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May 25th, 2018
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  1. > source("https://bioconductor.org/biocLite.R")
  2. Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
  3. > biocLite("Rsubread")
  4. BioC_mirror: https://bioconductor.org
  5. Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).
  6. Installing package(s) ‘Rsubread’
  7. trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/Rsubread_1.30.2.tar.gz'
  8. Content type 'appslication/x-gzip' length 9397481 bytes (9.0 MB)
  9. ==================================================
  10. downloaded 9.0 MB
  11.  
  12. * installing *source* package ‘Rsubread’ ...
  13. @@@@@ The operating system is Linux.
  14. ** libs
  15. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c HelperFunctions.c -o HelperFunctions.o
  16. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c LRMbase-index.c -o LRMbase-index.o
  17. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c LRMchro-event.c -o LRMchro-event.o
  18. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c LRMfile-io.c -o LRMfile-io.o
  19. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c LRMhashtable.c -o LRMhashtable.o
  20. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c LRMhelper.c -o LRMhelper.o
  21. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c LRMseek-zlib.c -o LRMseek-zlib.o
  22. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
  23. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c R_wrappser.c -o R_wrappser.o
  24. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c SNPCalling.c -o SNPCalling.o
  25. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c aligner.c -o aligner.o
  26. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c atgcContent.c -o atgcContent.o
  27. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c build-sam-index.c -o build-sam-index.o
  28. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c core-bigtable.c -o core-bigtable.o
  29. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c core-indel.c -o core-indel.o
  30. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c core-interface-aligner.c -o core-interface-aligner.o
  31. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c core-interface-subjunc.c -o core-interface-subjunc.o
  32. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c core-junction.c -o core-junction.o
  33. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c core.c -o core.o
  34. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c detection-calls.c -o detection-calls.o
  35. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c detectionCall.c -o detectionCall.o
  36. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c detectionCallAnnotation.c -o detectionCallAnnotation.o
  37. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c exon-algorithms.c -o exon-algorithms.o
  38. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c exon-align-indel.c -o exon-align-indel.o
  39. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c exon-align.c -o exon-align.o
  40. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c fullscan.c -o fullscan.o
  41. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c fusion-align.c -o fusion-align.o
  42. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c gene-algorithms.c -o gene-algorithms.o
  43. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c gene-value-index.c -o gene-value-index.o
  44. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c hashtable.c -o hashtable.o
  45. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c index-builder.c -o index-builder.o
  46. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c input-files.c -o input-files.o
  47. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c interval_merge.c -o interval_merge.o
  48. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c long-hashtable.c -o long-hashtable.o
  49. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c longread-mappsing.c -o longread-mappsing.o
  50. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c mergeVCF.c -o mergeVCF.o
  51. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c processExons.c -o processExons.o
  52. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c propmappsed.c -o propmappsed.o
  53. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c qualityScores.c -o qualityScores.o
  54. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c read-repair.c -o read-repair.o
  55. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c readSummary.c -o readSummary.o
  56. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c removeDupReads.c -o removeDupReads.o
  57. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c sam2bed.c -o sam2bed.o
  58. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c sambam-file.c -o sambam-file.o
  59. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c seek-zlib.c -o seek-zlib.o
  60. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c sorted-hashtable.c -o sorted-hashtable.o
  61. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c sublog.c -o sublog.o
  62. gcc -std=gnu99 -I"/apps/R-3.5.0/lib64/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.30.2\"" -fpic -I/apps/zlib-1.2.8/include -I/apps/curl-7.49.1/include/curl -I/apps/bzip2-1.0.6/include -I/apps/xz-5.2.2/include -I/apps/pcre-8.39b/include -c tx-unique.c -o tx-unique.o
  63. gcc -std=gnu99 -shared -L/apps/R-3.5.0/lib64/R/lib -L/apps/curl-7.49.1/lib -L/apps/bzip2-1.0.6/lib -L/apps/zlib-1.2.8/lib -L/apps/xz-5.2.2/lib -L/apps/pcre-8.39b/lib -L/apps/texinfo-5.2/texinfo-5.2/gnulib/lib -o Rsubread.so HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrappser.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o fullscan.o fusion-align.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-files.o interval_merge.o long-hashtable.o longread-mappsing.o mergeVCF.o processExons.o propmappsed.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON -L/apps/R-3.5.0/lib64/R/lib -lR
  64. installing to /apps/R-3.5.0/lib64/R/library/Rsubread/libs
  65. ** R
  66. ** inst
  67. ** byte-compile and prepare package for lazy loading
  68. ** help
  69. *** installing help indices
  70. ** building package indices
  71. ** installing vignettes
  72. ** testing if installed package can be loaded
  73. Error: package or namespace load failed for ‘Rsubread’ in dyn.load(file, DLLpath = DLLpath, ...):
  74. unable to load shared object '/apps/R-3.5.0/lib64/R/library/Rsubread/libs/Rsubread.so':
  75. /apps/R-3.5.0/lib64/R/library/Rsubread/libs/Rsubread.so: undefined symbol: LRM_gehash_get_bucket
  76. Error: loading failed
  77. Execution halted
  78. ERROR: loading failed
  79. * removing ‘/apps/R-3.5.0/lib64/R/library/Rsubread’
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