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BioC 3.1: CHECK report for DOQTL on moscato2

This page was generated on 2015-10-09 09:31:19 -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: rm -rf DOQTL.buildbin-libdir DOQTL.Rcheck && mkdir DOQTL.buildbin-libdir DOQTL.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DOQTL.buildbin-libdir DOQTL_1.2.0.tar.gz >DOQTL.Rcheck\00install.out 2>&1 && cp DOQTL.Rcheck\00install.out DOQTL-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=DOQTL.buildbin-libdir --install="check:DOQTL-install.out" --force-multiarch --no-vignettes --timings DOQTL_1.2.0.tar.gz
StartedAt: 2015-10-09 01:17:54 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:24:28 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 394.5 seconds
RetCode: 0
Status:  OK  
CheckDir: DOQTL.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DOQTL.buildbin-libdir DOQTL.Rcheck && mkdir DOQTL.buildbin-libdir DOQTL.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DOQTL.buildbin-libdir DOQTL_1.2.0.tar.gz >DOQTL.Rcheck\00install.out 2>&1 && cp DOQTL.Rcheck\00install.out DOQTL-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=DOQTL.buildbin-libdir --install="check:DOQTL-install.out" --force-multiarch --no-vignettes --timings DOQTL_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/DOQTL.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'DOQTL' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-3.1-bioc/meat/DOQTL.buildbin-libdir/DOQTL/libs/i386/DOQTL.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-3.1-bioc/meat/DOQTL.buildbin-libdir/DOQTL/libs/x64/DOQTL.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [18s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
categorize.variants 0.67   0.02    8.44
** running examples for arch 'x64' ... [19s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
categorize.variants 1.17   0.04    7.81
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [42s]
 [42s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [39s]
 [39s] 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: 1 NOTE
See
  'E:/biocbld/bbs-3.1-bioc/meat/DOQTL.Rcheck/00check.log'
for details.

DOQTL.Rcheck/00install.out:


install for i386

* installing *source* package 'DOQTL' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c DOrec.c -o DOrec.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c DOstep.c -o DOstep.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c DOstep_Rwrappers.c -o DOstep_Rwrappers.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c addlog.c -o addlog.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c emission_prob.c -o emission_prob.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c filter.smooth.allele.c -o filter.smooth.allele.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c filter.smooth.intensity.c -o filter.smooth.intensity.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c kinship.c -o kinship.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ri4hap.c -o ri4hap.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c transition.c -o transition.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c update.alleles.c -o update.alleles.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c update.c -o update.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c viterbi.c -o viterbi.o
gcc -m32 -shared -s -static-libgcc -o DOQTL.dll tmp.def 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 -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/DOQTL.buildbin-libdir/DOQTL/libs/i386
** 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'

install for x64

* installing *source* package 'DOQTL' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c DOrec.c -o DOrec.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c DOstep.c -o DOstep.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c DOstep_Rwrappers.c -o DOstep_Rwrappers.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c addlog.c -o addlog.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c emission_prob.c -o emission_prob.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c filter.smooth.allele.c -o filter.smooth.allele.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c filter.smooth.intensity.c -o filter.smooth.intensity.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c init.c -o init.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c kinship.c -o kinship.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ri4hap.c -o ri4hap.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c transition.c -o transition.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c update.alleles.c -o update.alleles.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c update.c -o update.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c viterbi.c -o viterbi.o
gcc -m64 -shared -s -static-libgcc -o DOQTL.dll tmp.def 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 -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/meat/DOQTL.buildbin-libdir/DOQTL/libs/x64
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'DOQTL' as DOQTL_1.2.0.zip
* DONE (DOQTL)

DOQTL.Rcheck/examples_i386/DOQTL-Ex.timings:

nameusersystemelapsed
add.missing.F1s000
add.slash000
addLog000
addLogVector000
assoc.map000
assoc.plot000
bayesint000
calc.genoprob000
calc.genoprob.alleles000
calc.genoprob.intensity000
categorize.variants0.670.028.44
cc.trans.probs000
cluster.strains0.390.030.42
coef.doqtl0.460.060.53
coefplot000
colSumsLog000
condense.model.probs000
convert.allele.calls000
convert.genes.to.GRanges000
convert.genotypes000
convert.variants.to.GRanges0.470.030.50
convert.variants.to.numeric0.560.041.54
create.Rdata.files000
create.genotype.states000
create.html.page000
do.colors000
do.states000
do.trans.probs000
do2sanger000
emission.probs.allele000
estimate.cluster.params000
example.genes000
example.pheno000
example.qtl000
example.snps000
extract.raw.data000
fast.qtlrel000
fill.in.snps000
filter.geno.probs000
filter.samples000
find.overlapping.genes000
gene.plot000
generic.trans.probs000
genome.plots000
genome.summary.plots000
get.chr.lengths000
get.do.states000
get.gene.name000
get.machine.precision000
get.max.geno000
get.mgi.features000
get.num.auto000
get.pattern.variants0.260.000.27
get.strains000
get.trans.probs000
get.variants000
html.report000
intensity.plots000
kinship000
muga.snps.to.keep0.030.020.05
normalize.batches000
plot.doqtl000
pxg.plot000
qtl.LRS000
qtl.heatmap000
qtl.qtlrel000
qtl.simulate000
rankZ000
read.vcf000
scanone000
scanone.eqtl000
scanone.perm000
sdp.plot000
sex.predict000
snp.plot000
summarize.genotype.transitions000
variant.plot000
write.founder.genomes000

DOQTL.Rcheck/examples_x64/DOQTL-Ex.timings:

nameusersystemelapsed
add.missing.F1s000
add.slash000
addLog0.010.000.01
addLogVector000
assoc.map000
assoc.plot000
bayesint000
calc.genoprob000
calc.genoprob.alleles000
calc.genoprob.intensity000
categorize.variants1.170.047.81
cc.trans.probs000
cluster.strains0.640.020.66
coef.doqtl0.590.150.75
coefplot000
colSumsLog000
condense.model.probs0.020.000.02
convert.allele.calls000
convert.genes.to.GRanges000
convert.genotypes000
convert.variants.to.GRanges0.670.020.68
convert.variants.to.numeric0.280.030.32
create.Rdata.files000
create.genotype.states000
create.html.page000
do.colors000
do.states000
do.trans.probs000
do2sanger000
emission.probs.allele0.010.000.02
estimate.cluster.params000
example.genes000
example.pheno000
example.qtl000
example.snps000
extract.raw.data000
fast.qtlrel000
fill.in.snps000
filter.geno.probs0.010.000.02
filter.samples000
find.overlapping.genes000
gene.plot000
generic.trans.probs000
genome.plots000
genome.summary.plots000
get.chr.lengths000
get.do.states000
get.gene.name000
get.machine.precision000
get.max.geno000
get.mgi.features000
get.num.auto000
get.pattern.variants0.730.020.75
get.strains000
get.trans.probs000
get.variants0.010.000.01
html.report000
intensity.plots000
kinship000
muga.snps.to.keep0.050.010.07
normalize.batches000
plot.doqtl000
pxg.plot000
qtl.LRS000
qtl.heatmap000
qtl.qtlrel000
qtl.simulate000
rankZ000
read.vcf000
scanone000
scanone.eqtl000
scanone.perm000
sdp.plot000
sex.predict000
snp.plot000
summarize.genotype.transitions000
variant.plot000
write.founder.genomes000