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BioC 3.4: CHECK report for podkat on zin1

This page was generated on 2016-09-21 03:39:45 -0700 (Wed, 21 Sep 2016).

Package 911/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
podkat 1.5.3
Ulrich Bodenhofer
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/podkat
Last Changed Rev: 120621 / Revision: 121152
Last Changed Date: 2016-08-31 04:52:04 -0700 (Wed, 31 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: podkat
Version: 1.5.3
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings podkat_1.5.3.tar.gz
StartedAt: 2016-09-20 10:40:14 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:44:42 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 268.5 seconds
RetCode: 0
Status:  OK 
CheckDir: podkat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings podkat_1.5.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/podkat.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.5.3’
* 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 ... 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 874Kb to 762Kb
  consider running tools::compactPDF() on these files
* 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   19.392  2.692  26.455
assocTest-methods 11.980  0.020  12.026
plot-methods       9.156  0.212   9.534
* 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-3.4-bioc/meat/podkat.Rcheck/00check.log’
for details.


podkat.Rcheck/00install.out:

* 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 ‘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
* DONE (podkat)

podkat.Rcheck/podkat-Ex.timings:

nameusersystemelapsed
AssocTestResult-class0.9360.0120.953
AssocTestResultRanges-class1.8600.0321.951
GenotypeMatrix-class2.4040.0242.476
NullModel-class2.2200.0122.232
VariantInfo-class0.2080.0040.213
assocTest-methods11.980 0.02012.026
computeKernel0.0000.0040.004
filterResult-methods1.5760.0001.590
genotypeMatrix-methods0.4360.0120.454
hgA0.0160.0000.018
nullModel-methods1.4320.0041.436
p.adjust-methods1.4480.0041.512
partitionRegions-methods0.6920.0040.697
plot-methods9.1560.2129.534
podkat-package1.4640.0041.472
print-methods1.4560.0001.461
qqplot-methods2.4080.0002.416
readGenotypeMatrix-methods0.1960.0000.196
readRegionsFromBedFile0.0320.0000.030
readSampleNamesFromVcfHeader0.0160.0000.015
readVariantInfo-methods0.2200.0000.221
sort-methods1.4640.0041.475
split-methods1.3520.0001.384
unmasked-datasets0.3720.0000.376
unmaskedRegions19.392 2.69226.455
weightFuncs0.0080.0000.007
weights-methods1.6360.0001.654