| Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:26 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the BitSeq package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BitSeq.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 208/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Antti Honkela
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| Package: BitSeq |
| Version: 1.42.0 |
| Command: chmod a+r BitSeq -R && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data BitSeq |
| StartedAt: 2023-04-10 17:27:11 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 17:27:35 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 24.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
###
### chmod a+r BitSeq -R && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data BitSeq
###
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* checking for file 'BitSeq/DESCRIPTION' ... OK
* preparing 'BitSeq':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package 'BitSeq' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ArgumentParser.cpp -o ArgumentParser.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CollapsedSampler.cpp -o CollapsedSampler.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FileHeader.cpp -o FileHeader.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GibbsParameters.cpp -o GibbsParameters.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GibbsSampler.cpp -o GibbsSampler.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MyTimer.cpp -o MyTimer.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PosteriorSamples.cpp -o PosteriorSamples.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadDistribution.cpp -o ReadDistribution.o
In file included from ReadDistribution.cpp:7:
ReadDistribution.h:13:10: fatal error: bam.h: No such file or directory
13 | #include "bam.h"
| ^~~~~~~
compilation terminated.
make: *** [F:/biocbuild/bbs-3.16-bioc/R/etc/x64/Makeconf:260: ReadDistribution.o] Error 1
ERROR: compilation failed for package 'BitSeq'
* removing 'F:/biocbuild/bbs-3.16-bioc/tmpdir/Rtmp0uWrrq/Rinst32d4df178c5/BitSeq'
-----------------------------------
ERROR: package installation failed