BioC 3.5: CHECK report for qsea on toluca2

Package: qsea

Version: 1.1.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings qsea_1.1.8.tar.gz

StartedAt: 2017-04-23 08:25:25 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 08:30:27 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 302.4 seconds

RetCode: 0

Status:  OK

CheckDir: qsea.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings qsea_1.1.8.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/qsea.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.8’
* 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     19.492  0.798  20.446
addCNV             9.247  0.379   9.691
addPatternDensity  6.008  0.570   6.641
* 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
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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)

name	user	system	elapsed
addCNV	9.247	0.379	9.691
addContrast	2.504	0.103	2.614
addCoverage	2.780	0.186	2.980
addEnrichmentParameters	0.540	0.014	0.556
addLibraryFactors	1.182	0.115	1.317
addNewSamples	19.492	0.798	20.446
addOffset	0.394	0.024	0.419
addPatternDensity	6.008	0.570	6.641
createQseaSet	0.249	0.012	0.263
example	0.295	0.010	0.307
fitNBglm	1.385	0.070	1.489
getPCA	0.771	0.053	0.829
isSignificant	1.664	0.060	1.739
makeTable	2.070	0.090	2.172
normMethod	0.002	0.001	0.003
plotCNV	0.314	0.009	0.329
plotCoverage	0.963	0.052	1.033
plotEnrichmentProfile	0.449	0.013	0.465
plotPCA	0.713	0.045	0.764
qseaGLM-class	0.001	0.000	0.002
qseaPCA-class	0.001	0.000	0.001
qseaSet-class	0.002	0.000	0.001
regionStats	0.820	0.010	0.837