Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOP[Q]RSTUVWXYZ

This page was generated on 2024-06-18 17:59 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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

Package 1657/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QuasR 1.44.0  (landing page)
Michael Stadler
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/QuasR
git_branch: RELEASE_3_19
git_last_commit: 7508987
git_last_commit_date: 2024-04-30 10:30:09 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


BUILD BIN results for QuasR on palomino3

To the developers/maintainers of the QuasR package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: QuasR
Version: 1.44.0
Command: rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL --build --library=QuasR.buildbin-libdir QuasR_1.44.0.tar.gz
StartedAt: 2024-06-17 17:24:44 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 17:31:10 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 385.6 seconds
RetCode: 0
Status:   OK  
PackageFile: QuasR_1.44.0.zip
PackageFileSize: 6.985 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL --build --library=QuasR.buildbin-libdir QuasR_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* installing *source* package 'QuasR' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_QuasR.cpp -o R_init_QuasR.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bam_cat.c -o bam_cat.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bam_plbuf.c -o bam_plbuf.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cat_bam.c -o cat_bam.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c count_alignments.c -o count_alignments.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c count_alignments_subregions.c -o count_alignments_subregions.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c count_junctions.cpp -o count_junctions.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c export_wig.c -o export_wig.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c extract_unmapped_reads.c -o extract_unmapped_reads.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c filter_hisat2.c -o filter_hisat2.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c idxstats_bam.c -o idxstats_bam.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c merge_reorder_sam.cpp -o merge_reorder_sam.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c profile_alignments.c -o profile_alignments.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c quantify_methylation.cpp -o quantify_methylation.o
quantify_methylation.cpp: In function 'SEXPREC* quantify_methylation_singleAlignments(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
quantify_methylation.cpp:1077:57: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
 1077 |         Rf_error("result structures are incompatible (%ld/%lu/%lu); fatal error in quantify_methylation_singleAlignments\n",
      |                                                       ~~^
      |                                                         |
      |                                                         long int
      |                                                       %lld
 1078 |                  resLength, data.Cid.size(), data.meth.size());
      |                  ~~~~~~~~~                               
      |                  |
      |                  R_xlen_t {aka long long int}
quantify_methylation.cpp:1077:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector<unsigned int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1077 |         Rf_error("result structures are incompatible (%ld/%lu/%lu); fatal error in quantify_methylation_singleAlignments\n",
      |                                                           ~~^
      |                                                             |
      |                                                             long unsigned int
      |                                                           %llu
 1078 |                  resLength, data.Cid.size(), data.meth.size());
      |                             ~~~~~~~~~~~~~~~                  
      |                                          |
      |                                          std::vector<unsigned int>::size_type {aka long long unsigned int}
quantify_methylation.cpp:1077:65: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
 1077 |         Rf_error("result structures are incompatible (%ld/%lu/%lu); fatal error in quantify_methylation_singleAlignments\n",
      |                                                               ~~^
      |                                                                 |
      |                                                                 long unsigned int
      |                                                               %llu
 1078 |                  resLength, data.Cid.size(), data.meth.size());
      |                                              ~~~~~~~~~~~~~~~~    
      |                                                            |
      |                                                            std::vector<int>::size_type {aka long long unsigned int}
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sam_opts.c -o sam_opts.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sam_utils.c -o sam_utils.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c split_sam_chr.c -o split_sam_chr.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utilities.c -o utilities.o
g++ -std=gnu++17 -shared -s -static-libgcc -o QuasR.dll tmp.def 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 F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/meat/QuasR.buildbin-libdir/00LOCK-QuasR/00new/QuasR/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'QuasR' as QuasR_1.44.0.zip
* DONE (QuasR)