Wei Shi
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/Rsubread |
| git_branch: RELEASE_3_14 |
| git_last_commit: 9fde88e |
| git_last_commit_date: 2022-03-16 23:02:15 -0400 (Wed, 16 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:05:53 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the Rsubread package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rsubread.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1664/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rsubread 2.8.2 (landing page) Wei Shi
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Rsubread |
| Version: 2.8.2 |
| Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL Rsubread |
| StartedAt: 2022-04-12 03:12:12 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 03:12:48 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 35.5 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL Rsubread
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘Rsubread’ ...
** using staged installation
@@@@@ The operating system is Linux.
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c HelperFunctions.c -o HelperFunctions.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c LRMbase-index.c -o LRMbase-index.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c LRMchro-event.c -o LRMchro-event.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c LRMfile-io.c -o LRMfile-io.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c LRMhashtable.c -o LRMhashtable.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c LRMhelper.c -o LRMhelper.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c LRMseek-zlib.c -o LRMseek-zlib.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c R_wrapper.c -o R_wrapper.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c RsimReads.c -o RsimReads.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c SNPCalling.c -o SNPCalling.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c aligner.c -o aligner.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c atgcContent.c -o atgcContent.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c build-sam-index.c -o build-sam-index.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c core-bigtable.c -o core-bigtable.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c core-indel.c -o core-indel.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c core-interface-aligner.c -o core-interface-aligner.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c core-junction.c -o core-junction.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c core.c -o core.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c detection-calls.c -o detection-calls.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c detectionCall.c -o detectionCall.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c detectionCallAnnotation.c -o detectionCallAnnotation.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c exon-algorithms.c -o exon-algorithms.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c exon-align-indel.c -o exon-align-indel.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c exon-align.c -o exon-align.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c flattenAnnotations.c -o flattenAnnotations.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c fullscan.c -o fullscan.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c fusion-align.c -o fusion-align.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c gen_rand_reads.c -o gen_rand_reads.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c gene-algorithms.c -o gene-algorithms.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c gene-value-index.c -o gene-value-index.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c hashtable.c -o hashtable.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c index-builder.c -o index-builder.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c input-blc.c -o input-blc.o
input-blc.c: In function ‘cacheBCL_qualTest_BAMmode’:
input-blc.c:1006:53: warning: variable ‘lane_str’ set but not used [-Wunused-but-set-variable]
1006 | char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL;
| ^~~~~~~~
input-blc.c:1006:31: warning: variable ‘sample_barcode’ set but not used [-Wunused-but-set-variable]
1006 | char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL;
| ^~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c input-files.c -o input-files.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c interval_merge.c -o interval_merge.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c long-hashtable.c -o long-hashtable.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c longread-mapping.c -o longread-mapping.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c mergeVCF.c -o mergeVCF.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c processExons.c -o processExons.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c propmapped.c -o propmapped.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c qualityScores.c -o qualityScores.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c read-repair.c -o read-repair.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c readSummary.c -o readSummary.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c removeDupReads.c -o removeDupReads.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c sam2bed.c -o sam2bed.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c sambam-file.c -o sambam-file.o
sambam-file.c: In function ‘SamBam_writer_sort_bins_to_BAM’:
sambam-file.c:2379:24: warning: variable ‘last_written_BAI_chro’ set but not used [-Wunused-but-set-variable]
2379 | int old_chro_no = -1, last_written_BAI_chro = -1;
| ^~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c seek-zlib.c -o seek-zlib.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c sorted-hashtable.c -o sorted-hashtable.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c sublog.c -o sublog.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.8.2\"" -fpic -g -O2 -Wall -c tx-unique.c -o tx-unique.o
gcc -shared -L/home/biocbuild/bbs-3.14-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-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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)