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This page was generated on 2023-02-01 11:05:35 -0500 (Wed, 01 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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

INSTALL results for GenomicAlignments on nebbiolo1


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 771/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicAlignments 1.35.0  (landing page)
Hervé Pagès
Snapshot Date: 2023-01-31 14:00:20 -0500 (Tue, 31 Jan 2023)
git_url: https://git.bioconductor.org/packages/GenomicAlignments
git_branch: master
git_last_commit: 06a6074
git_last_commit_date: 2022-11-01 11:08:59 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: GenomicAlignments
Version: 1.35.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GenomicAlignments
StartedAt: 2023-01-31 15:12:10 -0500 (Tue, 31 Jan 2023)
EndedAt: 2023-01-31 15:12:42 -0500 (Tue, 31 Jan 2023)
EllapsedTime: 32.6 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GenomicAlignments
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘GenomicAlignments’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function ‘cigar_ranges’:
cigar_utils.c:676:30: warning: ‘f_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  676 |                         f_elt++;
      |                         ~~~~~^~
cigar_utils.c:674:43: warning: ‘range_buf1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  674 |                         *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
      |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cigar_utils.c:674:37: warning: ‘breakpoint’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  674 |                         *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
      |                          ~~~~~~~~~~~^~~
cigar_utils.c:626:29: 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:708:29: warning: ‘flag_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  708 |                         if (*flag_elt == NA_INTEGER) {
      |                             ^~~~~~~~~
cigar_utils.c: In function ‘cigar_narrow’:
cigar_utils.c:883:20: warning: ‘Roffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  883 |                 if (offset == Roffset)
      |                    ^
cigar_utils.c:854:22: note: ‘Roffset’ was declared here
  854 |         int Loffset, Roffset, buf_offset;
      |                      ^~~~~~~
cigar_utils.c:881:20: warning: ‘Loffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  881 |                 if (offset == Loffset)
      |                    ^
cigar_utils.c:854:13: note: ‘Loffset’ was declared here
  854 |         int Loffset, Roffset, buf_offset;
      |             ^~~~~~~
cigar_utils.c: In function ‘cigar_qnarrow’:
cigar_utils.c:1074:20: warning: ‘Roffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1074 |                 if (offset == Roffset)
      |                    ^
cigar_utils.c:1045:22: note: ‘Roffset’ was declared here
 1045 |         int Loffset, Roffset, buf_offset;
      |                      ^~~~~~~
cigar_utils.c:1072:20: warning: ‘Loffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1072 |                 if (offset == Loffset)
      |                    ^
cigar_utils.c:1045:13: note: ‘Loffset’ was declared here
 1045 |         int Loffset, Roffset, buf_offset;
      |             ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
encodeOverlaps_methods.c: In function ‘overlap_encoding’:
encodeOverlaps_methods.c:182:9: warning: ‘out_nelt0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  182 |         CharAE_delete_at(out, out_nelt0, j1 * nrow);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
encodeOverlaps_methods.c:99:13: note: ‘out_nelt0’ was declared here
   99 |         int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
      |             ^~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-GenomicAlignments/00new/GenomicAlignments/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 (GenomicAlignments)