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 13:13:26 -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: /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 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings podkat_1.10.0.tar.gz
###
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* 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.
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)
podkat.Rcheck/podkat-Ex.timings
| name | user | system | elapsed | |
| AssocTestResult-class | 1.236 | 0.044 | 1.282 | |
| AssocTestResultRanges-class | 1.840 | 0.000 | 1.841 | |
| GenotypeMatrix-class | 2.836 | 0.040 | 2.876 | |
| NullModel-class | 2.184 | 0.008 | 2.193 | |
| VariantInfo-class | 0.22 | 0.00 | 0.22 | |
| assocTest-methods | 15.128 | 0.212 | 15.353 | |
| computeKernel | 0.036 | 0.000 | 0.036 | |
| filterResult-methods | 1.520 | 0.004 | 1.523 | |
| genotypeMatrix-methods | 0.964 | 0.016 | 0.981 | |
| hgA | 0.020 | 0.000 | 0.022 | |
| nullModel-methods | 1.328 | 0.024 | 1.357 | |
| p.adjust-methods | 1.236 | 0.004 | 1.238 | |
| partitionRegions-methods | 0.664 | 0.000 | 0.664 | |
| plot-methods | 14.536 | 0.200 | 14.753 | |
| podkat-package | 1.2 | 0.0 | 1.2 | |
| print-methods | 1.120 | 0.000 | 1.122 | |
| qqplot-methods | 2.116 | 0.000 | 2.122 | |
| readGenotypeMatrix-methods | 0.172 | 0.000 | 0.171 | |
| readRegionsFromBedFile | 0.040 | 0.000 | 0.041 | |
| readSampleNamesFromVcfHeader | 0.012 | 0.000 | 0.012 | |
| readVariantInfo-methods | 0.248 | 0.000 | 0.248 | |
| sort-methods | 1.108 | 0.000 | 1.108 | |
| split-methods | 2.060 | 0.032 | 2.092 | |
| unmasked-datasets | 0.480 | 0.000 | 0.479 | |
| unmaskedRegions | 21.380 | 2.960 | 28.819 | |
| weightFuncs | 0.004 | 0.000 | 0.006 | |
| weights-methods | 1.376 | 0.004 | 1.380 | |