| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 12:00:51 -0400 (Tue, 09 Apr 2019).
| Package 188/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| bsseq 1.19.3 Kasper Daniel Hansen
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | ERROR | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: bsseq |
| Version: 1.19.3 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/bsseq_1.19.3.tar.gz && rm -rf bsseq.buildbin-libdir && mkdir bsseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bsseq.buildbin-libdir bsseq_1.19.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL bsseq_1.19.3.zip && rm bsseq_1.19.3.tar.gz bsseq_1.19.3.zip |
| StartedAt: 2019-04-08 20:08:43 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 20:12:31 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 228.8 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/bsseq_1.19.3.tar.gz && rm -rf bsseq.buildbin-libdir && mkdir bsseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bsseq.buildbin-libdir bsseq_1.19.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL bsseq_1.19.3.zip && rm bsseq_1.19.3.tar.gz bsseq_1.19.3.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 2083k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2083k 100 2083k 0 0 5775k 0 --:--:-- --:--:-- --:--:-- 5870k
install for i386
* installing *source* package 'bsseq' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c check_M_and_Cov.cpp -o check_M_and_Cov.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o bsseq.dll tmp.def check_M_and_Cov.o init.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/bsseq.buildbin-libdir/00LOCK-bsseq/00new/bsseq/libs/i386
** R
** data
*** moving datasets to lazyload DB
Registered S3 method overwritten by 'R.oo':
method from
throw.default R.methodsS3
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'bsseq'
finding HTML links ... done
BS.chr22 html
BSmooth html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSmooth.Rd:38: file link 'getHDF5DumpChunkDim' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSmooth.Rd:40: file link 'getHDF5DumpChunkDim' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSmooth.Rd:43: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSmooth.Rd:44: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSmooth.Rd:67: file link 'getRealizationBackend' in package 'DelayedArray' does not exist and so has been treated as a topic
BSmooth.fstat html
BSmooth.tstat html
BSseq-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSseq-class.Rd:137: file link 'setRealizationBackend' in package 'DelayedArray' does not exist and so has been treated as a topic
BSseq html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSseq.Rd:34: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
BSseqStat-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSseqStat-class.Rd:27: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
BSseqTstat-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/BSseqTstat-class.Rd:27: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
FWGRanges-class html
computeStat html
data.frame2GRanges html
dmrFinder html
findLoci html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/findLoci.Rd:44: file link 'vmatchPattern' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/findLoci.Rd:45: file link 'vmatchPattern' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/findLoci.Rd:55: file link 'vmatchPattern' in package 'Biostrings' does not exist and so has been treated as a topic
fisherTests html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/fisherTests.Rd:55: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
getCoverage html
getMeth html
getStats html
goodnessOfFit html
hasGRanges-class html
internals html
plotRegion html
read.bismark html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:36: file link 'rowRanges' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:73: file link 'getHDF5DumpChunkDim' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:75: file link 'getHDF5DumpChunkDim' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:78: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:79: file link 'getHDF5DumpCompressionLevel' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:91: file link 'tempdir' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp8CSEKb/R.INSTALL11a4288b6659/bsseq/man/read.bismark.Rd:177: file link 'getRealizationBackend' in package 'DelayedArray' does not exist and so has been treated as a topic
read.bsmooth html
read.umtab html
smoothSds 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
install for x64
* installing *source* package 'bsseq' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c check_M_and_Cov.cpp -o check_M_and_Cov.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/beachmat/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o bsseq.dll tmp.def check_M_and_Cov.o init.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/bsseq.buildbin-libdir/bsseq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bsseq' as bsseq_1.19.3.zip
* DONE (bsseq)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'bsseq' successfully unpacked and MD5 sums checked