BioC 3.0: CHECK report for compcodeR on zin1

Package: compcodeR

Version: 1.2.1

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings compcodeR_1.2.1.tar.gz

StartedAt: 2015-04-09 22:51:07 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 22:55:04 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 236.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: compcodeR.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings compcodeR_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/compcodeR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-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 ‘1.2.1’
* 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 ... [4s/4s] 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 ... WARNING
Functions or methods with usage in documentation object 'HTSDiff.createRmd' but not in code:
  HTSDiff.createRmd

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' call not declared from: ‘HTSDiff’
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [176s/184s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
DESeq.nbinom.createRmd 80.533  0.388  86.530
DESeq.GLM.createRmd    13.444  0.368  14.196
EBSeq.createRmd        11.889  0.168  12.679
baySeq.createRmd       10.649  0.304  10.982
show-compData-method    8.913  0.196   9.123
convertcompDataToList   8.265  0.192   8.471
DESeq2.createRmd        6.077  0.352   7.099
* 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

WARNING: There were 2 warnings.
NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-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	13.444	0.368	14.196
DESeq.nbinom.createRmd	80.533	0.388	86.530
DESeq2.createRmd	6.077	0.352	7.099
DSS.createRmd	1.852	0.132	2.097
EBSeq.createRmd	11.889	0.168	12.679
HTSDiff.createRmd	0.004	0.000	0.004
NBPSeq.createRmd	0.652	0.116	0.862
NOISeq.prenorm.createRmd	4.288	0.164	4.486
SAMseq.createRmd	1.820	0.144	1.995
TCC.createRmd	3.028	0.140	3.256
baySeq.createRmd	10.649	0.304	10.982
checkDataObject	0.376	0.016	0.396
checkTableConsistency	1.452	0.112	1.583
check_compData	0.380	0.012	0.394
check_compData_results	1.104	0.080	1.196
compData	0.004	0.000	0.004
convertListTocompData	0.008	0.000	0.008
convertcompDataToList	8.265	0.192	8.471
edgeR.GLM.createRmd	1.684	0.072	1.768
edgeR.exact.createRmd	1.032	0.060	1.103
generateCodeHTMLs	0.876	0.068	0.955
generateSyntheticData	0.400	0.012	0.411
listcreateRmd	0.004	0.004	0.009
logcpm.limma.createRmd	0.884	0.064	0.996
runComparison	3.164	0.196	3.414
runComparisonGUI	0.000	0.000	0.001
runDiffExp	0.904	0.068	0.978
show-compData-method	8.913	0.196	9.123
sqrtcpm.limma.createRmd	0.676	0.076	0.763
summarizeSyntheticDataSet	1.576	0.064	1.644
ttest.createRmd	0.648	0.068	0.723
voom.limma.createRmd	0.880	0.052	0.944
voom.ttest.createRmd	0.704	0.072	0.787
vst.limma.createRmd	0.948	0.080	1.039
vst.ttest.createRmd	1.116	0.104	1.260