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This page was generated on 2023-03-27 11:05:28 -0400 (Mon, 27 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4480
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4276
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4304
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 GenomicAlignments on palomino4


To the developers/maintainers of the GenomicAlignments package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicAlignments.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 782/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicAlignments 1.34.1  (landing page)
Hervé Pagès
Snapshot Date: 2023-03-24 14:00:04 -0400 (Fri, 24 Mar 2023)
git_url: https://git.bioconductor.org/packages/GenomicAlignments
git_branch: RELEASE_3_16
git_last_commit: f65563c
git_last_commit_date: 2023-03-08 18:26:20 -0400 (Wed, 08 Mar 2023)
nebbiolo2Linux (Ubuntu 20.04.5 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 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GenomicAlignments
Version: 1.34.1
Command: rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.34.1.tar.gz
StartedAt: 2023-03-25 08:57:04 -0400 (Sat, 25 Mar 2023)
EndedAt: 2023-03-25 09:12:52 -0400 (Sat, 25 Mar 2023)
EllapsedTime: 948.5 seconds
RetCode: 0
Status:   OK  
PackageFile: GenomicAlignments_1.34.1.zip
PackageFileSize: 2.274 MiB

Command output

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### Running command:
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###   rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.34.1.tar.gz
###
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* installing *source* package 'GenomicAlignments' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:676:9: warning: 'f_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
  676 |    f_elt++;
      |    ~~~~~^~
cigar_utils.c:674:22: warning: 'range_buf1' may be used uninitialized in this function [-Wmaybe-uninitialized]
  674 |    *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
      |                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this function [-Wmaybe-uninitialized]
  674 |    *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
      |     ~~~~~~~~~~~^~~
cigar_utils.c:626:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
  626 |    if (*flag_elt == NA_INTEGER) {
      |        ^~~~~~~~~
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:708:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
  708 |    if (*flag_elt == NA_INTEGER) {
      |        ^~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.16-bioc/R/library/IRanges/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
encodeOverlaps_methods.c: In function 'overlap_encoding':
encodeOverlaps_methods.c:182:2: warning: 'out_nelt0' may be used uninitialized in this function [-Wmaybe-uninitialized]
  182 |  CharAE_delete_at(out, out_nelt0, j1 * nrow);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
encodeOverlaps_methods.c:99:6: note: 'out_nelt0' was declared here
   99 |  int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
      |      ^~~~~~~~~
gcc -shared -s -static-libgcc -o GenomicAlignments.dll tmp.def IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/meat/GenomicAlignments.buildbin-libdir/00LOCK-GenomicAlignments/00new/GenomicAlignments/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 'GenomicAlignments' as GenomicAlignments_1.34.1.zip
* DONE (GenomicAlignments)