Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q [R] S  T  U  V  W  X  Y  Z 

BioC 3.5: INSTALL report for Rsubread on malbec2

This page was generated on 2017-08-16 13:13:53 -0400 (Wed, 16 Aug 2017).

Package 1155/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsubread 1.26.1
Wei Shi
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/Rsubread
Last Changed Rev: 131224 / Revision: 131943
Last Changed Date: 2017-07-14 01:14:10 -0400 (Fri, 14 Jul 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64 [ OK ] OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rsubread
Version: 1.26.1
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD INSTALL Rsubread
StartedAt: 2017-08-15 17:58:18 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 17:58:45 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 26.8 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD INSTALL Rsubread
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.5-bioc/R/library’
* installing *source* package ‘Rsubread’ ...
@@@@@ The operating system is Linux.
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c HelperFunctions.c -o HelperFunctions.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c R_wrapper.c -o R_wrapper.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c SNPCalling.c -o SNPCalling.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c aligner.c -o aligner.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c atgcContent.c -o atgcContent.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c build-sam-index.c -o build-sam-index.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c core-bigtable.c -o core-bigtable.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c core-indel.c -o core-indel.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c core-interface-aligner.c -o core-interface-aligner.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c core-junction.c -o core-junction.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c core.c -o core.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c detectionCall.c -o detectionCall.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c detectionCallAnnotation.c -o detectionCallAnnotation.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c exon-algorithms.c -o exon-algorithms.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c exon-align-indel.c -o exon-align-indel.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c exon-align.c -o exon-align.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c fullscan.c -o fullscan.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c fusion-align.c -o fusion-align.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c gene-algorithms.c -o gene-algorithms.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c gene-value-index.c -o gene-value-index.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c hashtable.c -o hashtable.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c index-builder.c -o index-builder.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c input-files.c -o input-files.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c interval_merge.c -o interval_merge.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c long-hashtable.c -o long-hashtable.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c mergeVCF.c -o mergeVCF.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c processExons.c -o processExons.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c propmapped.c -o propmapped.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c qualityScores.c -o qualityScores.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c read-repair.c -o read-repair.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c readSummary.c -o readSummary.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c removeDupReads.c -o removeDupReads.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c sam2bed.c -o sam2bed.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c sambam-file.c -o sambam-file.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c seek-zlib.c -o seek-zlib.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c sorted-hashtable.c -o sorted-hashtable.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c sublog.c -o sublog.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.1\"" -w -fpic  -g -O2  -Wall -c tx-unique.c -o tx-unique.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o Rsubread.so HelperFunctions.o R_wrapper.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 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 mergeVCF.o processExons.o propmapped.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/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/R/library/Rsubread/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rsubread)