BioC 3.2: CHECK report for compcodeR on perceval

Package: compcodeR

Version: 1.5.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings compcodeR_1.5.3.tar.gz

StartedAt: 2015-08-23 23:31:47 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 23:37:47 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 359.7 seconds

RetCode: 0

Status:  OK

CheckDir: compcodeR.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 compcodeR_1.5.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/compcodeR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘compcodeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compcodeR’ version ‘1.5.3’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘rpanel’
* 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 ‘compcodeR’ can be installed ... [6s/6s] 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 ... NOTE
'library' or 'require' call to ‘rpanel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [286s/288s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   70.529  5.599  76.939
NBPSeq.createRmd         48.497  4.851  53.527
convertcompDataToList    20.760 10.514  31.082
show-compData-method     20.670 10.316  30.828
DESeq.GLM.createRmd      13.370  1.168  15.060
EBSeq.createRmd          12.579  1.271  13.974
DESeq2.createRmd          8.748  1.154   9.994
NOISeq.prenorm.createRmd  8.549  0.867   9.519
baySeq.createRmd          7.956  0.724   8.593
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/compcodeR.Rcheck/00check.log’
for details.

* installing *source* package ‘compcodeR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (compcodeR)

name	user	system	elapsed
DESeq.GLM.createRmd	13.370	1.168	15.060
DESeq.nbinom.createRmd	70.529	5.599	76.939
DESeq2.createRmd	8.748	1.154	9.994
DSS.createRmd	2.448	0.271	2.848
EBSeq.createRmd	12.579	1.271	13.974
NBPSeq.createRmd	48.497	4.851	53.527
NOISeq.prenorm.createRmd	8.549	0.867	9.519
SAMseq.createRmd	2.083	0.391	2.453
TCC.createRmd	3.738	0.361	4.111
baySeq.createRmd	7.956	0.724	8.593
checkDataObject	0.558	0.119	0.663
checkTableConsistency	1.745	0.220	1.930
check_compData	0.495	0.087	0.569
check_compData_results	1.136	0.155	1.275
compData	0.004	0.000	0.004
convertListTocompData	0.006	0.000	0.007
convertcompDataToList	20.760	10.514	31.082
edgeR.GLM.createRmd	1.907	0.210	2.077
edgeR.exact.createRmd	1.198	0.149	1.329
generateCodeHTMLs	1.066	0.162	1.223
generateSyntheticData	0.514	0.075	0.579
listcreateRmd	0.027	0.001	0.028
logcpm.limma.createRmd	0.905	0.111	1.036
runComparison	3.793	0.455	4.398
runComparisonGUI	0.001	0.000	0.002
runDiffExp	1.213	0.160	1.350
show-compData-method	20.670	10.316	30.828
sqrtcpm.limma.createRmd	0.857	0.141	0.977
summarizeSyntheticDataSet	2.135	0.245	2.393
ttest.createRmd	0.913	0.109	1.006
voom.limma.createRmd	1.191	0.160	1.323
voom.ttest.createRmd	0.961	0.131	1.073
vst.limma.createRmd	1.401	0.166	1.544
vst.ttest.createRmd	1.322	0.139	1.442