BioC 3.1: CHECK report for podkat on zin2

Package: podkat

Version: 1.0.3

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings podkat_1.0.3.tar.gz

StartedAt: 2015-10-09 04:22:30 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:27:36 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 306.7 seconds

RetCode: 0

Status:  OK

CheckDir: podkat.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings podkat_1.0.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/podkat.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.0.3’
* 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 ... [57s/57s] 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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘podkat.pdf’ from 852Kb to 738Kb
  consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [87s/91s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
unmaskedRegions   20.068  1.681  26.146
assocTest-methods 14.065  0.068  14.124
plot-methods      10.654  0.072  10.720
* 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
  ‘/home/biocbuild/bbs-3.1-bioc/meat/podkat.Rcheck/00check.log’
for details.

* installing *source* package ‘podkat’ ...
** libs
g++ -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c R_init_podkat.cpp -o R_init_podkat.o
g++ -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c bernoulliExact.cpp -o bernoulliExact.o
g++ -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c checkAndFixGenotype.cpp -o checkAndFixGenotype.o
g++ -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c cumMax.cpp -o cumMax.o
g++ -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c doubleMale.cpp -o doubleMale.o
g++ -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c kernels.cpp -o kernels.o
g++ -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c pValues.cpp -o pValues.o
g++ -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c partitionRegions.cpp -o partitionRegions.o
g++ -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c qfc.cpp -o qfc.o
g++ -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c readGenotypeMatrix.cpp -o readGenotypeMatrix.o
g++ -I/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include"   -fpic  -g -O2  -Wall -c readVariantInfo.cpp -o readVariantInfo.o
g++ -shared -L/home/biocbuild/bbs-3.1-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-3.1-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/podkat.Rcheck/podkat/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘p.adjust’ from package ‘stats’ in package ‘podkat’
Creating a generic function for ‘coefficients’ 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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (podkat)

name	user	system	elapsed
AssocTestResult-class	0.802	0.008	0.831
AssocTestResultRanges-class	2.244	0.024	2.271
GenotypeMatrix-class	2.338	0.020	2.368
NullModel-class	2.751	0.020	2.777
VariantInfo-class	0.334	0.004	0.338
assocTest-methods	14.065	0.068	14.124
computeKernel	0.005	0.000	0.005
filterResult-methods	2.295	0.000	2.294
genotypeMatrix-methods	0.560	0.012	0.571
hgA	0.031	0.000	0.031
nullModel-methods	1.665	0.005	1.668
p.adjust-methods	2.036	0.007	2.045
partitionRegions-methods	1.158	0.005	1.162
plot-methods	10.654	0.072	10.720
podkat-package	2.010	0.000	2.009
print-methods	1.996	0.004	1.998
qqplot-methods	3.644	0.000	3.642
readGenotypeMatrix-methods	0.314	0.000	0.313
readRegionsFromBedFile	0.025	0.000	0.026
readSampleNamesFromVcfHeader	0.017	0.000	0.016
readVariantInfo-methods	0.368	0.000	0.377
sort-methods	1.982	0.000	1.981
split-methods	1.809	0.004	1.835
unmasked-datasets	0.867	0.004	0.871
unmaskedRegions	20.068	1.681	26.146
weightFuncs	0.006	0.000	0.006
weights-methods	2.704	0.009	2.727