Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 12:20:18 -0400 (Tue, 09 Apr 2019).
Package 450/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
DOQTL 1.19.0 Daniel Gatti
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | ERROR | skipped | skipped | |||||||
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: DOQTL |
Version: 1.19.0 |
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DOQTL_1.19.0.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_1.19.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DOQTL_1.19.0.zip && rm DOQTL_1.19.0.tar.gz DOQTL_1.19.0.zip |
StartedAt: 2019-04-08 20:44:53 -0400 (Mon, 08 Apr 2019) |
EndedAt: 2019-04-08 20:46:38 -0400 (Mon, 08 Apr 2019) |
EllapsedTime: 105.8 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DOQTL_1.19.0.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_1.19.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DOQTL_1.19.0.zip && rm DOQTL_1.19.0.tar.gz DOQTL_1.19.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 7 4042k 7 304k 0 0 4868k 0 --:--:-- --:--:-- --:--:-- 5428k 100 4042k 100 4042k 0 0 39.6M 0 --:--:-- --:--:-- --:--:-- 42.4M install for i386 * installing *source* package 'DOQTL' ... ** 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/Rtmp8U4JDi/R.INSTALL2238395021ce/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 ** 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 '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 * MD5 sums packaged installation of 'DOQTL' as DOQTL_1.19.0.zip * DONE (DOQTL) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'DOQTL' successfully unpacked and MD5 sums checked