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BioC 3.0: CHECK report for DOQTL on perceval

This page was generated on 2015-04-10 09:59:58 -0700 (Fri, 10 Apr 2015).

Package 251/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DOQTL 1.0.0
Daniel Gatti
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/DOQTL
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: DOQTL
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DOQTL_1.0.0.tar.gz
StartedAt: 2015-04-10 00:54:01 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:01:21 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 439.8 seconds
RetCode: 0
Status:  OK 
CheckDir: DOQTL.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DOQTL_1.0.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/DOQTL.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DOQTL/DESCRIPTION’ ... OK
* this is package ‘DOQTL’ version ‘1.0.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DOQTL’ can be installed ... [49s/51s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/29s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
categorize.variants 1.857  0.087   9.734
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [45s/55s]
 [46s/55s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

DOQTL.Rcheck/00install.out:

* installing *source* package ‘DOQTL’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c DOrec.c -o DOrec.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c DOstep.c -o DOstep.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c DOstep_Rwrappers.c -o DOstep_Rwrappers.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c addlog.c -o addlog.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c emission_prob.c -o emission_prob.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c filter.smooth.allele.c -o filter.smooth.allele.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c filter.smooth.intensity.c -o filter.smooth.intensity.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c init.c -o init.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c kinship.c -o kinship.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ri4hap.c -o ri4hap.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c transition.c -o transition.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c update.alleles.c -o update.alleles.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c update.c -o update.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c viterbi.c -o viterbi.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o DOQTL.so DOrec.o DOstep.o DOstep_Rwrappers.o addlog.o emission_prob.o filter.smooth.allele.o filter.smooth.intensity.o init.o kinship.o ri4hap.o transition.o update.alleles.o update.o viterbi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/DOQTL.Rcheck/DOQTL/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DOQTL)

DOQTL.Rcheck/DOQTL-Ex.timings:

nameusersystemelapsed
add.missing.F1s0.0000.0000.001
add.slash0.0020.0010.004
addLog0.0010.0000.001
addLogVector0.0020.0000.002
assoc.map0.0010.0000.001
assoc.plot0.0010.0000.001
bayesint000
calc.genoprob0.0000.0000.001
calc.genoprob.alleles0.0010.0010.001
calc.genoprob.intensity0.0010.0000.001
categorize.variants1.8570.0879.734
cc.trans.probs000
cluster.strains0.7800.0580.839
coef.doqtl0.6740.4031.079
coefplot000
colSumsLog0.0020.0000.002
condense.model.probs0.0000.0000.001
convert.allele.calls0.0010.0000.000
convert.genes.to.GRanges0.0010.0000.000
convert.genotypes0.0010.0000.000
convert.variants.to.GRanges0.7100.0410.753
convert.variants.to.numeric0.6690.0510.721
create.Rdata.files0.0000.0010.000
create.genotype.states0.0020.0000.003
create.html.page000
do.colors0.0040.0000.004
do.states0.0010.0000.002
do.trans.probs0.0000.0000.001
do2sanger0.0010.0000.001
emission.probs.allele0.0010.0000.001
estimate.cluster.params0.0010.0000.000
example.genes0.0020.0000.003
example.pheno0.0060.0000.007
example.qtl0.0010.0000.001
example.snps0.0020.0010.002
extract.raw.data0.0010.0000.001
fast.qtlrel0.0000.0000.001
fill.in.snps0.0000.0010.001
filter.geno.probs0.0010.0000.000
filter.samples0.0010.0000.000
find.overlapping.genes0.0010.0000.001
gene.plot0.0000.0000.001
generic.trans.probs000
genome.plots0.0010.0000.001
genome.summary.plots0.0010.0000.001
get.chr.lengths0.0050.0000.005
get.do.states0.0020.0000.002
get.gene.name0.0000.0000.001
get.machine.precision0.0010.0000.001
get.max.geno0.0010.0000.001
get.mgi.features000
get.num.auto000
get.pattern.variants0.8250.0500.885
get.strains0.0010.0000.001
get.trans.probs0.0000.0000.001
get.variants0.0010.0000.001
html.report000
intensity.plots0.0010.0010.001
kinship0.0010.0000.000
muga.snps.to.keep0.1220.0400.162
normalize.batches0.0000.0000.001
plot.doqtl0.0010.0000.000
pxg.plot000
qtl.LRS0.0010.0000.001
qtl.heatmap0.0000.0000.001
qtl.qtlrel0.0010.0000.001
qtl.simulate000
rankZ0.0020.0000.003
read.vcf0.0010.0000.001
scanone0.0000.0000.002
scanone.eqtl0.0000.0000.001
scanone.perm0.0000.0000.001
sdp.plot0.0010.0000.001
sex.predict0.0010.0000.001
snp.plot0.0010.0000.001
summarize.genotype.transitions0.0010.0000.001
variant.plot0.0010.0000.000
write.founder.genomes0.0010.0000.001