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) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:51:12 -0400 (Tue, 16 Apr 2019).
| Package 1174/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| podkat 1.14.0 Ulrich Bodenhofer
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: podkat |
| Version: 1.14.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:podkat.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings podkat_1.14.0.tar.gz |
| StartedAt: 2019-04-16 02:09:46 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:14:36 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 289.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: podkat.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:podkat.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings podkat_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/podkat.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.14.0’
* 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 ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
R 1.0Mb
libs 4.1Mb
* 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 ‘/home/biocbuild/bbs-3.8-bioc/R/library/podkat/libs/podkat.so’:
Found ‘stderr’, 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
unmaskedRegions 27.136 2.956 35.354
assocTest-methods 13.368 0.504 13.914
plot-methods 11.516 0.296 11.828
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.8-bioc/meat/podkat.Rcheck/00check.log’
for details.
podkat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL podkat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘podkat’ ... ** libs g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c bernoulliExact.cpp -o bernoulliExact.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c checkAndFixGenotype.cpp -o checkAndFixGenotype.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c cumMax.cpp -o cumMax.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c doubleMale.cpp -o doubleMale.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c kernels.cpp -o kernels.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c pValues.cpp -o pValues.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c partitionRegions.cpp -o partitionRegions.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c qfc.cpp -o qfc.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c readGenotypeMatrix.cpp -o readGenotypeMatrix.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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-3.8-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-3.8-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.8-bioc/R/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)
podkat.Rcheck/podkat-Ex.timings
| name | user | system | elapsed | |
| AssocTestResult-class | 0.676 | 0.024 | 0.712 | |
| AssocTestResultRanges-class | 1.336 | 0.092 | 1.431 | |
| GenotypeMatrix-class | 3.452 | 0.028 | 3.485 | |
| NullModel-class | 1.536 | 0.008 | 1.545 | |
| VariantInfo-class | 0.228 | 0.000 | 0.227 | |
| assocTest-methods | 13.368 | 0.504 | 13.914 | |
| computeKernel | 0.004 | 0.000 | 0.003 | |
| filterResult-methods | 1.152 | 0.004 | 1.158 | |
| genotypeMatrix-methods | 0.628 | 0.004 | 0.634 | |
| hgA | 0.016 | 0.000 | 0.014 | |
| nullModel-methods | 0.732 | 0.016 | 0.748 | |
| p.adjust-methods | 1 | 0 | 1 | |
| partitionRegions-methods | 0.544 | 0.000 | 0.545 | |
| plot-methods | 11.516 | 0.296 | 11.828 | |
| podkat-package | 1.568 | 0.004 | 1.584 | |
| print-methods | 1.028 | 0.008 | 1.038 | |
| qqplot-methods | 2.256 | 0.000 | 2.266 | |
| readGenotypeMatrix-methods | 0.388 | 0.004 | 0.389 | |
| readRegionsFromBedFile | 0.036 | 0.000 | 0.048 | |
| readSampleNamesFromVcfHeader | 0.032 | 0.000 | 0.030 | |
| readVariantInfo-methods | 0.46 | 0.00 | 0.46 | |
| sort-methods | 1.140 | 0.004 | 1.143 | |
| split-methods | 2.460 | 0.032 | 2.493 | |
| unmasked-datasets | 0.376 | 0.000 | 0.374 | |
| unmaskedRegions | 27.136 | 2.956 | 35.354 | |
| weightFuncs | 0.004 | 0.000 | 0.004 | |
| weights-methods | 1.592 | 0.000 | 1.593 | |