Hervé Pagès
| Snapshot Date: 2024-11-21 13:40 -0500 (Thu, 21 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/pwalign |
| git_branch: devel |
| git_last_commit: faf38f6 |
| git_last_commit_date: 2024-10-29 11:29:52 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-22 11:34 -0500 (Fri, 22 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4742 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4456 |
| 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 1608/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pwalign 1.3.0 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the pwalign package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pwalign.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: pwalign |
| Version: 1.3.0 |
| Command: rm -rf pwalign.buildbin-libdir && mkdir pwalign.buildbin-libdir && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL --build --library=pwalign.buildbin-libdir pwalign_1.3.0.tar.gz |
| StartedAt: 2024-11-22 08:08:54 -0500 (Fri, 22 Nov 2024) |
| EndedAt: 2024-11-22 08:09:36 -0500 (Fri, 22 Nov 2024) |
| EllapsedTime: 41.9 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: pwalign_1.3.0.zip |
| PackageFileSize: 755.5 KiB |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf pwalign.buildbin-libdir && mkdir pwalign.buildbin-libdir && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL --build --library=pwalign.buildbin-libdir pwalign_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* installing *source* package 'pwalign' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_pairwiseAlignment.c -o R_init_pairwiseAlignment.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Biostrings/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c align_utils.c -o align_utils.o
align_utils.c: In function 'PairwiseAlignmentsSingleSubject_align_aligned':
align_utils.c:234:78: warning: 'indelStartPattern' may be used uninitialized [-Wmaybe-uninitialized]
234 | if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:223:21: note: 'indelStartPattern' was declared here
223 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
| ^~~~~~~~~~~~~~~~~
align_utils.c:240:55: warning: 'indelWidthPattern' may be used uninitialized [-Wmaybe-uninitialized]
240 | for (k = 0; k < indelWidthPattern; k++) {
| ~~^~~~~~~~~~~~~~~~~~~
align_utils.c:223:40: note: 'indelWidthPattern' was declared here
223 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
| ^~~~~~~~~~~~~~~~~
align_utils.c:233:63: warning: 'indelStartSubject' may be used uninitialized [-Wmaybe-uninitialized]
233 | if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
| ~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:223:59: note: 'indelStartSubject' was declared here
223 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
| ^~~~~~~~~~~~~~~~~
align_utils.c:252:42: warning: 'indelWidthSubject' may be used uninitialized [-Wmaybe-uninitialized]
252 | jPattern += indelWidthSubject;
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:223:78: note: 'indelWidthSubject' was declared here
223 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
| ^~~~~~~~~~~~~~~~~
gcc -shared -s -static-libgcc -o pwalign.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_pairwiseAlignment.o S4Vectors_stubs.o XVector_stubs.o align_pairwiseAlignment.o align_utils.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/meat/pwalign.buildbin-libdir/00LOCK-pwalign/00new/pwalign/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'insertion' in package 'pwalign'
Creating a new generic function for 'deletion' in package 'pwalign'
Creating a new generic function for 'unaligned' in package 'pwalign'
Creating a new generic function for 'aligned' in package 'pwalign'
Creating a new generic function for 'indel' in package 'pwalign'
Creating a new generic function for 'nindel' in package 'pwalign'
Creating a new generic function for 'PairwiseAlignments' in package 'pwalign'
Creating a new generic function for 'alignedPattern' in package 'pwalign'
Creating a new generic function for 'alignedSubject' in package 'pwalign'
Creating a new generic function for 'PairwiseAlignmentsSingleSubject' in package 'pwalign'
Creating a new generic function for 'nedit' in package 'pwalign'
Creating a new generic function for 'mismatchTable' in package 'pwalign'
Creating a new generic function for 'mismatchSummary' in package 'pwalign'
Creating a new generic function for 'compareStrings' in package 'pwalign'
Creating a new generic function for 'pid' in package 'pwalign'
Creating a new generic function for 'pairwiseAlignment' in package 'pwalign'
Creating a new generic function for 'stringDist' in package 'pwalign'
** 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 'pwalign' as pwalign_1.3.0.zip
* DONE (pwalign)