BioC 3.1: CHECK report for compcodeR on zin2

Package: compcodeR

Version: 1.4.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings compcodeR_1.4.0.tar.gz

StartedAt: 2015-10-08 23:52:44 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:57:28 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 284.3 seconds

RetCode: 0

Status:  OK

CheckDir: compcodeR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings compcodeR_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-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 ‘1.4.0’
* 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/5s] 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 ... [154s/224s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   77.543  0.423 113.088
EBSeq.createRmd          10.943  0.115  15.162
DESeq.GLM.createRmd       9.438  0.290  13.069
show-compData-method      7.408  0.223  10.226
convertcompDataToList     7.282  0.187  11.451
baySeq.createRmd          6.523  0.287   9.865
NOISeq.prenorm.createRmd  5.625  0.286   8.955
DESeq2.createRmd          4.488  0.343   6.724
* 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-3.1-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	9.438	0.290	13.069
DESeq.nbinom.createRmd	77.543	0.423	113.088
DESeq2.createRmd	4.488	0.343	6.724
DSS.createRmd	1.242	0.097	2.388
EBSeq.createRmd	10.943	0.115	15.162
NBPSeq.createRmd	0.513	0.065	1.073
NOISeq.prenorm.createRmd	5.625	0.286	8.955
SAMseq.createRmd	1.345	0.086	2.240
TCC.createRmd	2.415	0.065	3.644
baySeq.createRmd	6.523	0.287	9.865
checkDataObject	0.307	0.016	0.594
checkTableConsistency	1.226	0.116	2.192
check_compData	0.305	0.016	0.458
check_compData_results	0.652	0.076	0.910
compData	0.003	0.000	0.003
convertListTocompData	0.001	0.004	0.005
convertcompDataToList	7.282	0.187	11.451
edgeR.GLM.createRmd	1.438	0.064	2.071
edgeR.exact.createRmd	0.834	0.044	1.024
generateCodeHTMLs	0.687	0.075	1.155
generateSyntheticData	0.313	0.012	0.387
listcreateRmd	0.008	0.000	0.008
logcpm.limma.createRmd	0.519	0.057	1.167
runComparison	2.447	0.187	4.325
runComparisonGUI	0	0	0
runDiffExp	0.691	0.049	0.940
show-compData-method	7.408	0.223	10.226
sqrtcpm.limma.createRmd	0.478	0.063	0.747
summarizeSyntheticDataSet	1.137	0.076	1.541
ttest.createRmd	0.540	0.053	1.155
voom.limma.createRmd	0.678	0.077	1.348
voom.ttest.createRmd	0.579	0.053	1.313
vst.limma.createRmd	0.987	0.119	1.723
vst.ttest.createRmd	0.673	0.080	1.193