| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:30:23 -0400 (Wed, 16 Oct 2019).
| Package 458/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Daniel Gatti
| 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 |
| Package: DOQTL |
| Version: 1.20.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DOQTL_1.20.0.tar.gz && rm -rf DOQTL.buildbin-libdir && mkdir DOQTL.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DOQTL.buildbin-libdir DOQTL_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DOQTL_1.20.0.zip && rm DOQTL_1.20.0.tar.gz DOQTL_1.20.0.zip |
| StartedAt: 2019-10-15 21:10:06 -0400 (Tue, 15 Oct 2019) |
| EndedAt: 2019-10-15 21:12:39 -0400 (Tue, 15 Oct 2019) |
| EllapsedTime: 152.3 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/DOQTL_1.20.0.tar.gz && rm -rf DOQTL.buildbin-libdir && mkdir DOQTL.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DOQTL.buildbin-libdir DOQTL_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DOQTL_1.20.0.zip && rm DOQTL_1.20.0.tar.gz DOQTL_1.20.0.zip
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install for i386
* installing *source* package 'DOQTL' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c DOrec.c -o DOrec.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c DOstep.c -o DOstep.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c DOstep_Rwrappers.c -o DOstep_Rwrappers.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c addlog.c -o addlog.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c emission_prob.c -o emission_prob.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c emission_prob2.c -o emission_prob2.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c filter.smooth.allele.c -o filter.smooth.allele.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c filter.smooth.intensity.c -o filter.smooth.intensity.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c kinship.c -o kinship.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ri4hap.c -o ri4hap.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c transition.c -o transition.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c update.alleles.c -o update.alleles.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c update.c -o update.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o DOQTL.dll tmp.def DOrec.o DOstep.o DOstep_Rwrappers.o addlog.o emission_prob.o emission_prob2.o filter.smooth.allele.o filter.smooth.intensity.o init.o kinship.o ri4hap.o transition.o update.alleles.o update.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/DOQTL.buildbin-libdir/00LOCK-DOQTL/00new/DOQTL/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'scanOne(y = pheno, x = addcovar, ': unused argument (intcovar = intcovar)
** help
*** installing help indices
converting help for package 'DOQTL'
finding HTML links ... done
add.missing.F1s html
add.sig.thr html
add.slash html
addLog html
addLogVector html
assoc.map html
assoc.plot html
assoc.scan1 html
assoc.scan2 html
bayesint html
calc.genoprob html
calc.genoprob.alleles html
calc.genoprob.intensity html
categorize.variants html
cc.trans.probs html
cluster.strains html
coef.doqtl html
coefplot html
colSumsLog html
condense.model.probs html
condense.sanger.snps html
convert.allele.calls html
convert.genes.to.GRanges html
convert.genotypes html
convert.variants.to.GRanges html
convert.variants.to.numeric html
create.Rdata.files html
create.genotype.states html
create.html.page html
do.colors html
do.states html
do.trans.probs html
do2sanger html
emission.probs.allele html
estimate.cluster.params html
example.genes html
example.pheno html
example.qtl html
example.snps html
extract.raw.data html
fast.qtlrel html
fill.in.snps html
filter.geno.probs html
filter.samples html
find.overlapping.genes html
gene.plot html
generic.trans.probs html
genome.plots html
genome.summary.plots html
get.chr.lengths html
get.do.states html
get.gene.name html
get.machine.precision html
get.max.geno html
get.mgi.features html
get.num.auto html
get.pattern.variants html
get.pgw html
get.sig.thr html
get.strains html
get.trans.probs html
get.variants html
hmm html
html.report html
impute.genotypes html
intensity.plots html
internal_functions html
interpolate.markers html
kinship html
muga.snps.to.keep html
normalize.batches html
parameter.update html
plot.doqtl html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpC4IJV5/R.INSTALL24ec6057ee1/DOQTL/man/plot.doqtl.Rd:20: missing link 'get.sig.thr()'
pxg.plot html
qtl.LRS html
qtl.heatmap html
qtl.qtlrel html
qtl.simulate html
rankZ html
read.vcf html
scanone html
scanone.assoc html
scanone.eqtl html
scanone.perm html
sdp.plot html
sex.predict html
snp.plot html
summarize.genotype.transitions html
update_from_r html
variant.plot html
write.founder.genomes html
write.results html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'DOQTL' is deprecated and will be removed from Bioconductor
version 3.10
** testing if installed package can be loaded from final location
Warning: Package 'DOQTL' is deprecated and will be removed from Bioconductor
version 3.10
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'DOQTL' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c DOrec.c -o DOrec.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c DOstep.c -o DOstep.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c DOstep_Rwrappers.c -o DOstep_Rwrappers.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c addlog.c -o addlog.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c emission_prob.c -o emission_prob.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c emission_prob2.c -o emission_prob2.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c filter.smooth.allele.c -o filter.smooth.allele.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c filter.smooth.intensity.c -o filter.smooth.intensity.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c kinship.c -o kinship.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ri4hap.c -o ri4hap.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c transition.c -o transition.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c update.alleles.c -o update.alleles.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c update.c -o update.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o DOQTL.dll tmp.def DOrec.o DOstep.o DOstep_Rwrappers.o addlog.o emission_prob.o emission_prob2.o filter.smooth.allele.o filter.smooth.intensity.o init.o kinship.o ri4hap.o transition.o update.alleles.o update.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/DOQTL.buildbin-libdir/DOQTL/libs/x64
** testing if installed package can be loaded
Warning: Package 'DOQTL' is deprecated and will be removed from Bioconductor
version 3.10
* MD5 sums
packaged installation of 'DOQTL' as DOQTL_1.20.0.zip
* DONE (DOQTL)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'DOQTL' successfully unpacked and MD5 sums checked