| Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:37 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
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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. |
| Package 750/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicAlignments 1.31.2 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GenomicAlignments |
| Version: 1.31.2 |
| Command: rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.31.2.tar.gz |
| StartedAt: 2022-03-17 21:10:53 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 21:13:30 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 156.7 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: GenomicAlignments_1.31.2.zip |
| PackageFileSize: 2.496 MiB |
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### Running command:
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### rm -rf GenomicAlignments.buildbin-libdir && mkdir GenomicAlignments.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicAlignments.buildbin-libdir GenomicAlignments_1.31.2.tar.gz
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* installing *source* package 'GenomicAlignments' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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]
f_elt++;
~~~~~^~
cigar_utils.c:674:22: warning: 'range_buf1' may be used uninitialized in this function [-Wmaybe-uninitialized]
*(breakpoint++) = IntPairAE_get_nelt(range_buf1);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this function [-Wmaybe-uninitialized]
*(breakpoint++) = IntPairAE_get_nelt(range_buf1);
~~~~~~~~~~~^~~
cigar_utils.c:626:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
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]
if (*flag_elt == NA_INTEGER) {
^~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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]
CharAE_set_nelt(out, out_nelt0 + j2 * nrow);
~~~~~~~~~~^~~~~~~~~~~
encodeOverlaps_methods.c:99:6: note: 'out_nelt0' was declared here
int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
^~~~~~~~~
C:/rtools40/mingw64/bin/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:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-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
converting help for package 'GenomicAlignments'
finding HTML links ... done
GAlignmentPairs-class html
finding level-2 HTML links ... done
GAlignments-class html
GAlignmentsList-class html
GappedReads-class html
OverlapEncodings-class html
cigar-utils html
coordinate-mapping-methods html
coverage-methods html
encodeOverlaps-methods html
findCompatibleOverlaps-methods html
findMateAlignment html
findOverlaps-methods html
findSpliceOverlaps-methods html
intra-range-methods html
junctions-methods html
pileLettersAt html
readGAlignments html
sequenceLayer html
setops-methods html
stackStringsFromGAlignments html
summarizeOverlaps-methods html
** 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_1.31.2.zip
* DONE (GenomicAlignments)