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This page was generated on 2022-01-17 11:05:45 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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? here 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 745/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicAlignments 1.31.2  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/GenomicAlignments
git_branch: master
git_last_commit: 6043a0a
git_last_commit_date: 2021-11-03 18:06:15 -0500 (Wed, 03 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'BiocGenerics' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GenomicAlignments
Version: 1.31.2
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL GenomicAlignments
StartedAt: 2022-01-16 15:15:43 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 15:16:11 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 28.2 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL GenomicAlignments
###
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘GenomicAlignments’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-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:676:9: 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) {
      |        ^~~~~~~~~
cigar_utils.c: In function ‘cigar_narrow’:
cigar_utils.c:880:6: warning: ‘Roffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  880 |   if (offset == Roffset)
      |      ^
cigar_utils.c:852:15: note: ‘Roffset’ was declared here
  852 |  int Loffset, Roffset, buf_offset;
      |               ^~~~~~~
cigar_utils.c:878:6: warning: ‘Loffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  878 |   if (offset == Loffset)
      |      ^
cigar_utils.c:852:6: note: ‘Loffset’ was declared here
  852 |  int Loffset, Roffset, buf_offset;
      |      ^~~~~~~
cigar_utils.c: In function ‘cigar_qnarrow’:
cigar_utils.c:1064:6: warning: ‘Roffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1064 |   if (offset == Roffset)
      |      ^
cigar_utils.c:1036:15: note: ‘Roffset’ was declared here
 1036 |  int Loffset, Roffset, buf_offset;
      |               ^~~~~~~
cigar_utils.c:1062:6: warning: ‘Loffset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1062 |   if (offset == Loffset)
      |      ^
cigar_utils.c:1036:6: note: ‘Loffset’ was declared here
 1036 |  int Loffset, Roffset, buf_offset;
      |      ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.15-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:180:33: warning: ‘out_nelt0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  180 |  CharAE_set_nelt(out, out_nelt0 + j2 * 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 -L/home/biocbuild/bbs-3.15-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-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-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)