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CHECK report for podkat on merida1

This page was generated on 2019-04-16 11:58:29 -0400 (Tue, 16 Apr 2019).

Package 1174/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
podkat 1.14.0
Ulrich Bodenhofer
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/podkat
Branch: RELEASE_3_8
Last Commit: 5166924
Last Changed Date: 2018-10-30 11:41:57 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: podkat
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:podkat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings podkat_1.14.0.tar.gz
StartedAt: 2019-04-16 01:57:54 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:03:57 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 362.3 seconds
RetCode: 0
Status:  OK 
CheckDir: podkat.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:podkat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings podkat_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/podkat.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.14.0’
* 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 ... 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 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 ... NOTE
assocTest.TabixFile: no visible global function definition for ‘path’
readGenotypeMatrix.TabixFile: no visible global function definition for
  ‘path’
readSampleNamesFromVcfHeader: no visible global function definition for
  ‘path’
readVariantInfo.TabixFile: no visible global function definition for
  ‘path’
weights.AssocTestResultRanges.TabixFile: no visible global function
  definition for ‘path’
assocTest,TabixFile-NullModel: no visible global function definition
  for ‘path’
readGenotypeMatrix,TabixFile-GRanges: no visible global function
  definition for ‘path’
readVariantInfo,TabixFile-GRanges: no visible global function
  definition for ‘path’
Undefined global functions or variables:
  path
* 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 ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/podkat/libs/podkat.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
unmaskedRegions   64.485  5.281  70.189
assocTest-methods 13.694  0.567  14.334
plot-methods      11.381  0.555  11.991
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/podkat.Rcheck/00check.log’
for details.



Installation output

podkat.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL podkat
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘podkat’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_podkat.cpp -o R_init_podkat.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c bernoulliExact.cpp -o bernoulliExact.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c checkAndFixGenotype.cpp -o checkAndFixGenotype.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c cumMax.cpp -o cumMax.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c doubleMale.cpp -o doubleMale.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c kernels.cpp -o kernels.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c pValues.cpp -o pValues.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c partitionRegions.cpp -o partitionRegions.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c qfc.cpp -o qfc.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c readGenotypeMatrix.cpp -o readGenotypeMatrix.o
In file included from readGenotypeMatrix.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:128:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion]
    inline void warning(const std::string& message) {        // #nocov start
                                                    ^
1 warning generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c readVariantInfo.cpp -o readVariantInfo.o
In file included from readVariantInfo.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/RcppCommon.h:128:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/Rcpp/exceptions.h:109:53: warning: all paths through this function will call itself [-Winfinite-recursion]
    inline void warning(const std::string& message) {        // #nocov start
                                                    ^
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/podkat/libs
** R
** data
** inst
** byte-compile and prepare 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-class0.6660.0320.703
AssocTestResultRanges-class1.9110.1462.064
GenotypeMatrix-class3.3970.0933.503
NullModel-class1.8880.1212.022
VariantInfo-class0.3750.0040.381
assocTest-methods13.694 0.56714.334
computeKernel0.0040.0010.005
filterResult-methods2.0780.0502.139
genotypeMatrix-methods0.9510.0631.020
hgA0.0220.0020.025
nullModel-methods1.1160.0991.222
p.adjust-methods1.1770.0121.190
partitionRegions-methods0.5300.0030.535
plot-methods11.381 0.55511.991
podkat-package1.3440.0291.381
print-methods1.4450.0111.468
qqplot-methods2.3890.0082.407
readGenotypeMatrix-methods0.3680.0030.374
readRegionsFromBedFile0.0430.0080.052
readSampleNamesFromVcfHeader0.0250.0010.026
readVariantInfo-methods0.3100.0020.312
sort-methods1.4220.0071.434
split-methods2.6170.1472.776
unmasked-datasets0.4070.0140.423
unmaskedRegions64.485 5.28170.189
weightFuncs0.0080.0020.009
weights-methods1.6400.0071.654