BioC 3.5: CHECK report for qsea on malbec2

Package: qsea

Version: 1.2.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings qsea_1.2.0.tar.gz

StartedAt: 2017-10-18 01:43:47 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:47:33 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 225.6 seconds

RetCode: 0

Status:  OK

CheckDir: qsea.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings qsea_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/qsea.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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     18.864  0.064  19.399
addCNV             6.740  0.056   6.817
addPatternDensity  5.780  0.068   5.852
* 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

* installing *source* package ‘qsea’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c lm.c -o lm.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o qsea.so lm.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/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)

name	user	system	elapsed
addCNV	6.740	0.056	6.817
addContrast	1.460	0.020	1.479
addCoverage	2.488	0.020	2.512
addEnrichmentParameters	0.312	0.000	0.309
addLibraryFactors	0.852	0.000	0.853
addNewSamples	18.864	0.064	19.399
addOffset	0.252	0.000	0.253
addPatternDensity	5.780	0.068	5.852
createQseaSet	0.144	0.004	0.148
example	0.236	0.000	0.234
fitNBglm	0.808	0.004	0.812
getPCA	0.568	0.004	0.572
isSignificant	0.900	0.000	0.901
makeTable	1.184	0.004	1.189
normMethod	0.004	0.000	0.002
plotCNV	0.208	0.000	0.207
plotCoverage	0.588	0.016	0.605
plotEnrichmentProfile	0.272	0.000	0.272
plotPCA	0.484	0.008	0.494
qseaGLM-class	0.004	0.000	0.001
qseaPCA-class	0.000	0.000	0.001
qseaSet-class	0	0	0
regionStats	0.520	0.000	0.522