BioC 3.2: CHECK report for sSeq on perceval

Package: sSeq

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sSeq_1.8.0.tar.gz

StartedAt: 2015-11-10 09:51:57 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 09:57:56 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 359.7 seconds

RetCode: 0

Status:  OK

CheckDir: sSeq.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 sSeq_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/sSeq.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sSeq’ version ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘sSeq’ can be installed ... [2s/2s] 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 ‘caTools’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘caTools’ ‘RColorBrewer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ecdfAUC: no visible global function definition for ‘trapz’
plotDispersion: no visible global function definition for ‘brewer.pal’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [337s/337s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
nbTestSH       105.344  5.635 110.982
getTgroup      103.521  4.473 107.999
sSeq-package   100.863  4.847 105.715
plotDispersion   4.854  0.408   5.266
* 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/sSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘sSeq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (sSeq)

name	user	system	elapsed
Hammer2months	0.067	0.007	0.074
Sultan	0.073	0.005	0.079
Tuch	0.070	0.003	0.074
countsTable	0.017	0.003	0.019
drawMA_vol	0.412	0.001	0.413
ecdfAUC	0.018	0.001	0.019
equalSpace	0.431	0.008	0.440
exactNBtest1	0.001	0.000	0.001
getAdjustDisp	0.365	0.004	0.369
getNormFactor	0.019	0.003	0.024
getQ	1.928	0.119	2.048
getT	2.238	0.190	2.429
getTgroup	103.521	4.473	107.999
nbTestSH	105.344	5.635	110.982
plotDispersion	4.854	0.408	5.266
rnbinomMV	0.003	0.000	0.003
rowVars	0.001	0.001	0.001
sSeq-package	100.863	4.847	105.715
sim	0.588	0.017	0.605