| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:36:49 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 819/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicAlignments 1.38.2 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.38.2 |
| Command: rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.38.2.tar.gz |
| StartedAt: 2024-04-16 07:03:51 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 07:04:52 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 60.8 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: GenomicAlignments_1.38.2.zip |
| PackageFileSize: 2.267 MiB |
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### Running command:
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### rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.38.2.tar.gz
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* installing *source* package 'GenomicAlignments' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 [-Wmaybe-uninitialized]
676 | f_elt++;
| ~~~~~^~
cigar_utils.c:593:41: note: 'f_elt' was declared here
593 | const int *flag_elt, *pos_elt, *f_elt;
| ^~~~~
In function 'parse_cigar_ranges',
inlined from 'cigar_ranges' at cigar_utils.c:660:12:
cigar_utils.c:213:21: warning: 'range_buf1' may be used uninitialized [-Wmaybe-uninitialized]
213 | buf_nelt0 = IntPairAE_get_nelt(range_buf);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:590:20: note: 'range_buf1' was declared here
590 | IntPairAE *range_buf1;
| ^~~~~~~~~~
cigar_utils.c:674:37: warning: 'breakpoint' may be used uninitialized [-Wmaybe-uninitialized]
674 | *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
| ~~~~~~~~~~~^~~
cigar_utils.c:588:62: note: 'breakpoint' was declared here
588 | int cigar_len, space0, pos_len, f_is_NULL, ans_len, *breakpoint,
| ^~~~~~~~~~
cigar_utils.c:542:25: warning: 'ans_breakpoints' may be used uninitialized [-Wmaybe-uninitialized]
542 | new_PartitioningByEnd("PartitioningByEnd",
| ^~~~~~~~~~~~~~~~~~~~~
cigar_utils.c:587:19: note: 'ans_breakpoints' was declared here
587 | SEXP ans, ans_breakpoints, f_levels, cigar_elt;
| ^~~~~~~~~~~~~~~
cigar_utils.c:626:29: warning: 'flag_elt' may be used uninitialized [-Wmaybe-uninitialized]
626 | if (*flag_elt == NA_INTEGER) {
| ^~~~~~~~~
cigar_utils.c:593:20: note: 'flag_elt' was declared here
593 | const int *flag_elt, *pos_elt, *f_elt;
| ^~~~~~~~
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:708:29: warning: 'flag_elt' may be used uninitialized [-Wmaybe-uninitialized]
708 | if (*flag_elt == NA_INTEGER) {
| ^~~~~~~~~
cigar_utils.c:698:20: note: 'flag_elt' was declared here
698 | const int *flag_elt;
| ^~~~~~~~
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
coordinate_mapping_methods.c: In function 'to_ref':
coordinate_mapping_methods.c:219:6: warning: 'n' may be used uninitialized [-Wmaybe-uninitialized]
219 | if (n == 0)
| ^
coordinate_mapping_methods.c:172:7: note: 'n' was declared here
172 | int n, offset = 0, OPL, query_consumed = 0;
| ^
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
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:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-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_1.38.2.zip
* DONE (GenomicAlignments)