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BioC 3.1: CHECK report for DOQTL on petty

This page was generated on 2015-10-09 09:36:37 -0700 (Fri, 09 Oct 2015).

Package 271/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DOQTL 1.2.0
Daniel Gatti
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/DOQTL
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DOQTL
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DOQTL_1.2.0.tar.gz
StartedAt: 2015-10-08 22:41:01 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 22:47:04 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 363.9 seconds
RetCode: 0
Status:  OK 
CheckDir: DOQTL.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DOQTL_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/DOQTL.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.2.0’
* 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 ... [43s/44s] 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 ... [16s/34s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
categorize.variants 1.501  0.069  19.431
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [43s/51s]
 [43s/52s] 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

Status: OK

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-3.1-bioc/meat/DOQTL.Rcheck/DOQTL/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (DOQTL)

DOQTL.Rcheck/DOQTL-Ex.timings:

nameusersystemelapsed
add.missing.F1s000
add.slash0.0020.0000.003
addLog0.0010.0000.001
addLogVector0.0020.0000.002
assoc.map0.0000.0000.001
assoc.plot000
bayesint000
calc.genoprob0.0010.0000.001
calc.genoprob.alleles0.0010.0000.001
calc.genoprob.intensity0.0010.0000.001
categorize.variants 1.501 0.06919.431
cc.trans.probs0.0010.0000.001
cluster.strains0.6470.0160.664
coef.doqtl0.8140.3991.212
coefplot0.0010.0000.001
colSumsLog0.0020.0010.002
condense.model.probs0.0000.0000.001
convert.allele.calls0.0010.0000.002
convert.genes.to.GRanges0.0010.0000.001
convert.genotypes0.0010.0000.001
convert.variants.to.GRanges0.7240.0350.762
convert.variants.to.numeric0.6560.0320.689
create.Rdata.files0.0010.0000.001
create.genotype.states0.0040.0000.004
create.html.page0.0010.0000.000
do.colors0.0030.0000.002
do.states0.0020.0010.003
do.trans.probs0.0010.0000.001
do2sanger0.0010.0000.001
emission.probs.allele0.0010.0000.001
estimate.cluster.params0.0010.0000.000
example.genes0.0020.0000.002
example.pheno0.0060.0010.006
example.qtl0.0000.0000.001
example.snps0.0010.0010.002
extract.raw.data0.0010.0000.001
fast.qtlrel0.0010.0000.001
fill.in.snps0.0010.0000.000
filter.geno.probs0.0010.0000.001
filter.samples0.0010.0000.001
find.overlapping.genes0.0010.0000.001
gene.plot0.0010.0000.001
generic.trans.probs0.0010.0000.001
genome.plots0.0010.0000.001
genome.summary.plots0.0010.0000.001
get.chr.lengths0.0090.0010.009
get.do.states0.0010.0000.002
get.gene.name000
get.machine.precision0.0000.0000.001
get.max.geno0.0010.0000.001
get.mgi.features0.0010.0000.002
get.num.auto0.0010.0000.002
get.pattern.variants0.3670.0320.402
get.strains0.0000.0000.001
get.trans.probs0.0010.0000.001
get.variants0.0020.0000.001
html.report0.0000.0000.001
intensity.plots0.0010.0000.001
kinship0.0010.0000.001
muga.snps.to.keep0.1390.0350.175
normalize.batches0.0010.0000.002
plot.doqtl0.0010.0000.002
pxg.plot0.0010.0000.001
qtl.LRS0.0010.0000.001
qtl.heatmap0.0010.0000.001
qtl.qtlrel0.0010.0000.001
qtl.simulate0.0010.0000.001
rankZ0.0020.0010.003
read.vcf000
scanone0.0000.0000.001
scanone.eqtl0.0010.0000.001
scanone.perm0.0010.0000.001
sdp.plot0.0010.0000.002
sex.predict0.0010.0010.001
snp.plot0.0010.0000.002
summarize.genotype.transitions0.0000.0000.001
variant.plot0.0000.0000.001
write.founder.genomes0.0010.0000.001