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R 3.6.0 Rsamtools install error

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  1. > library(BiocManager)
  2. Bioconductor version 3.9 (BiocManager 1.30.4), ?BiocManager::install for help
  3.  
  4. > BiocManager::install("Rhtslib")
  5. Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
  6. Installing package(s) 'Rhtslib'
  7. trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/Rhtslib_1.15.6.tar.gz'
  8. Content type 'application/x-gzip' length 1469387 bytes (1.4 MB)
  9. ==================================================
  10. downloaded 1.4 MB
  11.  
  12. * installing *source* package ‘Rhtslib’ ...
  13. ** using non-staged installation via StagedInstall field
  14. ** libs
  15. cd "htslib-1.7" && make -f "/usr/lib/R/etc/Makeconf" -f "Makefile.Rhtslib"
  16. make[1]: Entering directory '/tmp/RtmpQlTtc2/R.INSTALL35be1d4cf162/Rhtslib/src/htslib-1.7'
  17. Makefile.Rhtslib:128: warning: overriding recipe for target '.c.o'
  18. /usr/lib/R/etc/Makeconf:167: warning: ignoring old recipe for target '.c.o'
  19. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o kfunc.o kfunc.c
  20. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o knetfile.o knetfile.c
  21. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o kstring.o kstring.c
  22. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
  23. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o bgzf.o bgzf.c
  24. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o errmod.o errmod.c
  25. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o faidx.o faidx.c
  26. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o hfile.o hfile.c
  27. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o hfile_net.o hfile_net.c
  28. echo '#define HTS_VERSION "1.7"' > version.h
  29. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o hts.o hts.c
  30. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o hts_os.o hts_os.c
  31. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o md5.o md5.c
  32. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o multipart.o multipart.c
  33. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o probaln.o probaln.c
  34. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o realn.o realn.c
  35. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o regidx.o regidx.c
  36. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o sam.o sam.c
  37. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
  38. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o vcf_sweep.o vcf_sweep.c
  39. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o tbx.o tbx.c
  40. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o textutils.o textutils.c
  41. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o thread_pool.o thread_pool.c
  42. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o vcf.o vcf.c
  43. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o vcfutils.o vcfutils.c
  44. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
  45. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/cram_decode.o cram/cram_decode.c
  46. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/cram_encode.o cram/cram_encode.c
  47. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/cram_external.o cram/cram_external.c
  48. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/cram_index.o cram/cram_index.c
  49. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/cram_io.o cram/cram_io.c
  50. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/cram_samtools.o cram/cram_samtools.c
  51. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/cram_stats.o cram/cram_stats.c
  52. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/files.o cram/files.c
  53. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/mFILE.o cram/mFILE.c
  54. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
  55. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
  56. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/rANS_static.o cram/rANS_static.c
  57. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/sam_header.o cram/sam_header.c
  58. gcc -std=gnu99 -g -Wall -O2 -I.  -c -o cram/string_alloc.o cram/string_alloc.c
  59. 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
  60. ranlib libhts.a
  61. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o kfunc.pico kfunc.c
  62. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o knetfile.pico knetfile.c
  63. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o kstring.pico kstring.c
  64. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
  65. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o bgzf.pico bgzf.c
  66. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o errmod.pico errmod.c
  67. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o faidx.pico faidx.c
  68. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o hfile.pico hfile.c
  69. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o hfile_net.pico hfile_net.c
  70. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o hts.pico hts.c
  71. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o hts_os.pico hts_os.c
  72. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o md5.pico md5.c
  73. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o multipart.pico multipart.c
  74. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o probaln.pico probaln.c
  75. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o realn.pico realn.c
  76. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o regidx.pico regidx.c
  77. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o sam.pico sam.c
  78. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
  79. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o vcf_sweep.pico vcf_sweep.c
  80. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o tbx.pico tbx.c
  81. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o textutils.pico textutils.c
  82. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o thread_pool.pico thread_pool.c
  83. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o vcf.pico vcf.c
  84. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o vcfutils.pico vcfutils.c
  85. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
  86. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
  87. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
  88. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/cram_external.pico cram/cram_external.c
  89. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/cram_index.pico cram/cram_index.c
  90. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/cram_io.pico cram/cram_io.c
  91. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
  92. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
  93. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/files.pico cram/files.c
  94. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/mFILE.pico cram/mFILE.c
  95. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
  96. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
  97. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/rANS_static.pico cram/rANS_static.c
  98. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/sam_header.pico cram/sam_header.c
  99. gcc -std=gnu99 -g -Wall -O2 -I.  -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
  100. 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
  101. ln -sf libhts.so libhts.so.2
  102. make[1]: Leaving directory '/tmp/RtmpQlTtc2/R.INSTALL35be1d4cf162/Rhtslib/src/htslib-1.7'
  103. mkdir -p "/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include/htslib"
  104. cd "htslib-1.7/htslib" && cp * "/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include/htslib" && cd .. && cp textutils_internal.h hts_internal.h "/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include"
  105. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/zlibbioc/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c R_init_Rhtslib.c -o R_init_Rhtslib.o
  106. mkdir -p "/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/usrlib"
  107. cd "htslib-1.7" && cp libhts.so libhts.a "/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/usrlib"
  108. cd "/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/usrlib" && ln -s libhts.so libhts.so.2
  109. gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rhtslib.so R_init_Rhtslib.o -L/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/usrlib -Wl,-rpath,/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/usrlib -lhts -lz -lm -lbz2 -llzma -lpthread -L/usr/lib/R/lib -lR
  110. mkdir -p "/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/testdata/tabix"
  111. cd "htslib-1.7/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/home/ben/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/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/testdata/tabix" 2>/dev/null || true)
  112. installing to /home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/libs
  113. ** R
  114. ** inst
  115. ** byte-compile and prepare package for lazy loading
  116. ** help
  117. *** installing help indices
  118. ** building package indices
  119. ** installing vignettes
  120. ** testing if installed package can be loaded
  121. * DONE (Rhtslib)
  122.  
  123. The downloaded source packages are in
  124.     ‘/tmp/RtmpTwKoJm/downloaded_packages’
  125.  
  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/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c Biostrings_stubs.c -o Biostrings_stubs.o
  138. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
  139. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c IRanges_stubs.c -o IRanges_stubs.o
  140. g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -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/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -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/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c R_init_Rsamtools.c -o R_init_Rsamtools.o
  143. g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -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/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c S4Vectors_stubs.c -o S4Vectors_stubs.o
  145. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c XVector_stubs.c -o XVector_stubs.o
  146. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c as_bam.c -o as_bam.o
  147. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c bam.c -o bam.o
  148. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c bam_data.c -o bam_data.o
  149. g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -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/ben/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/ben/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/ben/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/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c bam_plbuf.c -o bam_plbuf.o
  170. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c bam_sort.c -o bam_sort.o
  171. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c bambuffer.c -o bambuffer.o
  172. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -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/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c bcffile.c -o bcffile.o
  178. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c encode.c -o encode.o
  179. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c fafile.c -o fafile.o
  180. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c idxstats.c -o idxstats.o
  181. In file included from /home/ben/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/ben/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/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c io_sam.c -o io_sam.o
  192. In file included from /home/ben/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/ben/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/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -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/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -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/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c pileupbam.c -o pileupbam.o
  204. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c sam.c -o sam.o
  205. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c sam_opts.c -o sam_opts.o
  206. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c sam_utils.c -o sam_utils.o
  207. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c samtools_patch.c -o samtools_patch.o
  208. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c scan_bam_data.c -o scan_bam_data.o
  209. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -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/ben/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/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c tagfilter.c -o tagfilter.o
  219. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -c utilities.c -o utilities.o
  220. gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/S4Vectors/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/IRanges/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/XVector/include" -I"/home/ben/R/x86_64-pc-linux-gnu-library/3.6/Biostrings/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Dinline="" -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/ben/R/x86_64-pc-linux-gnu-library/3.6/Rhtslib/usrlib -Wl,-rpath,/home/ben/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/ben/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/ben/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so':
  233.   /home/ben/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/ben/R/x86_64-pc-linux-gnu-library/3.6/Rsamtools’
  238.  
  239. The downloaded source packages are in
  240.     ‘/tmp/RtmpTwKoJm/downloaded_packages’
  241. Warning message:
  242. In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  243.   installation of package ‘Rsamtools’ had non-zero exit status
  244.  
  245. > sessionInfo()
  246. R version 3.6.0 (2019-04-26)
  247. Platform: x86_64-pc-linux-gnu (64-bit)
  248. Running under: Ubuntu 18.04.2 LTS
  249.  
  250. Matrix products: default
  251. BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
  252. LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
  253.  
  254. locale:
  255.  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
  256.  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                
  257.  [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C      
  258.  
  259. attached base packages:
  260. [1] stats     graphics  grDevices utils     datasets  methods   base    
  261.  
  262. other attached packages:
  263. [1] BiocManager_1.30.4
  264.  
  265. loaded via a namespace (and not attached):
  266. [1] compiler_3.6.0 tools_3.6.0
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