BioC 3.2: CHECK report for compcodeR on linux1.bioconductor.org

Package: compcodeR

Version: 1.6.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings compcodeR_1.6.0.tar.gz

StartedAt: 2015-10-27 02:24:48 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:29:15 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 266.6 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_1.6.0.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 ‘1.6.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [225s/224s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   84.267  0.330  84.712
NBPSeq.createRmd         57.268  0.219  57.574
DESeq.GLM.createRmd      10.779  0.411  11.077
EBSeq.createRmd          10.841  0.127  10.940
baySeq.createRmd          8.860  0.267   8.956
show-compData-method      7.846  0.145   7.900
convertcompDataToList     7.428  0.131   7.464
DESeq2.createRmd          6.857  0.279   6.956
NOISeq.prenorm.createRmd  5.036  0.232   5.147
* 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	10.779	0.411	11.077
DESeq.nbinom.createRmd	84.267	0.330	84.712
DESeq2.createRmd	6.857	0.279	6.956
DSS.createRmd	1.861	0.097	1.938
EBSeq.createRmd	10.841	0.127	10.940
NBPSeq.createRmd	57.268	0.219	57.574
NOISeq.prenorm.createRmd	5.036	0.232	5.147
SAMseq.createRmd	1.304	0.076	1.351
TCC.createRmd	2.907	0.128	3.012
baySeq.createRmd	8.860	0.267	8.956
checkDataObject	0.266	0.017	0.274
checkTableConsistency	1.046	0.099	1.122
check_compData	0.307	0.017	0.316
check_compData_results	0.705	0.045	0.733
compData	0.002	0.000	0.003
convertListTocompData	0.001	0.005	0.004
convertcompDataToList	7.428	0.131	7.464
edgeR.GLM.createRmd	1.391	0.081	1.441
edgeR.exact.createRmd	1.278	0.121	1.395
generateCodeHTMLs	0.614	0.060	0.656
generateSyntheticData	0.276	0.013	0.280
listcreateRmd	0.007	0.000	0.007
logcpm.limma.createRmd	0.456	0.043	0.485
runComparison	2.548	0.186	2.700
runComparisonGUI	0	0	0
runDiffExp	0.637	0.058	0.679
show-compData-method	7.846	0.145	7.900
sqrtcpm.limma.createRmd	0.466	0.052	0.507
summarizeSyntheticDataSet	1.058	0.061	1.093
ttest.createRmd	0.493	0.035	0.515
voom.limma.createRmd	0.643	0.046	0.673
voom.ttest.createRmd	0.496	0.078	0.560
vst.limma.createRmd	0.682	0.055	0.721
vst.ttest.createRmd	1.017	0.075	1.076