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CHECK report for podkat on malbec1

This page was generated on 2018-04-12 13:13:26 -0400 (Thu, 12 Apr 2018).

Package 1052/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
podkat 1.10.0
Ulrich Bodenhofer
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/podkat
Branch: RELEASE_3_6
Last Commit: 45abe14
Last Changed Date: 2017-10-30 12:40:50 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: podkat
Version: 1.10.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings podkat_1.10.0.tar.gz
StartedAt: 2018-04-12 01:52:01 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:56:54 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 292.9 seconds
RetCode: 0
Status:  OK 
CheckDir: podkat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings podkat_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/podkat.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.10.0’
* 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 ‘podkat’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
* 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   21.380  2.960  28.819
assocTest-methods 15.128  0.212  15.353
plot-methods      14.536  0.200  14.753
* 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-3.6-bioc/meat/podkat.Rcheck/00check.log’
for details.



Installation output

podkat.Rcheck/00install.out

* installing *source* package ‘podkat’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_podkat.cpp -o R_init_podkat.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c bernoulliExact.cpp -o bernoulliExact.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c checkAndFixGenotype.cpp -o checkAndFixGenotype.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c cumMax.cpp -o cumMax.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c doubleMale.cpp -o doubleMale.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c kernels.cpp -o kernels.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c pValues.cpp -o pValues.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c partitionRegions.cpp -o partitionRegions.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c qfc.cpp -o qfc.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c readGenotypeMatrix.cpp -o readGenotypeMatrix.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c readVariantInfo.cpp -o readVariantInfo.o
g++ -shared -L/home/biocbuild/bbs-3.6-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-3.6-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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)

Tests output


Example timings

podkat.Rcheck/podkat-Ex.timings

nameusersystemelapsed
AssocTestResult-class1.2360.0441.282
AssocTestResultRanges-class1.8400.0001.841
GenotypeMatrix-class2.8360.0402.876
NullModel-class2.1840.0082.193
VariantInfo-class0.220.000.22
assocTest-methods15.128 0.21215.353
computeKernel0.0360.0000.036
filterResult-methods1.5200.0041.523
genotypeMatrix-methods0.9640.0160.981
hgA0.0200.0000.022
nullModel-methods1.3280.0241.357
p.adjust-methods1.2360.0041.238
partitionRegions-methods0.6640.0000.664
plot-methods14.536 0.20014.753
podkat-package1.20.01.2
print-methods1.1200.0001.122
qqplot-methods2.1160.0002.122
readGenotypeMatrix-methods0.1720.0000.171
readRegionsFromBedFile0.0400.0000.041
readSampleNamesFromVcfHeader0.0120.0000.012
readVariantInfo-methods0.2480.0000.248
sort-methods1.1080.0001.108
split-methods2.0600.0322.092
unmasked-datasets0.4800.0000.479
unmaskedRegions21.380 2.96028.819
weightFuncs0.0040.0000.006
weights-methods1.3760.0041.380