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) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:40:37 -0400 (Thu, 12 Apr 2018).
| Package 1052/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| podkat 1.10.0 Ulrich Bodenhofer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| Package: podkat |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings podkat_1.10.0.tar.gz |
| StartedAt: 2018-04-12 07:47:13 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 07:53:37 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 384.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: podkat.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings podkat_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/podkat.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.10.0’
* 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 ... 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’ ... 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 49.23 4.313 54.623
assocTest-methods 17.33 0.577 18.232
plot-methods 12.91 0.505 13.645
* 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
podkat.Rcheck/00install.out
* 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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/RcppCommon.h:138:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/exceptions.h:106:53: 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/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/RcppCommon.h:138:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/exceptions.h:106:53: 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/3.4/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.4/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 /Users/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)
podkat.Rcheck/podkat-Ex.timings
| name | user | system | elapsed | |
| AssocTestResult-class | 1.394 | 0.053 | 1.473 | |
| AssocTestResultRanges-class | 2.299 | 0.041 | 2.362 | |
| GenotypeMatrix-class | 3.811 | 0.070 | 3.926 | |
| NullModel-class | 1.931 | 0.085 | 2.050 | |
| VariantInfo-class | 0.310 | 0.003 | 0.319 | |
| assocTest-methods | 17.330 | 0.577 | 18.232 | |
| computeKernel | 0.044 | 0.001 | 0.046 | |
| filterResult-methods | 1.545 | 0.012 | 1.579 | |
| genotypeMatrix-methods | 1.003 | 0.046 | 1.061 | |
| hgA | 0.017 | 0.002 | 0.019 | |
| nullModel-methods | 0.924 | 0.066 | 1.007 | |
| p.adjust-methods | 1.263 | 0.013 | 1.287 | |
| partitionRegions-methods | 0.748 | 0.012 | 0.770 | |
| plot-methods | 12.910 | 0.505 | 13.645 | |
| podkat-package | 1.404 | 0.013 | 1.451 | |
| print-methods | 1.329 | 0.008 | 1.377 | |
| qqplot-methods | 2.462 | 0.008 | 2.518 | |
| readGenotypeMatrix-methods | 0.263 | 0.003 | 0.279 | |
| readRegionsFromBedFile | 0.060 | 0.002 | 0.063 | |
| readSampleNamesFromVcfHeader | 0.018 | 0.001 | 0.019 | |
| readVariantInfo-methods | 0.349 | 0.003 | 0.363 | |
| sort-methods | 1.307 | 0.007 | 1.331 | |
| split-methods | 2.680 | 0.180 | 2.976 | |
| unmasked-datasets | 0.649 | 0.007 | 0.662 | |
| unmaskedRegions | 49.230 | 4.313 | 54.623 | |
| weightFuncs | 0.008 | 0.001 | 0.009 | |
| weights-methods | 1.451 | 0.009 | 1.485 | |