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BioC 3.5: CHECK report for qsea on veracruz2

This page was generated on 2017-10-18 14:34:46 -0400 (Wed, 18 Oct 2017).

Package 1040/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qsea 1.2.0
Matthias Lienhard
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/qsea
Branch: RELEASE_3_5
Last Commit: 33311bd
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: qsea
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings qsea_1.2.0.tar.gz
StartedAt: 2017-10-18 07:42:13 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 07:46:45 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 271.9 seconds
RetCode: 0
Status:  OK 
CheckDir: qsea.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings qsea_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/qsea.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qsea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qsea’ version ‘1.2.0’
* 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 ‘qsea’ 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... 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
addNewSamples     20.257  0.819  21.739
addCNV             8.199  0.358   8.820
addPatternDensity  5.621  0.561   6.389
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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

qsea.Rcheck/00install.out:

* installing *source* package ‘qsea’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c lm.c -o lm.o
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 qsea.so lm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/qsea.Rcheck/qsea/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (qsea)

qsea.Rcheck/qsea-Ex.timings:

nameusersystemelapsed
addCNV8.1990.3588.820
addContrast2.0510.0822.230
addCoverage2.7190.1702.980
addEnrichmentParameters0.4700.0190.501
addLibraryFactors0.9210.0901.034
addNewSamples20.257 0.81921.739
addOffset0.3290.0190.365
addPatternDensity5.6210.5616.389
createQseaSet0.2450.0140.266
example0.2650.0110.293
fitNBglm1.1680.0721.271
getPCA0.7100.0480.787
isSignificant1.4520.0591.549
makeTable1.8040.0651.912
normMethod0.0020.0000.003
plotCNV0.2980.0080.314
plotCoverage0.8400.0510.917
plotEnrichmentProfile0.3690.0130.392
plotPCA0.6700.0370.731
qseaGLM-class0.0020.0000.002
qseaPCA-class0.0010.0000.002
qseaSet-class0.0010.0000.002
regionStats0.7040.0140.740