BioC 3.3: CHECK report for podkat on linux2.bioconductor.org
This page was generated on 2015-10-27 12:12:54 -0400 (Tue, 27 Oct 2015).
podkat 1.3.0
Ulrich Bodenhofer
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/podkat | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
Summary
| Package: podkat |
| Version: 1.3.0 |
| Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings podkat_1.3.0.tar.gz |
| StartedAt: 2015-10-27 06:50:06 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 06:55:02 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 296.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: podkat.Rcheck |
| Warnings: 0 |
Command output
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###
### Running command:
###
### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings podkat_1.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/podkat.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.3.0’
* 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 ... [52s/52s] 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘podkat’ for: ‘residuals’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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 ... [83s/86s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
unmaskedRegions 21.080 1.387 25.189
assocTest-methods 15.092 0.196 15.288
plot-methods 10.682 0.152 10.838
* 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-3.3-bioc/meat/podkat.Rcheck/00check.log’
for details.
podkat.Rcheck/00install.out:
* installing *source* package ‘podkat’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c R_init_podkat.cpp -o R_init_podkat.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c bernoulliExact.cpp -o bernoulliExact.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c checkAndFixGenotype.cpp -o checkAndFixGenotype.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c cumMax.cpp -o cumMax.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c doubleMale.cpp -o doubleMale.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c kernels.cpp -o kernels.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c pValues.cpp -o pValues.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c partitionRegions.cpp -o partitionRegions.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c qfc.cpp -o qfc.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c readGenotypeMatrix.cpp -o readGenotypeMatrix.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c readVariantInfo.cpp -o readVariantInfo.o
g++ -shared -L/home/biocbuild/bbs-3.3-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-3.3-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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 ‘coefficients’ 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 | 0.738 | 0.012 | 0.750 |
|
| AssocTestResultRanges-class | 1.712 | 0.004 | 1.718 |
|
| GenotypeMatrix-class | 2.450 | 0.032 | 2.484 |
|
| NullModel-class | 2.802 | 0.016 | 2.825 |
|
| VariantInfo-class | 0.516 | 0.004 | 0.524 |
|
| assocTest-methods | 15.092 | 0.196 | 15.288 |
|
| computeKernel | 0.006 | 0.000 | 0.005 |
|
| filterResult-methods | 1.883 | 0.000 | 1.883 |
|
| genotypeMatrix-methods | 0.504 | 0.012 | 0.515 |
|
| hgA | 0.025 | 0.000 | 0.024 |
|
| nullModel-methods | 1.493 | 0.000 | 1.494 |
|
| p.adjust-methods | 1.587 | 0.004 | 1.590 |
|
| partitionRegions-methods | 0.913 | 0.000 | 0.913 |
|
| plot-methods | 10.682 | 0.152 | 10.838 |
|
| podkat-package | 1.597 | 0.004 | 1.602 |
|
| print-methods | 1.578 | 0.004 | 1.581 |
|
| qqplot-methods | 3.324 | 0.000 | 3.324 |
|
| readGenotypeMatrix-methods | 0.516 | 0.000 | 0.516 |
|
| readRegionsFromBedFile | 0.031 | 0.000 | 0.031 |
|
| readSampleNamesFromVcfHeader | 0.021 | 0.000 | 0.020 |
|
| readVariantInfo-methods | 0.551 | 0.000 | 0.550 |
|
| sort-methods | 1.738 | 0.000 | 1.737 |
|
| split-methods | 1.284 | 0.004 | 1.289 |
|
| unmasked-datasets | 0.642 | 0.004 | 0.647 |
|
| unmaskedRegions | 21.080 | 1.387 | 25.189 |
|
| weightFuncs | 0.005 | 0.000 | 0.005 |
|
| weights-methods | 1.77 | 0.00 | 1.77 |
|