API tools faq
paste
Advertisement
NdAK11

Rsamtools logs

NdAK11
May 2nd, 2019
113
0
Never
Add comment
Not a member of Pastebin yet? Sign Up, it unlocks many cool features!
R 54.46 KB | None | 0 0
raw download clone embed print report
  1. > library(BiocManager)
  2. Bioconductor version 3.9 (BiocManager 1.30.4), ?BiocManager::install for help
  3. > BiocManager::install('Rhtslib') # for Rsamtools
  4. Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
  5. Installing package(s) 'Rhtslib'
  6. trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/Rhtslib_1.15.6.tar.gz'
  7. Content type 'application/x-gzip' length 1469387 bytes (1.4 MB)
  8. ==================================================
  9. downloaded 1.4 MB
  10.  
  11. * installing *source* package ‘Rhtslib’ ...
  12. ** using non-staged installation via StagedInstall field
  13. ** libs
  14. cd "htslib-1.7" && make -f "/usr/lib/R/etc/Makeconf" -f "Makefile.Rhtslib"
  15. make[1]: Entering directory '/tmp/Rtmp3kDa06/R.INSTALL8b1d75b351a/Rhtslib/src/htslib-1.7'
  16. Makefile.Rhtslib:128: warning: overriding recipe for target '.c.o'
  17. /usr/lib/R/etc/Makeconf:167: warning: ignoring old recipe for target '.c.o'
  18. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o kfunc.o kfunc.c
  19. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o knetfile.o knetfile.c
  20. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o kstring.o kstring.c
  21. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
  22. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o bgzf.o bgzf.c
  23. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o errmod.o errmod.c
  24. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o faidx.o faidx.c
  25. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o hfile.o hfile.c
  26. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o hfile_net.o hfile_net.c
  27. echo '#define HTS_VERSION "1.7"' > version.h
  28. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o hts.o hts.c
  29. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o hts_os.o hts_os.c
  30. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o md5.o md5.c
  31. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o multipart.o multipart.c
  32. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o probaln.o probaln.c
  33. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o realn.o realn.c
  34. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o regidx.o regidx.c
  35. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o sam.o sam.c
  36. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
  37. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o vcf_sweep.o vcf_sweep.c
  38. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o tbx.o tbx.c
  39. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o textutils.o textutils.c
  40. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o thread_pool.o thread_pool.c
  41. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o vcf.o vcf.c
  42. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o vcfutils.o vcfutils.c
  43. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
  44. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/cram_decode.o cram/cram_decode.c
  45. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/cram_encode.o cram/cram_encode.c
  46. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/cram_external.o cram/cram_external.c
  47. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/cram_index.o cram/cram_index.c
  48. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/cram_io.o cram/cram_io.c
  49. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/cram_samtools.o cram/cram_samtools.c
  50. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/cram_stats.o cram/cram_stats.c
  51. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/files.o cram/files.c
  52. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/mFILE.o cram/mFILE.c
  53. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
  54. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
  55. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/rANS_static.o cram/rANS_static.c
  56. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/sam_header.o cram/sam_header.c
  57. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/string_alloc.o cram/string_alloc.c
  58. ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
  59. ranlib libhts.a
  60. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o kfunc.pico kfunc.c
  61. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o knetfile.pico knetfile.c
  62. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o kstring.pico kstring.c
  63. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
  64. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o bgzf.pico bgzf.c
  65. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o errmod.pico errmod.c
  66. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o faidx.pico faidx.c
  67. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o hfile.pico hfile.c
  68. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o hfile_net.pico hfile_net.c
  69. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o hts.pico hts.c
  70. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o hts_os.pico hts_os.c
  71. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o md5.pico md5.c
  72. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o multipart.pico multipart.c
  73. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o probaln.pico probaln.c
  74. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o realn.pico realn.c
  75. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o regidx.pico regidx.c
  76. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o sam.pico sam.c
  77. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
  78. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o vcf_sweep.pico vcf_sweep.c
  79. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o tbx.pico tbx.c
  80. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o textutils.pico textutils.c
  81. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o thread_pool.pico thread_pool.c
  82. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o vcf.pico vcf.c
  83. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o vcfutils.pico vcfutils.c
  84. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
  85. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
  86. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
  87. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/cram_external.pico cram/cram_external.c
  88. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/cram_index.pico cram/cram_index.c
  89. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/cram_io.pico cram/cram_io.c
  90. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
  91. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
  92. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/files.pico cram/files.c
  93. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/mFILE.pico cram/mFILE.c
  94. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
  95. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
  96. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/rANS_static.pico cram/rANS_static.c
  97. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/sam_header.pico cram/sam_header.c
  98. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
  99. gcc -std=gnu99 -shared -Wl,-soname,libhts.so.2  -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico -lz -lm -lbz2 -llzma -lpthread
  100. ln -sf libhts.so libhts.so.2
  101. make[1]: Leaving directory '/tmp/Rtmp3kDa06/R.INSTALL8b1d75b351a/Rhtslib/src/htslib-1.7'
  102. mkdir -p "/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include/htslib"
  103. cd "htslib-1.7/htslib" && cp * "/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include/htslib" && cd .. && cp textutils_internal.h hts_internal.h "/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include"
  104. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/zlibbioc/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_Rhtslib.c -o R_init_Rhtslib.o
  105. mkdir -p "/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/usrlib"
  106. cd "htslib-1.7" && cp libhts.so libhts.a "/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/usrlib"
  107. cd "/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/usrlib" && ln -s libhts.so libhts.so.2
  108. gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rhtslib.so R_init_Rhtslib.o -L/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/usrlib -Wl,-rpath,/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/usrlib -lhts -lz -lm -lbz2 -llzma -lpthread -L/usr/lib/R/lib -lR
  109. mkdir -p "/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/testdata/tabix"
  110. cd "htslib-1.7/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/testdata/tabix" 2>/dev/null || true)
  111. installing to /home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/libs
  112. ** R
  113. ** inst
  114. ** byte-compile and prepare package for lazy loading
  115. ** help
  116. *** installing help indices
  117. ** building package indices
  118. ** installing vignettes
  119. ** testing if installed package can be loaded
  120. * DONE (Rhtslib)
  121.  
  122.  
  123.  
  124. > library(Rhtslib)
  125. Rhtslib htslib version 1.7-2
  126. > BiocManager::install("Rsamtools")
  127. Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
  128. Installing package(s) 'Rsamtools'
  129. trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/Rsamtools_1.99.6.tar.gz'
  130. Content type 'application/x-gzip' length 3032600 bytes (2.9 MB)
  131. ==================================================
  132. downloaded 2.9 MB
  133.  
  134. * installing *source* package ‘Rsamtools’ ...
  135. ** using staged installation
  136. ** libs
  137. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Biostrings_stubs.c -o Biostrings_stubs.o
  138. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
  139. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
  140. g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c PileupBuffer.cpp -o PileupBuffer.o
  141. g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c PosCacheColl.cpp -o PosCacheColl.o
  142. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_Rsamtools.c -o R_init_Rsamtools.o
  143. g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ResultManager.cpp -o ResultManager.o
  144. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
  145. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XVector_stubs.c -o XVector_stubs.o
  146. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c as_bam.c -o as_bam.o
  147. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam.c -o bam.o
  148. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam_data.c -o bam_data.o
  149. g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam_mate_iter.cpp -o bam_mate_iter.o
  150. In file included from /home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include/sam.h:29:0,
  151.                  from Template.h:9,
  152.                  from BamIterator.h:10,
  153.                  from BamRangeIterator.h:7,
  154.                  from bam_mate_iter.cpp:2:
  155. BamRangeIterator.h: In member function ‘virtual void BamRangeIterator::finalize_inprogress(bamFile)’:
  156. /home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include/bam.h:57:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)���, declared with attribute warn_unused_result [-Wunused-result]
  157.  #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
  158.                                 ~~~~~~~~~^~~~~~~~~~~~~~
  159. BamRangeIterator.h:138:9: note: in expansion of macro ‘bam_seek’
  160.          bam_seek(bfile, pos, SEEK_SET);
  161.          ^~~~~~~~
  162. BamIterator.h: In constructor ‘BamIterator::BamIterator(bamFile, const bam_index_t*)’:
  163. /home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include/bam.h:57:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’, declared with attribute warn_unused_result [-Wunused-result]
  164.  #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
  165.                                 ~~~~~~~~~^~~~~~~~~~~~~~
  166. BamIterator.h:87:9: note: in expansion of macro ‘bam_seek’
  167.          bam_seek(bfile, 0, 0);
  168.          ^~~~~~~~
  169. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam_plbuf.c -o bam_plbuf.o
  170. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam_sort.c -o bam_sort.o
  171. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bambuffer.c -o bambuffer.o
  172. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bamfile.c -o bamfile.o
  173. bamfile.c: In function ‘bamfile_isincomplete’:
  174. bamfile.c:165:13: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
  175.              bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
  176.              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  177. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bcffile.c -o bcffile.o
  178. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c encode.c -o encode.o
  179. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fafile.c -o fafile.o
  180. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c idxstats.c -o idxstats.o
  181. In file included from /home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include/sam.h:29:0,
  182.                  from bamfile.h:5,
  183.                  from idxstats.c:1:
  184. idxstats.c: In function ‘idxstats_bamfile’:
  185. /home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
  186.  #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
  187.                                 ^~~~~~~~~~~~~~~~~~~~~~~
  188. idxstats.c:20:5: note: in expansion of macro ‘bam_seek’
  189.      bam_seek(fp, 0, 0);
  190.      ^~~~~~~~
  191. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c io_sam.c -o io_sam.o
  192. In file included from /home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include/sam.h:29:0,
  193.                  from io_sam.c:2:
  194. io_sam.c: In function ‘_scan_bam_all’:
  195. /home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
  196.  #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
  197.                                 ^~~~~~~~~~~~~~~~~~~~~~~
  198. io_sam.c:304:5: note: in expansion of macro ‘bam_seek’
  199.      bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
  200.      ^~~~~~~~
  201. g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
  202. g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pileup.cpp -o pileup.o
  203. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pileupbam.c -o pileupbam.o
  204. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sam.c -o sam.o
  205. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sam_opts.c -o sam_opts.o
  206. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sam_utils.c -o sam_utils.o
  207. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c samtools_patch.c -o samtools_patch.o
  208. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c scan_bam_data.c -o scan_bam_data.o
  209. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tabixfile.c -o tabixfile.o
  210. tabixfile.c: In function ‘index_tabix’:
  211. tabixfile.c:190:5: warning: ‘bgzf_is_bgzf’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
  212.      if (bgzf_is_bgzf(fn) != 1)
  213.      ^~
  214. In file included from tabixfile.c:3:0:
  215. /home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include/htslib/bgzf.h:243:9: note: declared here
  216.      int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
  217.          ^~~~~~~~~~~~
  218. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tagfilter.c -o tagfilter.o
  219. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utilities.c -o utilities.o
  220. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zip_compression.c -o zip_compression.o
  221. g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rsamtools.so Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o -L/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/usrlib -Wl,-rpath,/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/usrlib -lhts -lz -lm -lbz2 -llzma -lpthread -L/usr/lib/R/lib -lR
  222. installing to /home/rad/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-Rsamtools/00new/Rsamtools/libs
  223. ** R
  224. ** inst
  225. ** byte-compile and prepare package for lazy loading
  226. ** help
  227. *** installing help indices
  228. ** building package indices
  229. ** installing vignettes
  230. ** testing if installed package can be loaded from temporary location
  231. Error: package or namespace load failed for ‘Rsamtools’ in dyn.load(file, DLLpath = DLLpath, ...):
  232.  unable to load shared object '/home/rad/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so':
  233.   /home/rad/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so: undefined symbol: faidx_fetch_seq2
  234. Error: loading failed
  235. Execution halted
  236. ERROR: loading failed
  237. * removing ‘/home/rad/R/x86_64-pc-linux-gnu-library/3.6/Rsamtools’
  238.  
  239. The downloaded source packages are in
  240.     ‘/tmp/RtmpVYytby/downloaded_packages’
  241. Update old packages: 'Rsamtools'
  242. Update all/some/none? [a/s/n]:
  243. a
  244. trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/Rsamtools_1.99.6.tar.gz'
  245. Content type 'application/x-gzip' length 3032600 bytes (2.9 MB)
  246. ==================================================
  247. downloaded 2.9 MB
  248.  
  249. * installing *source* package ‘Rsamtools’ ...
  250. ** using staged installation
  251. ** libs
  252. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Biostrings_stubs.c -o Biostrings_stubs.o
  253. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
  254. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
  255. g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c PileupBuffer.cpp -o PileupBuffer.o
  256. g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c PosCacheColl.cpp -o PosCacheColl.o
  257. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_Rsamtools.c -o R_init_Rsamtools.o
  258. g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ResultManager.cpp -o ResultManager.o
  259. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
  260. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XVector_stubs.c -o XVector_stubs.o
  261. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c as_bam.c -o as_bam.o
  262. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam.c -o bam.o
  263. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam_data.c -o bam_data.o
  264. g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam_mate_iter.cpp -o bam_mate_iter.o
  265. In file included from /usr/local/lib/R/site-library/Rhtslib/include/sam.h:29:0,
  266.                  from Template.h:9,
  267.                  from BamIterator.h:10,
  268.                  from BamRangeIterator.h:7,
  269.                  from bam_mate_iter.cpp:2:
  270. BamRangeIterator.h: In member function ‘virtual void BamRangeIterator::finalize_inprogress(bamFile)’:
  271. /usr/local/lib/R/site-library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’, declared with attribute warn_unused_result [-Wunused-result]
  272.  #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
  273.                                 ~~~~~~~~~^~~~~~~~~~~~~~
  274. BamRangeIterator.h:138:9: note: in expansion of macro ‘bam_seek’
  275.          bam_seek(bfile, pos, SEEK_SET);
  276.          ^~~~~~~~
  277. BamIterator.h: In constructor ‘BamIterator::BamIterator(bamFile, const bam_index_t*)’:
  278. /usr/local/lib/R/site-library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’, declared with attribute warn_unused_result [-Wunused-result]
  279.  #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
  280.                                 ~~~~~~~~~^~~~~~~~~~~~~~
  281. BamIterator.h:87:9: note: in expansion of macro ‘bam_seek’
  282.          bam_seek(bfile, 0, 0);
  283.          ^~~~~~~~
  284. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam_plbuf.c -o bam_plbuf.o
  285. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam_sort.c -o bam_sort.o
  286. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bambuffer.c -o bambuffer.o
  287. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bamfile.c -o bamfile.o
  288. bamfile.c: In function ‘bamfile_isincomplete’:
  289. bamfile.c:165:13: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
  290.              bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
  291.              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  292. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bcffile.c -o bcffile.o
  293. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c encode.c -o encode.o
  294. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fafile.c -o fafile.o
  295. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c idxstats.c -o idxstats.o
  296. In file included from /usr/local/lib/R/site-library/Rhtslib/include/sam.h:29:0,
  297.                  from bamfile.h:5,
  298.                  from idxstats.c:1:
  299. idxstats.c: In function ‘idxstats_bamfile’:
  300. /usr/local/lib/R/site-library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
  301.  #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
  302.                                 ^~~~~~~~~~~~~~~~~~~~~~~
  303. idxstats.c:20:5: note: in expansion of macro ‘bam_seek’
  304.      bam_seek(fp, 0, 0);
  305.      ^~~~~~~~
  306. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c io_sam.c -o io_sam.o
  307. In file included from /usr/local/lib/R/site-library/Rhtslib/include/sam.h:29:0,
  308.                  from io_sam.c:2:
  309. io_sam.c: In function ‘_scan_bam_all’:
  310. /usr/local/lib/R/site-library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
  311.  #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
  312.                                 ^~~~~~~~~~~~~~~~~~~~~~~
  313. io_sam.c:304:5: note: in expansion of macro ‘bam_seek’
  314.      bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
  315.      ^~~~~~~~
  316. g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
  317. g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pileup.cpp -o pileup.o
  318. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pileupbam.c -o pileupbam.o
  319. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sam.c -o sam.o
  320. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sam_opts.c -o sam_opts.o
  321. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sam_utils.c -o sam_utils.o
  322. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c samtools_patch.c -o samtools_patch.o
  323. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c scan_bam_data.c -o scan_bam_data.o
  324. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tabixfile.c -o tabixfile.o
  325. tabixfile.c: In function ‘index_tabix’:
  326. tabixfile.c:190:5: warning: ‘bgzf_is_bgzf’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
  327.      if (bgzf_is_bgzf(fn) != 1)
  328.      ^~
  329. In file included from tabixfile.c:3:0:
  330. /usr/local/lib/R/site-library/Rhtslib/include/htslib/bgzf.h:243:9: note: declared here
  331.      int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
  332.          ^~~~~~~~~~~~
  333. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tagfilter.c -o tagfilter.o
  334. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utilities.c -o utilities.o
  335. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VAQCff/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zip_compression.c -o zip_compression.o
  336. g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rsamtools.so Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o -L/usr/local/lib/R/site-library/Rhtslib/usrlib -Wl,-rpath,/usr/local/lib/R/site-library/Rhtslib/usrlib -lhts -lz -lm -lbz2 -llzma -lpthread -L/usr/lib/R/lib -lR
  337. installing to /usr/local/lib/R/site-library/00LOCK-Rsamtools/00new/Rsamtools/libs
  338. ** R
  339. ** inst
  340. ** byte-compile and prepare package for lazy loading
  341. ** help
  342. *** installing help indices
  343. ** building package indices
  344. ** installing vignettes
  345. ** testing if installed package can be loaded from temporary location
  346. Error: package or namespace load failed for ‘Rsamtools’ in dyn.load(file, DLLpath = DLLpath, ...):
  347.  unable to load shared object '/usr/local/lib/R/site-library/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so':
  348.   /usr/local/lib/R/site-library/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so: undefined symbol: faidx_fetch_seq2
  349. Error: loading failed
  350. Execution halted
  351. ERROR: loading failed
  352. * removing ‘/usr/local/lib/R/site-library/Rsamtools’
  353. * restoring previous ‘/usr/local/lib/R/site-library/Rsamtools’
  354.  
  355. The downloaded source packages are in
  356.     ‘/tmp/RtmpVYytby/downloaded_packages’
  357. Warning messages:
  358. 1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  359.   installation of package ‘Rsamtools’ had non-zero exit status
  360. 2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  361.   installation of package ‘Rsamtools’ had non-zero exit status
  362. >
Advertisement
Add Comment
Please, Sign In to add comment
Advertisement
Public Pastes
Advertisement
We use cookies for various purposes including analytics. By continuing to use Pastebin, you agree to our use of cookies as described in the Cookies Policy.  OK, I Understand
Not a member of Pastebin yet?
Sign Up, it unlocks many cool features!