BioC 3.2: CHECK report for compcodeR on oaxaca

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 22:49:37 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 22:55:34 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 357.3 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 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [5s/7s] 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 ... [217s/272s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   54.827  2.751  63.943
NBPSeq.createRmd         37.002  2.424  39.792
convertcompDataToList    10.435  5.810  16.448
show-compData-method     10.392  5.596  16.680
DESeq.GLM.createRmd      14.811  1.067  30.378
EBSeq.createRmd          11.123  0.509  14.299
baySeq.createRmd          9.101  0.546  10.232
DESeq2.createRmd          8.401  1.015  23.590
NOISeq.prenorm.createRmd  8.172  0.658  12.238
TCC.createRmd             2.676  0.189   8.465
DSS.createRmd             2.642  0.214   5.855
SAMseq.createRmd          1.859  0.225   5.160
* 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	14.811	1.067	30.378
DESeq.nbinom.createRmd	54.827	2.751	63.943
DESeq2.createRmd	8.401	1.015	23.590
DSS.createRmd	2.642	0.214	5.855
EBSeq.createRmd	11.123	0.509	14.299
NBPSeq.createRmd	37.002	2.424	39.792
NOISeq.prenorm.createRmd	8.172	0.658	12.238
SAMseq.createRmd	1.859	0.225	5.160
TCC.createRmd	2.676	0.189	8.465
baySeq.createRmd	9.101	0.546	10.232
checkDataObject	0.449	0.046	0.497
checkTableConsistency	1.509	0.131	1.679
check_compData	0.438	0.045	0.484
check_compData_results	0.991	0.080	1.096
compData	0.005	0.000	0.005
convertListTocompData	0.007	0.001	0.008
convertcompDataToList	10.435	5.810	16.448
edgeR.GLM.createRmd	1.733	0.135	1.871
edgeR.exact.createRmd	0.986	0.078	1.107
generateCodeHTMLs	1.377	0.090	1.472
generateSyntheticData	0.416	0.042	0.505
listcreateRmd	0.012	0.000	0.013
logcpm.limma.createRmd	0.739	0.081	0.823
runComparison	3.443	0.272	4.001
runComparisonGUI	0.001	0.000	0.001
runDiffExp	0.992	0.090	1.421
show-compData-method	10.392	5.596	16.680
sqrtcpm.limma.createRmd	0.696	0.073	0.773
summarizeSyntheticDataSet	2.024	0.142	2.334
ttest.createRmd	0.729	0.065	0.795
voom.limma.createRmd	0.969	0.079	1.075
voom.ttest.createRmd	0.768	0.069	0.852
vst.limma.createRmd	1.055	0.090	1.147
vst.ttest.createRmd	1.035	0.082	1.122