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This page was generated on 2022-06-24 11:08:26 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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

BUILD BIN results for QuasR on lconway


To the developers/maintainers of the QuasR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/QuasR.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.

raw results

Package 1532/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QuasR 1.37.1  (landing page)
Michael Stadler
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/QuasR
git_branch: master
git_last_commit: ff049af
git_last_commit_date: 2022-05-03 14:20:29 -0400 (Tue, 03 May 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    ERROR    OK  

Summary

Package: QuasR
Version: 1.37.1
Command: rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh QuasR_1.37.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R QuasR.buildbin-libdir
StartedAt: 2022-06-23 23:51:39 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 23:53:03 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 83.8 seconds
RetCode: 0
Status:   OK  
PackageFile: QuasR_1.37.1.tgz
PackageFileSize: 3.141 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh QuasR_1.37.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R QuasR.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=QuasR.buildbin-libdir QuasR_1.37.1.tar.gz'
>>>>>>> 

* installing *source* package ‘QuasR’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_QuasR.cpp -o R_init_QuasR.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bam_cat.c -o bam_cat.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bam_plbuf.c -o bam_plbuf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cat_bam.c -o cat_bam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_alignments.c -o count_alignments.o
count_alignments.c:110:50: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
    if((rinfo->absIsizeMin != NO_ISIZE_FILTER && abs(hit->core.isize) < rinfo->absIsizeMin) ||
                                                 ^
count_alignments.c:110:50: note: use function 'labs' instead
    if((rinfo->absIsizeMin != NO_ISIZE_FILTER && abs(hit->core.isize) < rinfo->absIsizeMin) ||
                                                 ^~~
                                                 labs
count_alignments.c:111:50: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
       (rinfo->absIsizeMax != NO_ISIZE_FILTER && abs(hit->core.isize) > rinfo->absIsizeMax))
                                                 ^
count_alignments.c:111:50: note: use function 'labs' instead
       (rinfo->absIsizeMax != NO_ISIZE_FILTER && abs(hit->core.isize) > rinfo->absIsizeMax))
                                                 ^~~
                                                 labs
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_alignments_subregions.c -o count_alignments_subregions.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_junctions.cpp -o count_junctions.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c export_wig.c -o export_wig.o
export_wig.c:49:49: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
    if((tcov->absIsizeMin != NO_ISIZE_FILTER && abs(hit->core.isize) < tcov->absIsizeMin) ||
                                                ^
export_wig.c:49:49: note: use function 'labs' instead
    if((tcov->absIsizeMin != NO_ISIZE_FILTER && abs(hit->core.isize) < tcov->absIsizeMin) ||
                                                ^~~
                                                labs
export_wig.c:50:49: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
       (tcov->absIsizeMax != NO_ISIZE_FILTER && abs(hit->core.isize) > tcov->absIsizeMax))
                                                ^
export_wig.c:50:49: note: use function 'labs' instead
       (tcov->absIsizeMax != NO_ISIZE_FILTER && abs(hit->core.isize) > tcov->absIsizeMax))
                                                ^~~
                                                labs
export_wig.c:62:127: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
                    hitPos = (int)((double)bam_calend(&(hit->core), bam1_cigar(hit)) -1 + ((double)hit->core.isize - hit->core.isize/abs(hit->core.isize)) /2);
                                                                                                                                     ^
export_wig.c:62:127: note: use function 'labs' instead
                    hitPos = (int)((double)bam_calend(&(hit->core), bam1_cigar(hit)) -1 + ((double)hit->core.isize - hit->core.isize/abs(hit->core.isize)) /2);
                                                                                                                                     ^~~
                                                                                                                                     labs
export_wig.c:64:99: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
                hitPos = (int)((double)hit->core.pos + ((double)hit->core.isize - hit->core.isize/abs(hit->core.isize)) /2);
                                                                                                  ^
export_wig.c:64:99: note: use function 'labs' instead
                hitPos = (int)((double)hit->core.pos + ((double)hit->core.isize - hit->core.isize/abs(hit->core.isize)) /2);
                                                                                                  ^~~
                                                                                                  labs
4 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c extract_unmapped_reads.c -o extract_unmapped_reads.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c filter_hisat2.c -o filter_hisat2.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c idxstats_bam.c -o idxstats_bam.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c merge_reorder_sam.cpp -o merge_reorder_sam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c profile_alignments.c -o profile_alignments.o
profile_alignments.c:121:50: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
    if((rinfo->absIsizeMin != NO_ISIZE_FILTER && abs(hit->core.isize) < rinfo->absIsizeMin) ||
                                                 ^
profile_alignments.c:121:50: note: use function 'labs' instead
    if((rinfo->absIsizeMin != NO_ISIZE_FILTER && abs(hit->core.isize) < rinfo->absIsizeMin) ||
                                                 ^~~
                                                 labs
profile_alignments.c:122:50: warning: absolute value function 'abs' given an argument of type 'const hts_pos_t' (aka 'const long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
       (rinfo->absIsizeMax != NO_ISIZE_FILTER && abs(hit->core.isize) > rinfo->absIsizeMax))
                                                 ^
profile_alignments.c:122:50: note: use function 'labs' instead
       (rinfo->absIsizeMax != NO_ISIZE_FILTER && abs(hit->core.isize) > rinfo->absIsizeMax))
                                                 ^~~
                                                 labs
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c quantify_methylation.cpp -o quantify_methylation.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c sam_opts.c -o sam_opts.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c sam_utils.c -o sam_utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c split_sam_chr.c -o split_sam_chr.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c utilities.c -o utilities.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o QuasR.so R_init_QuasR.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_opts.o sam_utils.o split_sam_chr.o utilities.o /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.16-bioc/meat/QuasR.buildbin-libdir/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)


>>>>>>> 
>>>>>>> FIXING LINKS FOR QuasR.buildbin-libdir/QuasR/libs/QuasR.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "QuasR.buildbin-libdir/QuasR/libs/QuasR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "QuasR.buildbin-libdir/QuasR/libs/QuasR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "QuasR.buildbin-libdir/QuasR/libs/QuasR.so"