| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:04:59 -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: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BitSeq |
| StartedAt: 2023-04-10 16:13:26 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 16:13:42 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 16.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.16-bioc/R/bin/R 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
* running ‘cleanup’
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘BitSeq’ ...
** using staged installation
configure: Version def: -DBS_VERSION=\"1.42.0\"
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking for g++ -std=gnu++14 option to support OpenMP... -fopenmp
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/Makevars.win
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.42.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c ArgumentParser.cpp -o ArgumentParser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.42.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c CollapsedSampler.cpp -o CollapsedSampler.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.42.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c FileHeader.cpp -o FileHeader.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.42.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c GibbsParameters.cpp -o GibbsParameters.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.42.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c GibbsSampler.cpp -o GibbsSampler.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.42.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c MyTimer.cpp -o MyTimer.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.42.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c PosteriorSamples.cpp -o PosteriorSamples.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.42.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.42.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rhtslib/include' -I/usr/local/include -I. -fopenmp -fpic -g -O2 -Wall -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: *** [/home/biocbuild/bbs-3.16-bioc/R/etc/Makeconf:176: ReadDistribution.o] Error 1
ERROR: compilation failed for package ‘BitSeq’
* removing ‘/tmp/RtmpqU8gVU/Rinst3f23bb10a52f44/BitSeq’
-----------------------------------
ERROR: package installation failed