| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:38 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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 829/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicAlignments 1.40.0 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the GenomicAlignments package: - 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 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. |
| Package: GenomicAlignments |
| Version: 1.40.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GenomicAlignments |
| StartedAt: 2024-10-16 16:02:14 -0400 (Wed, 16 Oct 2024) |
| EndedAt: 2024-10-16 16:02:49 -0400 (Wed, 16 Oct 2024) |
| EllapsedTime: 34.9 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GenomicAlignments
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘GenomicAlignments’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-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-3.19-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-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-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)