BioC 3.2: CHECK report for compcodeR on zin1

Package: compcodeR

Version: 1.5.3

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings compcodeR_1.5.3.tar.gz

StartedAt: 2015-08-23 22:49:56 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 22:54:06 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 250.2 seconds

RetCode: 0

Status:  OK

CheckDir: compcodeR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings compcodeR_1.5.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/compcodeR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [3s/3s] 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 ... [210s/211s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   77.543  0.350  78.798
NBPSeq.createRmd         54.164  0.141  54.435
EBSeq.createRmd          11.387  0.158  11.813
DESeq.GLM.createRmd       9.273  0.363   9.688
show-compData-method      7.119  0.169   7.241
convertcompDataToList     7.071  0.133   7.197
baySeq.createRmd          6.310  0.278   6.582
DESeq2.createRmd          5.188  0.377   5.610
NOISeq.prenorm.createRmd  5.217  0.261   5.434
* 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
  ‘/home/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	9.273	0.363	9.688
DESeq.nbinom.createRmd	77.543	0.350	78.798
DESeq2.createRmd	5.188	0.377	5.610
DSS.createRmd	1.737	0.141	1.972
EBSeq.createRmd	11.387	0.158	11.813
NBPSeq.createRmd	54.164	0.141	54.435
NOISeq.prenorm.createRmd	5.217	0.261	5.434
SAMseq.createRmd	1.678	0.138	1.846
TCC.createRmd	2.397	0.143	2.571
baySeq.createRmd	6.310	0.278	6.582
checkDataObject	0.299	0.048	0.347
checkTableConsistency	1.192	0.143	1.352
check_compData	0.347	0.012	0.355
check_compData_results	0.701	0.060	0.771
compData	0.003	0.000	0.003
convertListTocompData	0.005	0.000	0.005
convertcompDataToList	7.071	0.133	7.197
edgeR.GLM.createRmd	1.500	0.065	1.554
edgeR.exact.createRmd	0.848	0.086	0.943
generateCodeHTMLs	0.740	0.110	0.847
generateSyntheticData	0.302	0.024	0.323
listcreateRmd	0.009	0.000	0.009
logcpm.limma.createRmd	0.529	0.090	0.636
runComparison	2.989	0.256	3.250
runComparisonGUI	0	0	0
runDiffExp	0.648	0.080	0.722
show-compData-method	7.119	0.169	7.241
sqrtcpm.limma.createRmd	0.534	0.059	0.587
summarizeSyntheticDataSet	1.172	0.076	1.237
ttest.createRmd	0.517	0.049	0.561
voom.limma.createRmd	0.718	0.081	0.793
voom.ttest.createRmd	0.610	0.070	0.677
vst.limma.createRmd	0.809	0.098	0.906
vst.ttest.createRmd	0.814	0.073	0.898