BioC 3.3: CHECK report for compcodeR on linux2.bioconductor.org

Package: compcodeR

Version: 1.7.1

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings compcodeR_1.7.1.tar.gz

StartedAt: 2015-10-27 02:52:30 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:56:46 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 256.6 seconds

RetCode: 0

Status:  OK

CheckDir: compcodeR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings compcodeR_1.7.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/compcodeR.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.7.1’
* 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 ... [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 ... [216s/215s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   82.299  0.398  82.756
NBPSeq.createRmd         56.584  0.186  56.826
EBSeq.createRmd          12.243  0.103  12.334
DESeq.GLM.createRmd       9.828  0.343  10.013
show-compData-method      7.151  0.141   7.199
convertcompDataToList     6.583  0.193   6.689
baySeq.createRmd          6.226  0.228   6.332
NOISeq.prenorm.createRmd  5.606  0.197   5.668
DESeq2.createRmd          5.462  0.262   5.587
* 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-3.3-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	9.828	0.343	10.013
DESeq.nbinom.createRmd	82.299	0.398	82.756
DESeq2.createRmd	5.462	0.262	5.587
DSS.createRmd	1.503	0.094	1.574
EBSeq.createRmd	12.243	0.103	12.334
NBPSeq.createRmd	56.584	0.186	56.826
NOISeq.prenorm.createRmd	5.606	0.197	5.668
SAMseq.createRmd	1.404	0.079	1.453
TCC.createRmd	2.279	0.069	2.320
baySeq.createRmd	6.226	0.228	6.332
checkDataObject	0.264	0.021	0.277
checkTableConsistency	1.142	0.118	1.237
check_compData	0.356	0.038	0.384
check_compData_results	0.611	0.033	0.627
compData	0.001	0.000	0.003
convertListTocompData	0.004	0.000	0.004
convertcompDataToList	6.583	0.193	6.689
edgeR.GLM.createRmd	1.649	0.062	1.680
edgeR.exact.createRmd	0.706	0.051	0.742
generateCodeHTMLs	0.616	0.044	0.643
generateSyntheticData	0.272	0.017	0.280
listcreateRmd	0.009	0.000	0.009
logcpm.limma.createRmd	0.441	0.046	0.473
runComparison	2.673	0.299	2.933
runComparisonGUI	0	0	0
runDiffExp	0.610	0.082	0.677
show-compData-method	7.151	0.141	7.199
sqrtcpm.limma.createRmd	0.459	0.040	0.486
summarizeSyntheticDataSet	1.145	0.044	1.170
ttest.createRmd	0.456	0.056	0.499
voom.limma.createRmd	0.711	0.077	0.783
voom.ttest.createRmd	0.551	0.099	0.637
vst.limma.createRmd	0.719	0.068	0.775
vst.ttest.createRmd	0.587	0.077	0.650