Michael Stadler
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/QuasR |
| Branch: RELEASE_3_10 |
| Last Commit: 666a27b |
| Last Changed Date: 2019-10-29 13:08:36 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:07:25 -0400 (Wed, 15 Apr 2020).
| Package 1352/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| QuasR 1.26.0 Michael Stadler
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | [ OK ] | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: QuasR |
| Version: 1.26.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL QuasR |
| StartedAt: 2020-04-14 19:03:16 -0400 (Tue, 14 Apr 2020) |
| EndedAt: 2020-04-14 19:04:17 -0400 (Tue, 14 Apr 2020) |
| EllapsedTime: 60.7 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL QuasR
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘QuasR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c R_init_QuasR.cpp -o R_init_QuasR.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c bam.c -o bam.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c bam_cat.c -o bam_cat.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c bam_plbuf.c -o bam_plbuf.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c cat_bam.c -o cat_bam.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c count_alignments.c -o count_alignments.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c count_alignments_subregions.c -o count_alignments_subregions.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c count_junctions.cpp -o count_junctions.o
count_junctions.cpp: In function ‘int _addJunction(const bam1_t*, void*)’:
count_junctions.cpp:90:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = y = 0; i < hit->core.n_cigar; ++i) {
~~^~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c export_wig.c -o export_wig.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c extract_unmapped_reads.c -o extract_unmapped_reads.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c filter_hisat2.c -o filter_hisat2.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c idxstats_bam.c -o idxstats_bam.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c merge_reorder_sam.cpp -o merge_reorder_sam.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c profile_alignments.c -o profile_alignments.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c quantify_methylation.cpp -o quantify_methylation.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c sam.c -o sam.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c sam_utils.c -o sam_utils.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c split_sam_chr.c -o split_sam_chr.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -c utilities.c -o utilities.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o QuasR.so R_init_QuasR.o bam.o bam_cat.o bam_plbuf.o cat_bam.o convert_reads_id_bis_rc.o count_alignments.o count_alignments_subregions.o count_junctions.o export_wig.o extract_unmapped_reads.o filter_hisat2.o idxstats_bam.o merge_reorder_sam.o nucleotide_alignment_frequencies.o profile_alignments.o quantify_methylation.o remove_unmapped_from_sam.o sam.o sam_utils.o split_sam_chr.o utilities.o /home/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-QuasR/00new/QuasR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (QuasR)