibbons.C -o ../LINUXAMD64/DrawMolItemRibbons.o
  1506. Compiling DrawMolItemRibbons.C --> DrawMolItemRibbons.o ...
  1507. DrawMolItemRibbons.C: In member function 'void DrawMolItem::draw_spline_new(int, const float*, const float*, const int*, const float*, const float*, int, int, int)':
  1508. DrawMolItemRibbons.C:1484: warning: 'q[3][2]' may be used uninitialized in this function
  1509. DrawMolItemRibbons.C:1484: warning: 'q[3][1]' may be used uninitialized in this function
  1510. DrawMolItemRibbons.C:1484: warning: 'q[3][0]' may be used uninitialized in this function
  1511. DrawMolItemRibbons.C:1484: warning: 'q[2][2]' may be used uninitialized in this function
  1512. DrawMolItemRibbons.C:1484: warning: 'q[2][1]' may be used uninitialized in this function
  1513. DrawMolItemRibbons.C:1484: warning: 'q[2][0]' may be used uninitialized in this function
  1514. DrawMolItemRibbons.C:1484: warning: 'q[1][2]' may be used uninitialized in this function
  1515. DrawMolItemRibbons.C:1484: warning: 'q[1][1]' may be used uninitialized in this function
  1516. DrawMolItemRibbons.C:1484: warning: 'q[1][0]' may be used uninitialized in this function
  1517. DrawMolItemRibbons.C:1484: warning: 'q[0][2]' may be used uninitialized in this function
  1518. DrawMolItemRibbons.C:1484: warning: 'q[0][1]' may be used uninitialized in this function
  1519. DrawMolItemRibbons.C:1484: warning: 'q[0][0]' may be used uninitialized in this function
  1520. echo "Compiling " DrawMolItemMSMS.C " --> " DrawMolItemMSMS.o " ..."; \
  1521. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c DrawMolItemMSMS.C -o ../LINUXAMD64/DrawMolItemMSMS.o
  1522. Compiling DrawMolItemMSMS.C --> DrawMolItemMSMS.o ...
  1523. echo "Compiling " DrawMolItemNanoShaper.C " --> " DrawMolItemNanoShaper.o " ..."; \
  1524. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c DrawMolItemNanoShaper.C -o ../LINUXAMD64/DrawMolItemNanoShaper.o
  1525. Compiling DrawMolItemNanoShaper.C --> DrawMolItemNanoShaper.o ...
  1526. echo "Compiling " DrawMolItemRings.C " --> " DrawMolItemRings.o " ..."; \
  1527. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c DrawMolItemRings.C -o ../LINUXAMD64/DrawMolItemRings.o
  1528. Compiling DrawMolItemRings.C --> DrawMolItemRings.o ...
  1529. echo "Compiling " DrawMolItemOrbital.C " --> " DrawMolItemOrbital.o " ..."; \
  1530. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c DrawMolItemOrbital.C -o ../LINUXAMD64/DrawMolItemOrbital.o
  1531. Compiling DrawMolItemOrbital.C --> DrawMolItemOrbital.o ...
  1532. echo "Compiling " DrawMolItemQuickSurf.C " --> " DrawMolItemQuickSurf.o " ..."; \
  1533. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c DrawMolItemQuickSurf.C -o ../LINUXAMD64/DrawMolItemQuickSurf.o
  1534. Compiling DrawMolItemQuickSurf.C --> DrawMolItemQuickSurf.o ...
  1535. echo "Compiling " DrawMolItemSurface.C " --> " DrawMolItemSurface.o " ..."; \
  1536. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c DrawMolItemSurface.C -o ../LINUXAMD64/DrawMolItemSurface.o
  1537. Compiling DrawMolItemSurface.C --> DrawMolItemSurface.o ...
  1538. echo "Compiling " DrawMolItemVolume.C " --> " DrawMolItemVolume.o " ..."; \
  1539. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c DrawMolItemVolume.C -o ../LINUXAMD64/DrawMolItemVolume.o
  1540. Compiling DrawMolItemVolume.C --> DrawMolItemVolume.o ...
  1541. echo "Compiling " DrawForce.C " --> " DrawForce.o " ..."; \
  1542. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c DrawForce.C -o ../LINUXAMD64/DrawForce.o
  1543. Compiling DrawForce.C --> DrawForce.o ...
  1544. echo "Compiling " DrawRingsUtils.C " --> " DrawRingsUtils.o " ..."; \
  1545. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c DrawRingsUtils.C -o ../LINUXAMD64/DrawRingsUtils.o
  1546. Compiling DrawRingsUtils.C --> DrawRingsUtils.o ...
  1547. DrawRingsUtils.C: In function 'void hotcold_gradient_lerp(float, float*)':
  1548. DrawRingsUtils.C:48: warning: unused variable 'yellow2'
  1549. echo "Compiling " FileRenderList.C " --> " FileRenderList.o " ..."; \
  1550. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c FileRenderList.C -o ../LINUXAMD64/FileRenderList.o
  1551. Compiling FileRenderList.C --> FileRenderList.o ...
  1552. echo "Compiling " FileRenderer.C " --> " FileRenderer.o " ..."; \
  1553. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c FileRenderer.C -o ../LINUXAMD64/FileRenderer.o
  1554. Compiling FileRenderer.C --> FileRenderer.o ...
  1555. echo "Compiling " FPS.C " --> " FPS.o " ..."; \
  1556. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c FPS.C -o ../LINUXAMD64/FPS.o
  1557. Compiling FPS.C --> FPS.o ...
  1558. echo "Compiling " GelatoDisplayDevice.C " --> " GelatoDisplayDevice.o " ..."; \
  1559. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c GelatoDisplayDevice.C -o ../LINUXAMD64/GelatoDisplayDevice.o
  1560. Compiling GelatoDisplayDevice.C --> GelatoDisplayDevice.o ...
  1561. echo "Compiling " GeometryAngle.C " --> " GeometryAngle.o " ..."; \
  1562. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c GeometryAngle.C -o ../LINUXAMD64/GeometryAngle.o
  1563. Compiling GeometryAngle.C --> GeometryAngle.o ...
  1564. echo "Compiling " GeometryAtom.C " --> " GeometryAtom.o " ..."; \
  1565. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c GeometryAtom.C -o ../LINUXAMD64/GeometryAtom.o
  1566. Compiling GeometryAtom.C --> GeometryAtom.o ...
  1567. echo "Compiling " GeometryBond.C " --> " GeometryBond.o " ..."; \
  1568. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c GeometryBond.C -o ../LINUXAMD64/GeometryBond.o
  1569. Compiling GeometryBond.C --> GeometryBond.o ...
  1570. echo "Compiling " GeometryDihedral.C " --> " GeometryDihedral.o " ..."; \
  1571. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c GeometryDihedral.C -o ../LINUXAMD64/GeometryDihedral.o
  1572. Compiling GeometryDihedral.C --> GeometryDihedral.o ...
  1573. echo "Compiling " GeometryList.C " --> " GeometryList.o " ..."; \
  1574. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c GeometryList.C -o ../LINUXAMD64/GeometryList.o
  1575. Compiling GeometryList.C --> GeometryList.o ...
  1576. echo "Compiling " GeometryMol.C " --> " GeometryMol.o " ..."; \
  1577. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c GeometryMol.C -o ../LINUXAMD64/GeometryMol.o
  1578. Compiling GeometryMol.C --> GeometryMol.o ...
  1579. echo "Compiling " GeometrySpring.C " --> " GeometrySpring.o " ..."; \
  1580. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c GeometrySpring.C -o ../LINUXAMD64/GeometrySpring.o
  1581. Compiling GeometrySpring.C --> GeometrySpring.o ...
  1582. echo "Compiling " Hershey.C " --> " Hershey.o " ..."; \
  1583. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Hershey.C -o ../LINUXAMD64/Hershey.o
  1584. Compiling Hershey.C --> Hershey.o ...
  1585. echo "Compiling " HMDMgr.C " --> " HMDMgr.o " ..."; \
  1586. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c HMDMgr.C -o ../LINUXAMD64/HMDMgr.o
  1587. Compiling HMDMgr.C --> HMDMgr.o ...
  1588. HMDMgr.C:36: warning: 'void quat_rot_matrix(float*, const float*)' defined but not used
  1589. echo "Compiling " Inform.C " --> " Inform.o " ..."; \
  1590. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Inform.C -o ../LINUXAMD64/Inform.o
  1591. Compiling Inform.C --> Inform.o ...
  1592. echo "Compiling " ImageIO.C " --> " ImageIO.o " ..."; \
  1593. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c ImageIO.C -o ../LINUXAMD64/ImageIO.o
  1594. Compiling ImageIO.C --> ImageIO.o ...
  1595. echo "Compiling " Isosurface.C " --> " Isosurface.o " ..."; \
  1596. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Isosurface.C -o ../LINUXAMD64/Isosurface.o
  1597. Compiling Isosurface.C --> Isosurface.o ...
  1598. echo "Compiling " JRegex.C " --> " JRegex.o " ..."; \
  1599. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c JRegex.C -o ../LINUXAMD64/JRegex.o
  1600. Compiling JRegex.C --> JRegex.o ...
  1601. echo "Compiling " JString.C " --> " JString.o " ..."; \
  1602. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c JString.C -o ../LINUXAMD64/JString.o
  1603. Compiling JString.C --> JString.o ...
  1604. echo "Compiling " macosxvmdstart.C " --> " macosxvmdstart.o " ..."; \
  1605. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c macosxvmdstart.C -o ../LINUXAMD64/macosxvmdstart.o
  1606. Compiling macosxvmdstart.C --> macosxvmdstart.o ...
  1607. echo "Compiling " MaterialList.C " --> " MaterialList.o " ..."; \
  1608. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c MaterialList.C -o ../LINUXAMD64/MaterialList.o
  1609. Compiling MaterialList.C --> MaterialList.o ...
  1610. echo "Compiling " Matrix4.C " --> " Matrix4.o " ..."; \
  1611. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Matrix4.C -o ../LINUXAMD64/Matrix4.o
  1612. Compiling Matrix4.C --> Matrix4.o ...
  1613. echo "Compiling " MayaDisplayDevice.C " --> " MayaDisplayDevice.o " ..."; \
  1614. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c MayaDisplayDevice.C -o ../LINUXAMD64/MayaDisplayDevice.o
  1615. Compiling MayaDisplayDevice.C --> MayaDisplayDevice.o ...
  1616. echo "Compiling " MDFF.C " --> " MDFF.o " ..."; \
  1617. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c MDFF.C -o ../LINUXAMD64/MDFF.o
  1618. Compiling MDFF.C --> MDFF.o ...
  1619. echo "Compiling " Measure.C " --> " Measure.o " ..."; \
  1620. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Measure.C -o ../LINUXAMD64/Measure.o
  1621. Compiling Measure.C --> Measure.o ...
  1622. echo "Compiling " MeasureCluster.C " --> " MeasureCluster.o " ..."; \
  1623. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c MeasureCluster.C -o ../LINUXAMD64/MeasureCluster.o
  1624. Compiling MeasureCluster.C --> MeasureCluster.o ...
  1625. echo "Compiling " MeasurePBC.C " --> " MeasurePBC.o " ..."; \
  1626. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c MeasurePBC.C -o ../LINUXAMD64/MeasurePBC.o
  1627. Compiling MeasurePBC.C --> MeasurePBC.o ...
  1628. echo "Compiling " MeasureRDF.C " --> " MeasureRDF.o " ..."; \
  1629. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c MeasureRDF.C -o ../LINUXAMD64/MeasureRDF.o
  1630. Compiling MeasureRDF.C --> MeasureRDF.o ...
  1631. echo "Compiling " MeasureQCP.C " --> " MeasureQCP.o " ..."; \
  1632. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c MeasureQCP.C -o ../LINUXAMD64/MeasureQCP.o
  1633. Compiling MeasureQCP.C --> MeasureQCP.o ...
  1634. echo "Compiling " MeasureSurface.C " --> " MeasureSurface.o " ..."; \
  1635. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c MeasureSurface.C -o ../LINUXAMD64/MeasureSurface.o
  1636. Compiling MeasureSurface.C --> MeasureSurface.o ...
  1637. echo "Compiling " MeasureSymmetry.C " --> " MeasureSymmetry.o " ..."; \
  1638. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c MeasureSymmetry.C -o ../LINUXAMD64/MeasureSymmetry.o
  1639. Compiling MeasureSymmetry.C --> MeasureSymmetry.o ...
  1640. echo "Compiling " MobileInterface.C " --> " MobileInterface.o " ..."; \
  1641. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c MobileInterface.C -o ../LINUXAMD64/MobileInterface.o
  1642. Compiling MobileInterface.C --> MobileInterface.o ...
  1643. MobileInterface.C: In function 'int mobile_listener_poll(void*, float&, float&, float&, float&, float&, float&, int&, int&, int&, int*, float*, float*, int&, int&, JString&, JString&, int&, float&, float&, float&, JString&)':
  1644. MobileInterface.C:254: warning: dereferencing type-punned pointer will break strict-aliasing rules
  1645. MobileInterface.C:257: warning: dereferencing type-punned pointer will break strict-aliasing rules
  1646. echo "Compiling " MobileButtons.C " --> " MobileButtons.o " ..."; \
  1647. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c MobileButtons.C -o ../LINUXAMD64/MobileButtons.o
  1648. Compiling MobileButtons.C --> MobileButtons.o ...
  1649. echo "Compiling " MobileTracker.C " --> " MobileTracker.o " ..."; \
  1650. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c MobileTracker.C -o ../LINUXAMD64/MobileTracker.o
  1651. Compiling MobileTracker.C --> MobileTracker.o ...
  1652. echo "Compiling " Molecule.C " --> " Molecule.o " ..."; \
  1653. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Molecule.C -o ../LINUXAMD64/Molecule.o
  1654. Compiling Molecule.C --> Molecule.o ...
  1655. echo "Compiling " MoleculeList.C " --> " MoleculeList.o " ..."; \
  1656. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c MoleculeList.C -o ../LINUXAMD64/MoleculeList.o
  1657. Compiling MoleculeList.C --> MoleculeList.o ...
  1658. echo "Compiling " MoleculeGraphics.C " --> " MoleculeGraphics.o " ..."; \
  1659. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c MoleculeGraphics.C -o ../LINUXAMD64/MoleculeGraphics.o
  1660. Compiling MoleculeGraphics.C --> MoleculeGraphics.o ...
  1661. echo "Compiling " MolFilePlugin.C " --> " MolFilePlugin.o " ..."; \
  1662. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c MolFilePlugin.C -o ../LINUXAMD64/MolFilePlugin.o
  1663. Compiling MolFilePlugin.C --> MolFilePlugin.o ...
  1664. MolFilePlugin.C: In member function 'int MolFilePlugin::read_structure(Molecule*, int, int)':
  1665. MolFilePlugin.C:88: warning: comparison between signed and unsigned integer expressions
  1666. MolFilePlugin.C: In member function 'int MolFilePlugin::read_optional_structure(Molecule*, int)':
  1667. MolFilePlugin.C:410: warning: comparison between signed and unsigned integer expressions
  1668. echo "Compiling " Mouse.C " --> " Mouse.o " ..."; \
  1669. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Mouse.C -o ../LINUXAMD64/Mouse.o
  1670. Compiling Mouse.C --> Mouse.o ...
  1671. echo "Compiling " MSMSInterface.C " --> " MSMSInterface.o " ..."; \
  1672. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c MSMSInterface.C -o ../LINUXAMD64/MSMSInterface.o
  1673. Compiling MSMSInterface.C --> MSMSInterface.o ...
  1674. echo "Compiling " NanoShaperInterface.C " --> " NanoShaperInterface.o " ..."; \
  1675. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c NanoShaperInterface.C -o ../LINUXAMD64/NanoShaperInterface.o
  1676. Compiling NanoShaperInterface.C --> NanoShaperInterface.o ...
  1677. echo "Compiling " Orbital.C " --> " Orbital.o " ..."; \
  1678. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Orbital.C -o ../LINUXAMD64/Orbital.o
  1679. Compiling Orbital.C --> Orbital.o ...
  1680. echo "Compiling " OrbitalJIT.C " --> " OrbitalJIT.o " ..."; \
  1681. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c OrbitalJIT.C -o ../LINUXAMD64/OrbitalJIT.o
  1682. Compiling OrbitalJIT.C --> OrbitalJIT.o ...
  1683. echo "Compiling " PeriodicTable.C " --> " PeriodicTable.o " ..."; \
  1684. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c PeriodicTable.C -o ../LINUXAMD64/PeriodicTable.o
  1685. Compiling PeriodicTable.C --> PeriodicTable.o ...
  1686. echo "Compiling " P_JoystickTool.C " --> " P_JoystickTool.o " ..."; \
  1687. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c P_JoystickTool.C -o ../LINUXAMD64/P_JoystickTool.o
  1688. Compiling P_JoystickTool.C --> P_JoystickTool.o ...
  1689. echo "Compiling " P_TugTool.C " --> " P_TugTool.o " ..."; \
  1690. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c P_TugTool.C -o ../LINUXAMD64/P_TugTool.o
  1691. Compiling P_TugTool.C --> P_TugTool.o ...
  1692. echo "Compiling " P_GrabTool.C " --> " P_GrabTool.o " ..."; \
  1693. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c P_GrabTool.C -o ../LINUXAMD64/P_GrabTool.o
  1694. Compiling P_GrabTool.C --> P_GrabTool.o ...
  1695. echo "Compiling " P_PrintTool.C " --> " P_PrintTool.o " ..."; \
  1696. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c P_PrintTool.C -o ../LINUXAMD64/P_PrintTool.o
  1697. Compiling P_PrintTool.C --> P_PrintTool.o ...
  1698. echo "Compiling " P_PinchTool.C " --> " P_PinchTool.o " ..."; \
  1699. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c P_PinchTool.C -o ../LINUXAMD64/P_PinchTool.o
  1700. Compiling P_PinchTool.C --> P_PinchTool.o ...
  1701. echo "Compiling " P_UIVR.C " --> " P_UIVR.o " ..."; \
  1702. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c P_UIVR.C -o ../LINUXAMD64/P_UIVR.o
  1703. Compiling P_UIVR.C --> P_UIVR.o ...
  1704. echo "Compiling " P_Buttons.C " --> " P_Buttons.o " ..."; \
  1705. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c P_Buttons.C -o ../LINUXAMD64/P_Buttons.o
  1706. Compiling P_Buttons.C --> P_Buttons.o ...
  1707. echo "Compiling " P_Tracker.C " --> " P_Tracker.o " ..."; \
  1708. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c P_Tracker.C -o ../LINUXAMD64/P_Tracker.o
  1709. Compiling P_Tracker.C --> P_Tracker.o ...
  1710. echo "Compiling " P_Tool.C " --> " P_Tool.o " ..."; \
  1711. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c P_Tool.C -o ../LINUXAMD64/P_Tool.o
  1712. Compiling P_Tool.C --> P_Tool.o ...
  1713. echo "Compiling " P_CmdTool.C " --> " P_CmdTool.o " ..."; \
  1714. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c P_CmdTool.C -o ../LINUXAMD64/P_CmdTool.o
  1715. Compiling P_CmdTool.C --> P_CmdTool.o ...
  1716. echo "Compiling " P_SensorConfig.C " --> " P_SensorConfig.o " ..."; \
  1717. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c P_SensorConfig.C -o ../LINUXAMD64/P_SensorConfig.o
  1718. Compiling P_SensorConfig.C --> P_SensorConfig.o ...
  1719. echo "Compiling " ParseTree.C " --> " ParseTree.o " ..."; \
  1720. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c ParseTree.C -o ../LINUXAMD64/ParseTree.o
  1721. Compiling ParseTree.C --> ParseTree.o ...
  1722. ParseTree.C: In member function 'void ParseTree::eval_k_nearest(atomparser_node*, int, int*)':
  1723. ParseTree.C:979: warning: comparison between signed and unsigned integer expressions
  1724. echo "Compiling " PickList.C " --> " PickList.o " ..."; \
  1725. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c PickList.C -o ../LINUXAMD64/PickList.o
  1726. Compiling PickList.C --> PickList.o ...
  1727. echo "Compiling " PickModeAddBond.C " --> " PickModeAddBond.o " ..."; \
  1728. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c PickModeAddBond.C -o ../LINUXAMD64/PickModeAddBond.o
  1729. Compiling PickModeAddBond.C --> PickModeAddBond.o ...
  1730. echo "Compiling " PickModeCenter.C " --> " PickModeCenter.o " ..."; \
  1731. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c PickModeCenter.C -o ../LINUXAMD64/PickModeCenter.o
  1732. Compiling PickModeCenter.C --> PickModeCenter.o ...
  1733. echo "Compiling " PickModeForce.C " --> " PickModeForce.o " ..."; \
  1734. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c PickModeForce.C -o ../LINUXAMD64/PickModeForce.o
  1735. Compiling PickModeForce.C --> PickModeForce.o ...
  1736. echo "Compiling " PickModeList.C " --> " PickModeList.o " ..."; \
  1737. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c PickModeList.C -o ../LINUXAMD64/PickModeList.o
  1738. Compiling PickModeList.C --> PickModeList.o ...
  1739. echo "Compiling " PickModeMolLabel.C " --> " PickModeMolLabel.o " ..."; \
  1740. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c PickModeMolLabel.C -o ../LINUXAMD64/PickModeMolLabel.o
  1741. Compiling PickModeMolLabel.C --> PickModeMolLabel.o ...
  1742. echo "Compiling " PickModeMove.C " --> " PickModeMove.o " ..."; \
  1743. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c PickModeMove.C -o ../LINUXAMD64/PickModeMove.o
  1744. Compiling PickModeMove.C --> PickModeMove.o ...
  1745. echo "Compiling " PickModeUser.C " --> " PickModeUser.o " ..."; \
  1746. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c PickModeUser.C -o ../LINUXAMD64/PickModeUser.o
  1747. Compiling PickModeUser.C --> PickModeUser.o ...
  1748. echo "Compiling " PlainTextInterp.C " --> " PlainTextInterp.o " ..."; \
  1749. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c PlainTextInterp.C -o ../LINUXAMD64/PlainTextInterp.o
  1750. Compiling PlainTextInterp.C --> PlainTextInterp.o ...
  1751. echo "Compiling " PluginMgr.C " --> " PluginMgr.o " ..."; \
  1752. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c PluginMgr.C -o ../LINUXAMD64/PluginMgr.o
  1753. Compiling PluginMgr.C --> PluginMgr.o ...
  1754. echo "Compiling " POV3DisplayDevice.C " --> " POV3DisplayDevice.o " ..."; \
  1755. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c POV3DisplayDevice.C -o ../LINUXAMD64/POV3DisplayDevice.o
  1756. Compiling POV3DisplayDevice.C --> POV3DisplayDevice.o ...
  1757. echo "Compiling " PSDisplayDevice.C " --> " PSDisplayDevice.o " ..."; \
  1758. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c PSDisplayDevice.C -o ../LINUXAMD64/PSDisplayDevice.o
  1759. Compiling PSDisplayDevice.C --> PSDisplayDevice.o ...
  1760. echo "Compiling " QMData.C " --> " QMData.o " ..."; \
  1761. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c QMData.C -o ../LINUXAMD64/QMData.o
  1762. Compiling QMData.C --> QMData.o ...
  1763. echo "Compiling " QMTimestep.C " --> " QMTimestep.o " ..."; \
  1764. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c QMTimestep.C -o ../LINUXAMD64/QMTimestep.o
  1765. Compiling QMTimestep.C --> QMTimestep.o ...
  1766. echo "Compiling " QuickSurf.C " --> " QuickSurf.o " ..."; \
  1767. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c QuickSurf.C -o ../LINUXAMD64/QuickSurf.o
  1768. Compiling QuickSurf.C --> QuickSurf.o ...
  1769. QuickSurf.C: In function 'void vmd_gaussdensity_opt(int, int, const float*, const float*, const float*, float*, float*, const int*, float, float, float, float)':
  1770. QuickSurf.C:402: warning: 'gridspacing4_4' may be used uninitialized in this function
  1771. QuickSurf.C:474: warning: 'atomicnumfactor_4' may be used uninitialized in this function
  1772. QuickSurf.C:475: warning: 'arinv_4' may be used uninitialized in this function
  1773. QuickSurf.C:1034: warning: 'atomicnumfactor_4' may be used uninitialized in this function
  1774. QuickSurf.C:1035: warning: 'arinv_4' may be used uninitialized in this function
  1775. echo "Compiling " RadianceDisplayDevice.C " --> " RadianceDisplayDevice.o " ..."; \
  1776. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c RadianceDisplayDevice.C -o ../LINUXAMD64/RadianceDisplayDevice.o
  1777. Compiling RadianceDisplayDevice.C --> RadianceDisplayDevice.o ...
  1778. echo "Compiling " RayShadeDisplayDevice.C " --> " RayShadeDisplayDevice.o " ..."; \
  1779. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c RayShadeDisplayDevice.C -o ../LINUXAMD64/RayShadeDisplayDevice.o
  1780. Compiling RayShadeDisplayDevice.C --> RayShadeDisplayDevice.o ...
  1781. echo "Compiling " R3dDisplayDevice.C " --> " R3dDisplayDevice.o " ..."; \
  1782. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c R3dDisplayDevice.C -o ../LINUXAMD64/R3dDisplayDevice.o
  1783. Compiling R3dDisplayDevice.C --> R3dDisplayDevice.o ...
  1784. echo "Compiling " RenderManDisplayDevice.C " --> " RenderManDisplayDevice.o " ..."; \
  1785. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c RenderManDisplayDevice.C -o ../LINUXAMD64/RenderManDisplayDevice.o
  1786. Compiling RenderManDisplayDevice.C --> RenderManDisplayDevice.o ...
  1787. echo "Compiling " Scene.C " --> " Scene.o " ..."; \
  1788. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Scene.C -o ../LINUXAMD64/Scene.o
  1789. Compiling Scene.C --> Scene.o ...
  1790. echo "Compiling " SnapshotDisplayDevice.C " --> " SnapshotDisplayDevice.o " ..."; \
  1791. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c SnapshotDisplayDevice.C -o ../LINUXAMD64/SnapshotDisplayDevice.o
  1792. Compiling SnapshotDisplayDevice.C --> SnapshotDisplayDevice.o ...
  1793. echo "Compiling " Spaceball.C " --> " Spaceball.o " ..."; \
  1794. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Spaceball.C -o ../LINUXAMD64/Spaceball.o
  1795. Compiling Spaceball.C --> Spaceball.o ...
  1796. echo "Compiling " SpaceballButtons.C " --> " SpaceballButtons.o " ..."; \
  1797. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c SpaceballButtons.C -o ../LINUXAMD64/SpaceballButtons.o
  1798. Compiling SpaceballButtons.C --> SpaceballButtons.o ...
  1799. echo "Compiling " SpaceballTracker.C " --> " SpaceballTracker.o " ..."; \
  1800. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c SpaceballTracker.C -o ../LINUXAMD64/SpaceballTracker.o
  1801. Compiling SpaceballTracker.C --> SpaceballTracker.o ...
  1802. echo "Compiling " SpatialSearch.C " --> " SpatialSearch.o " ..."; \
  1803. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c SpatialSearch.C -o ../LINUXAMD64/SpatialSearch.o
  1804. Compiling SpatialSearch.C --> SpatialSearch.o ...
  1805. echo "Compiling " SpringTool.C " --> " SpringTool.o " ..."; \
  1806. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c SpringTool.C -o ../LINUXAMD64/SpringTool.o
  1807. Compiling SpringTool.C --> SpringTool.o ...
  1808. echo "Compiling " Stage.C " --> " Stage.o " ..."; \
  1809. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Stage.C -o ../LINUXAMD64/Stage.o
  1810. Compiling Stage.C --> Stage.o ...
  1811. echo "Compiling " STLDisplayDevice.C " --> " STLDisplayDevice.o " ..."; \
  1812. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c STLDisplayDevice.C -o ../LINUXAMD64/STLDisplayDevice.o
  1813. Compiling STLDisplayDevice.C --> STLDisplayDevice.o ...
  1814. echo "Compiling " Stride.C " --> " Stride.o " ..."; \
  1815. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Stride.C -o ../LINUXAMD64/Stride.o
  1816. Compiling Stride.C --> Stride.o ...
  1817. echo "Compiling " Surf.C " --> " Surf.o " ..."; \
  1818. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Surf.C -o ../LINUXAMD64/Surf.o
  1819. Compiling Surf.C --> Surf.o ...
  1820. echo "Compiling " SymbolTable.C " --> " SymbolTable.o " ..."; \
  1821. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c SymbolTable.C -o ../LINUXAMD64/SymbolTable.o
  1822. Compiling SymbolTable.C --> SymbolTable.o ...
  1823. echo "Compiling " TachyonDisplayDevice.C " --> " TachyonDisplayDevice.o " ..."; \
  1824. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c TachyonDisplayDevice.C -o ../LINUXAMD64/TachyonDisplayDevice.o
  1825. Compiling TachyonDisplayDevice.C --> TachyonDisplayDevice.o ...
  1826. echo "Compiling " Timestep.C " --> " Timestep.o " ..."; \
  1827. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Timestep.C -o ../LINUXAMD64/Timestep.o
  1828. Compiling Timestep.C --> Timestep.o ...
  1829. echo "Compiling " UIObject.C " --> " UIObject.o " ..."; \
  1830. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c UIObject.C -o ../LINUXAMD64/UIObject.o
  1831. Compiling UIObject.C --> UIObject.o ...
  1832. echo "Compiling " UIText.C " --> " UIText.o " ..."; \
  1833. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c UIText.C -o ../LINUXAMD64/UIText.o
  1834. Compiling UIText.C --> UIText.o ...
  1835. echo "Compiling " VMDApp.C " --> " VMDApp.o " ..."; \
  1836. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c VMDApp.C -o ../LINUXAMD64/VMDApp.o
  1837. Compiling VMDApp.C --> VMDApp.o ...
  1838. echo "Compiling " VMDCollab.C " --> " VMDCollab.o " ..."; \
  1839. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c VMDCollab.C -o ../LINUXAMD64/VMDCollab.o
  1840. Compiling VMDCollab.C --> VMDCollab.o ...
  1841. echo "Compiling " VMDDir.C " --> " VMDDir.o " ..."; \
  1842. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c VMDDir.C -o ../LINUXAMD64/VMDDir.o
  1843. Compiling VMDDir.C --> VMDDir.o ...
  1844. echo "Compiling " VMDDisplayList.C " --> " VMDDisplayList.o " ..."; \
  1845. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c VMDDisplayList.C -o ../LINUXAMD64/VMDDisplayList.o
  1846. Compiling VMDDisplayList.C --> VMDDisplayList.o ...
  1847. echo "Compiling " VMDMenu.C " --> " VMDMenu.o " ..."; \
  1848. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c VMDMenu.C -o ../LINUXAMD64/VMDMenu.o
  1849. Compiling VMDMenu.C --> VMDMenu.o ...
  1850. echo "Compiling " VMDQuat.C " --> " VMDQuat.o " ..."; \
  1851. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c VMDQuat.C -o ../LINUXAMD64/VMDQuat.o
  1852. Compiling VMDQuat.C --> VMDQuat.o ...
  1853. echo "Compiling " VMDTitle.C " --> " VMDTitle.o " ..."; \
  1854. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c VMDTitle.C -o ../LINUXAMD64/VMDTitle.o
  1855. Compiling VMDTitle.C --> VMDTitle.o ...
  1856. echo "Compiling " VMDThreads.C " --> " VMDThreads.o " ..."; \
  1857. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c VMDThreads.C -o ../LINUXAMD64/VMDThreads.o
  1858. Compiling VMDThreads.C --> VMDThreads.o ...
  1859. echo "Compiling " VolCPotential.C " --> " VolCPotential.o " ..."; \
  1860. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c VolCPotential.C -o ../LINUXAMD64/VolCPotential.o
  1861. Compiling VolCPotential.C --> VolCPotential.o ...
  1862. echo "Compiling " VolMapCreate.C " --> " VolMapCreate.o " ..."; \
  1863. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c VolMapCreate.C -o ../LINUXAMD64/VolMapCreate.o
  1864. Compiling VolMapCreate.C --> VolMapCreate.o ...
  1865. echo "Compiling " VolMapCreateILS.C " --> " VolMapCreateILS.o " ..."; \
  1866. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c VolMapCreateILS.C -o ../LINUXAMD64/VolMapCreateILS.o
  1867. Compiling VolMapCreateILS.C --> VolMapCreateILS.o ...
  1868. echo "Compiling " VolumetricData.C " --> " VolumetricData.o " ..."; \
  1869. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c VolumetricData.C -o ../LINUXAMD64/VolumetricData.o
  1870. Compiling VolumetricData.C --> VolumetricData.o ...
  1871. echo "Compiling " VolumeTexture.C " --> " VolumeTexture.o " ..."; \
  1872. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c VolumeTexture.C -o ../LINUXAMD64/VolumeTexture.o
  1873. Compiling VolumeTexture.C --> VolumeTexture.o ...
  1874. echo "Compiling " VrmlDisplayDevice.C " --> " VrmlDisplayDevice.o " ..."; \
  1875. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c VrmlDisplayDevice.C -o ../LINUXAMD64/VrmlDisplayDevice.o
  1876. Compiling VrmlDisplayDevice.C --> VrmlDisplayDevice.o ...
  1877. echo "Compiling " Vrml2DisplayDevice.C " --> " Vrml2DisplayDevice.o " ..."; \
  1878. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c Vrml2DisplayDevice.C -o ../LINUXAMD64/Vrml2DisplayDevice.o
  1879. Compiling Vrml2DisplayDevice.C --> Vrml2DisplayDevice.o ...
  1880. echo "Compiling " WavefrontDisplayDevice.C " --> " WavefrontDisplayDevice.o " ..."; \
  1881. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c WavefrontDisplayDevice.C -o ../LINUXAMD64/WavefrontDisplayDevice.o
  1882. Compiling WavefrontDisplayDevice.C --> WavefrontDisplayDevice.o ...
  1883. echo "Compiling " WKFThreads.C " --> " WKFThreads.o " ..."; \
  1884. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c WKFThreads.C -o ../LINUXAMD64/WKFThreads.o
  1885. Compiling WKFThreads.C --> WKFThreads.o ...
  1886. echo "Compiling " WKFUtils.C " --> " WKFUtils.o " ..."; \
  1887. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c WKFUtils.C -o ../LINUXAMD64/WKFUtils.o
  1888. Compiling WKFUtils.C --> WKFUtils.o ...
  1889. echo "Compiling " utilities.C " --> " utilities.o " ..."; \
  1890. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c utilities.C -o ../LINUXAMD64/utilities.o
  1891. Compiling utilities.C --> utilities.o ...
  1892. echo "Compiling " util_simd.C " --> " util_simd.o " ..."; \
  1893. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c util_simd.C -o ../LINUXAMD64/util_simd.o
  1894. Compiling util_simd.C --> util_simd.o ...
  1895. echo "Compiling " vmd.C " --> " vmd.o " ..."; \
  1896. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c vmd.C -o ../LINUXAMD64/vmd.o
  1897. Compiling vmd.C --> vmd.o ...
  1898. echo "Compiling " vmdmain.C " --> " vmdmain.o " ..."; \
  1899. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c vmdmain.C -o ../LINUXAMD64/vmdmain.o
  1900. Compiling vmdmain.C --> vmdmain.o ...
  1901. echo "Compiling " X3DDisplayDevice.C " --> " X3DDisplayDevice.o " ..."; \
  1902. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c X3DDisplayDevice.C -o ../LINUXAMD64/X3DDisplayDevice.o
  1903. Compiling X3DDisplayDevice.C --> X3DDisplayDevice.o ...
  1904. echo "Compiling " hash.c " --> " hash.o " ..."; \
  1905. gcc -m64 -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c hash.c -o ../LINUXAMD64/hash.o
  1906. Compiling hash.c --> hash.o ...
  1907. echo "Compiling " inthash.c " --> " inthash.o " ..."; \
  1908. gcc -m64 -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c inthash.c -o ../LINUXAMD64/inthash.o
  1909. Compiling inthash.c --> inthash.o ...
  1910. echo "Compiling " intstack.c " --> " intstack.o " ..."; \
  1911. gcc -m64 -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c intstack.c -o ../LINUXAMD64/intstack.o
  1912. Compiling intstack.c --> intstack.o ...
  1913. echo "Compiling " ptrstack.c " --> " ptrstack.o " ..."; \
  1914. gcc -m64 -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c ptrstack.c -o ../LINUXAMD64/ptrstack.o
  1915. Compiling ptrstack.c --> ptrstack.o ...
  1916. echo "Compiling " msmpot.c " --> " msmpot.o " ..."; \
  1917. gcc -m64 -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c msmpot.c -o ../LINUXAMD64/msmpot.o
  1918. Compiling msmpot.c --> msmpot.o ...
  1919. echo "Compiling " msmpot_compute.c " --> " msmpot_compute.o " ..."; \
  1920. gcc -m64 -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c msmpot_compute.c -o ../LINUXAMD64/msmpot_compute.o
  1921. Compiling msmpot_compute.c --> msmpot_compute.o ...
  1922. echo "Compiling " msmpot_cubic.c " --> " msmpot_cubic.o " ..."; \
  1923. gcc -m64 -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c msmpot_cubic.c -o ../LINUXAMD64/msmpot_cubic.o
  1924. Compiling msmpot_cubic.c --> msmpot_cubic.o ...
  1925. echo "Compiling " msmpot_setup.c " --> " msmpot_setup.o " ..."; \
  1926. gcc -m64 -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c msmpot_setup.c -o ../LINUXAMD64/msmpot_setup.o
  1927. Compiling msmpot_setup.c --> msmpot_setup.o ...
  1928. echo "Compiling " vmdsock.c " --> " vmdsock.o " ..."; \
  1929. gcc -m64 -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c vmdsock.c -o ../LINUXAMD64/vmdsock.o
  1930. Compiling vmdsock.c --> vmdsock.o ...
  1931. vmdsock.c: In function 'vmdsock_accept':
  1932. vmdsock.c:133: warning: pointer targets in passing argument 3 of 'accept' differ in signedness
  1933. /usr/include/sys/socket.h:214: note: expected 'socklen_t * __restrict__' but argument is of type 'int *'
  1934. echo "Compiling " vmddlopen.c " --> " vmddlopen.o " ..."; \
  1935. gcc -m64 -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c vmddlopen.c -o ../LINUXAMD64/vmddlopen.o
  1936. Compiling vmddlopen.c --> vmddlopen.o ...
  1937. echo "Compiling " pcre.c " --> " pcre.o " ..."; \
  1938. gcc -m64 -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c pcre.c -o ../LINUXAMD64/pcre.o
  1939. Compiling pcre.c --> pcre.o ...
  1940. echo "Compiling " fitrms.c " --> " fitrms.o " ..."; \
  1941. gcc -m64 -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -c fitrms.c -o ../LINUXAMD64/fitrms.o
  1942. Compiling fitrms.c --> fitrms.o ...
  1943. echo "Linking " vmd_LINUXAMD64 "..."; \
  1944. cd ../LINUXAMD64 ; \
  1945. if [ ! -r ./foobar ]; then \
  1946. ln -s ../src/foobar ./foobar ; \
  1947. fi; \
  1948. g++ -m64 -fno-for-scope -Wno-deprecated -Wall -O6 -ffast-math -DARCH_LINUXAMD64 -DVMDOPENGL -DVMDQUICKSURF -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -DVMDMSMS -DVMDNANOSHAPER -DVMDSTATICPLUGINS -I../plugins/include -I../plugins/LINUXAMD64/molfile -I. -I../src -o vmd_LINUXAMD64 OpenGLDisplayDevice.o OpenGLExtensions.o OpenGLRenderer.o OpenGLShader.o OpenGLCache.o androidvmdstart.o Animation.o ArtDisplayDevice.o AtomColor.o AtomParser.o AtomLexer.o AtomRep.o AtomSel.o Axes.o BaseMolecule.o Benchmark.o BondSearch.o CmdAnimate.o CmdColor.o CmdDisplay.o CmdLabel.o CmdMaterial.o CmdMenu.o CmdMol.o CmdRender.o CmdTrans.o CommandQueue.o CoorPluginData.o CUDAAccel.o DisplayDevice.o Displayable.o DisplayRocker.o DispCmds.o DrawMolecule.o DrawMolItem.o DrawMolItem2.o DrawMolItemRibbons.o DrawMolItemMSMS.o DrawMolItemNanoShaper.o DrawMolItemRings.o DrawMolItemOrbital.o DrawMolItemQuickSurf.o DrawMolItemSurface.o DrawMolItemVolume.o DrawForce.o DrawRingsUtils.o FileRenderList.o FileRenderer.o FPS.o GelatoDisplayDevice.o GeometryAngle.o GeometryAtom.o GeometryBond.o GeometryDihedral.o GeometryList.o GeometryMol.o GeometrySpring.o Hershey.o HMDMgr.o Inform.o ImageIO.o Isosurface.o JRegex.o JString.o macosxvmdstart.o MaterialList.o Matrix4.o MayaDisplayDevice.o MDFF.o Measure.o MeasureCluster.o MeasurePBC.o MeasureRDF.o MeasureQCP.o MeasureSurface.o MeasureSymmetry.o MobileInterface.o MobileButtons.o MobileTracker.o Molecule.o MoleculeList.o MoleculeGraphics.o MolFilePlugin.o Mouse.o MSMSInterface.o NanoShaperInterface.o Orbital.o OrbitalJIT.o PeriodicTable.o P_JoystickTool.o P_TugTool.o P_GrabTool.o P_PrintTool.o P_PinchTool.o P_UIVR.o P_Buttons.o P_Tracker.o P_Tool.o P_CmdTool.o P_SensorConfig.o ParseTree.o PickList.o PickModeAddBond.o PickModeCenter.o PickModeForce.o PickModeList.o PickModeMolLabel.o PickModeMove.o PickModeUser.o PlainTextInterp.o PluginMgr.o POV3DisplayDevice.o PSDisplayDevice.o QMData.o QMTimestep.o QuickSurf.o RadianceDisplayDevice.o RayShadeDisplayDevice.o R3dDisplayDevice.o RenderManDisplayDevice.o Scene.o SnapshotDisplayDevice.o Spaceball.o SpaceballButtons.o SpaceballTracker.o SpatialSearch.o SpringTool.o Stage.o STLDisplayDevice.o Stride.o Surf.o SymbolTable.o TachyonDisplayDevice.o Timestep.o UIObject.o UIText.o VMDApp.o VMDCollab.o VMDDir.o VMDDisplayList.o VMDMenu.o VMDQuat.o VMDTitle.o VMDThreads.o VolCPotential.o VolMapCreate.o VolMapCreateILS.o VolumetricData.o VolumeTexture.o VrmlDisplayDevice.o Vrml2DisplayDevice.o WavefrontDisplayDevice.o WKFThreads.o WKFUtils.o utilities.o util_simd.o vmd.o vmdmain.o X3DDisplayDevice.o hash.o inthash.o intstack.o ptrstack.o msmpot.o msmpot_compute.o msmpot_cubic.o msmpot_setup.o vmdsock.o vmddlopen.o pcre.o fitrms.o -L../plugins/LINUXAMD64/molfile -lGL -L/usr/X11R6/lib64 -lGL -lX11 -lmolfile_plugin -lm -ldl -rdynamic ;
  1949. Linking vmd_LINUXAMD64 ...
  1950. Stride.o: In function `ss_from_stride(DrawMolecule*)':
  1951. Stride.C:(.text+0x3f): warning: the use of `tempnam' is dangerous, better use `mkstemp'
  1952. echo No resource compiler required on this platform.
  1953. No resource compiler required on this platform.
  1954. mahmood@cluster:src$ make install
  1955. if [ ! -d "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd" ]; then \
  1956. mkdir -p "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd" ; \
  1957. fi ; \
  1958. if [ ! -d "/home/mahmood/namd/vmd-1.9.3/install/bin" ]; then \
  1959. mkdir -p "/home/mahmood/namd/vmd-1.9.3/install/bin" ; \
  1960. fi ; \
  1961. if [ ! -d "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd"/doc ]; then \
  1962. mkdir -p "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd"/doc; \
  1963. fi
  1964. cp ../Announcement "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd"
  1965. cp ../README "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd"
  1966. cp ../LICENSE "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd"
  1967. cp ../doc/ug.pdf "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd"/doc
  1968. if [ -f /home/mahmood/namd/vmd-1.9.3/install/lib/vmd/vmd_LINUXAMD64 ]; then \
  1969. mv -f "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd/vmd_LINUXAMD64" "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd/OLD_vmd_LINUXAMD64" ; rm -f "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd/OLD_vmd_LINUXAMD64" ; fi
  1970. cp ../LINUXAMD64/vmd_LINUXAMD64 "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd"
  1971. if [ -d "../lib/redistrib/lib_LINUXAMD64" ]; then \
  1972. cd ../lib/redistrib/lib_LINUXAMD64; tar -cf - ./* | \
  1973. (cd "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd" ; tar -xf -) \
  1974. fi ;
  1975. cp ../lib/stride/stride_LINUXAMD64 ../lib/surf/surf_LINUXAMD64 ../lib/tachyon/tachyon_LINUXAMD64 "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd"
  1976. cp: cannot stat `../lib/stride/stride_LINUXAMD64': No such file or directory
  1977. cp: cannot stat `../lib/surf/surf_LINUXAMD64': No such file or directory
  1978. cp: cannot stat `../lib/tachyon/tachyon_LINUXAMD64': No such file or directory
  1979. make: [install] Error 1 (ignored)
  1980. cd ..; tar -cf - scripts | \
  1981. (cd "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd" ; tar -xf -)
  1982. cd ../lib; tar -cf - scripts | \
  1983. (cd "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd" ; tar -xf -)
  1984. cd ..; tar -cf - python | \
  1985. (cd "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd"/scripts ; tar -xf -)
  1986. cd ..; tar -cf - plugins | \
  1987. (cd "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd" ; tar -xf -)
  1988. cd ..; tar -cf - shaders | \
  1989. (cd "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd" ; tar -xf -)
  1990. if [ -f ../LINUXAMD64/OptiXShaders.ptx ]; then \
  1991. cp ../LINUXAMD64/OptiXShaders.ptx "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd/shaders"; \
  1992. fi;
  1993. cp ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "/home/mahmood/namd/vmd-1.9.3/install/lib/vmd"
  1994. cd ../bin ; \
  1995. if [ -f run_vmd_tmp ]; then rm -f run_vmd_tmp; fi ; \
  1996. if [ ! -x "/bin/csh" ]; then \
  1997. echo "Info: /bin/csh shell not found, installing Bourne shell startup script instead" ; \
  1998. echo '#!/bin/sh' >> run_vmd_tmp ; \
  1999. echo 'defaultvmddir="/home/mahmood/namd/vmd-1.9.3/install/lib/vmd"' >> run_vmd_tmp ; \
  2000. echo 'vmdbasename=vmd' >> run_vmd_tmp ; \
  2001. cat vmd.sh >> run_vmd_tmp ; \
  2002. else \
  2003. echo '#!/bin/csh' >> run_vmd_tmp ; \
  2004. echo 'set defaultvmddir="/home/mahmood/namd/vmd-1.9.3/install/lib/vmd"' >> run_vmd_tmp ; \
  2005. echo 'set vmdbasename=vmd' >> run_vmd_tmp ; \
  2006. cat vmd.csh >> run_vmd_tmp ; \
  2007. fi ; \
  2008. chmod +x run_vmd_tmp ; \
  2009. cp run_vmd_tmp "/home/mahmood/namd/vmd-1.9.3/install/bin"/vmd ; \
  2010. rm -f run_vmd_tmp
  2011. echo Make sure "/home/mahmood/namd/vmd-1.9.3/install/bin"/vmd is in your path.
  2012. Make sure /home/mahmood/namd/vmd-1.9.3/install/bin/vmd is in your path.
  2013. echo "VMD installation complete. Enjoy!"
  2014. VMD installation complete. Enjoy!
  2015. mahmood@cluster:src$ export PATH=$PATH:/home/mahmood/namd/vmd-1.9.3/install/bin
  2016. mahmood@cluster:src$ vd
  2017. -bash: vd: command not found
  2018. mahmood@cluster:src$ vmd
  2019. Info) VMD for LINUXAMD64, version 1.9.3 (March 5, 2018)
  2020. Info) http://www.ks.uiuc.edu/Research/vmd/
  2021. Info) Email questions and bug reports to vmd@ks.uiuc.edu
  2022. Info) Please include this reference in published work using VMD:
  2023. Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
  2024. Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
  2025. Info) -------------------------------------------------------------
  2026. Info) Free system memory: 39GB (62%)
  2027. Warning) Detected X11 'Composite' extension: if incorrect display occurs
  2028. Warning) try disabling this X server option. Most OpenGL drivers
  2029. Warning) disable stereoscopic display when 'Composite' is enabled.
  2030. Info) OpenGL renderer: Gallium 0.4 on llvmpipe (LLVM 3.6, 128 bits)
  2031. Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
  2032. Info) Full GLSL rendering mode is available.
  2033. Info) Textures: 2-D (8192x8192), 3-D (512x512x512), Multitexture (8)
  2034. Info) Starting VMD text interpreter...
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