BioC 3.4: CHECK report for podkat on malbec1

Package: podkat

Version: 1.6.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings podkat_1.6.1.tar.gz

StartedAt: 2017-04-15 00:28:55 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:33:34 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 278.6 seconds

RetCode: 0

Status:  OK

CheckDir: podkat.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings podkat_1.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/podkat.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘podkat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘podkat’ version ‘1.6.1’
* 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 ‘podkat’ 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
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
unmaskedRegions   21.488  0.968  28.363
assocTest-methods 12.104  0.064  12.176
plot-methods      10.060  0.056  10.122
* 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

* installing *source* package ‘podkat’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c R_init_podkat.cpp -o R_init_podkat.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c bernoulliExact.cpp -o bernoulliExact.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c checkAndFixGenotype.cpp -o checkAndFixGenotype.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c cumMax.cpp -o cumMax.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c doubleMale.cpp -o doubleMale.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c kernels.cpp -o kernels.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c pValues.cpp -o pValues.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c partitionRegions.cpp -o partitionRegions.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c qfc.cpp -o qfc.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c readGenotypeMatrix.cpp -o readGenotypeMatrix.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c readVariantInfo.cpp -o readVariantInfo.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o podkat.so R_init_podkat.o bernoulliExact.o checkAndFixGenotype.o cumMax.o doubleMale.o kernels.o pValues.o partitionRegions.o qfc.o readGenotypeMatrix.o readVariantInfo.o /home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/podkat.Rcheck/podkat/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘p.adjust’ from package ‘stats’ in package ‘podkat’
Creating a generic function for ‘qqplot’ from package ‘stats’ in package ‘podkat’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (podkat)

name	user	system	elapsed
AssocTestResult-class	1.084	0.004	1.090
AssocTestResultRanges-class	1.672	0.040	1.715
GenotypeMatrix-class	2.640	0.028	2.673
NullModel-class	2.392	0.016	2.407
VariantInfo-class	0.192	0.000	0.194
assocTest-methods	12.104	0.064	12.176
computeKernel	0.004	0.000	0.004
filterResult-methods	1.348	0.000	1.351
genotypeMatrix-methods	0.432	0.012	0.443
hgA	0.016	0.000	0.019
nullModel-methods	0.916	0.004	0.917
p.adjust-methods	1.204	0.000	1.204
partitionRegions-methods	0.636	0.000	0.639
plot-methods	10.060	0.056	10.122
podkat-package	1.164	0.000	1.166
print-methods	1.164	0.004	1.171
qqplot-methods	2.168	0.000	2.169
readGenotypeMatrix-methods	0.300	0.000	0.301
readRegionsFromBedFile	0.028	0.000	0.028
readSampleNamesFromVcfHeader	0.016	0.000	0.015
readVariantInfo-methods	0.208	0.000	0.205
sort-methods	1.220	0.000	1.222
split-methods	1.968	0.008	1.977
unmasked-datasets	0.376	0.000	0.377
unmaskedRegions	21.488	0.968	28.363
weightFuncs	0.008	0.000	0.006
weights-methods	1.368	0.000	1.370