Wei Shi
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/Rsubread |
| Branch: RELEASE_3_12 |
| Last Commit: 04818c6 |
| Last Changed Date: 2021-03-15 23:46:01 -0400 (Mon, 15 Mar 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:28:55 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the Rsubread package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1586/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rsubread 2.4.3 (landing page) Wei Shi
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Rsubread |
| Version: 2.4.3 |
| Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL Rsubread |
| StartedAt: 2021-05-05 16:04:01 -0400 (Wed, 05 May 2021) |
| EndedAt: 2021-05-05 16:04:37 -0400 (Wed, 05 May 2021) |
| EllapsedTime: 35.8 seconds |
| RetCode: 0 |
| Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL Rsubread ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’ * installing *source* package ‘Rsubread’ ... ** using staged installation @@@@@ The operating system is Linux. ** libs gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c HelperFunctions.c -o HelperFunctions.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c LRMbase-index.c -o LRMbase-index.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c LRMchro-event.c -o LRMchro-event.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c LRMfile-io.c -o LRMfile-io.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c LRMhashtable.c -o LRMhashtable.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c LRMhelper.c -o LRMhelper.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c LRMseek-zlib.c -o LRMseek-zlib.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c R_wrapper.c -o R_wrapper.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c RsimReads.c -o RsimReads.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c SNPCalling.c -o SNPCalling.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c aligner.c -o aligner.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c atgcContent.c -o atgcContent.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c build-sam-index.c -o build-sam-index.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c core-bigtable.c -o core-bigtable.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c core-indel.c -o core-indel.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c core-interface-aligner.c -o core-interface-aligner.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c core-interface-subjunc.c -o core-interface-subjunc.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c core-junction.c -o core-junction.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c core.c -o core.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c detection-calls.c -o detection-calls.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c detectionCall.c -o detectionCall.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c detectionCallAnnotation.c -o detectionCallAnnotation.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c exon-algorithms.c -o exon-algorithms.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c exon-align-indel.c -o exon-align-indel.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c exon-align.c -o exon-align.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c flattenAnnotations.c -o flattenAnnotations.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c fullscan.c -o fullscan.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c fusion-align.c -o fusion-align.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c gen_rand_reads.c -o gen_rand_reads.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c gene-algorithms.c -o gene-algorithms.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c gene-value-index.c -o gene-value-index.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c hashtable.c -o hashtable.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c index-builder.c -o index-builder.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c input-blc.c -o input-blc.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c input-files.c -o input-files.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c interval_merge.c -o interval_merge.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c long-hashtable.c -o long-hashtable.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c longread-mapping.c -o longread-mapping.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c mergeVCF.c -o mergeVCF.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c processExons.c -o processExons.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c propmapped.c -o propmapped.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c qualityScores.c -o qualityScores.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c read-repair.c -o read-repair.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c readSummary.c -o readSummary.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c removeDupReads.c -o removeDupReads.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c sam2bed.c -o sam2bed.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c sambam-file.c -o sambam-file.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c seek-zlib.c -o seek-zlib.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c sorted-hashtable.c -o sorted-hashtable.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c sublog.c -o sublog.o gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.4.3\"" -fpic -g -O2 -Wall -c tx-unique.c -o tx-unique.o gcc -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/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_wrapper.o RsimReads.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 flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.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-3.12-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-Rsubread/00new/Rsubread/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ‘Rsubread.Rnw’ ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rsubread)