BioC 3.1: CHECK report for sSeq on zin2

Package: sSeq

Version: 1.6.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings sSeq_1.6.0.tar.gz

StartedAt: 2015-10-09 05:49:16 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:55:25 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 368.7 seconds

RetCode: 0

Status:  OK

CheckDir: sSeq.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 sSeq_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/sSeq.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 ‘sSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sSeq’ version ‘1.6.0’
* 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 ... [1s/1s] 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:
  ‘RColorBrewer’ ‘caTools’
  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 ... [355s/355s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
nbTestSH     117.349  0.296 117.748
getTgroup    115.477  0.175 115.752
sSeq-package 111.959  0.092 112.044
* 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/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	0.055	0.000	0.055
Sultan	0.059	0.004	0.063
Tuch	0.053	0.004	0.057
countsTable	0.015	0.000	0.015
drawMA_vol	0.332	0.000	0.332
ecdfAUC	0.016	0.000	0.016
equalSpace	0.335	0.004	0.338
exactNBtest1	0.001	0.000	0.001
getAdjustDisp	0.293	0.000	0.293
getNormFactor	0.017	0.000	0.017
getQ	1.734	0.016	1.749
getT	1.975	0.000	1.973
getTgroup	115.477	0.175	115.752
nbTestSH	117.349	0.296	117.748
plotDispersion	4.006	0.000	4.003
rnbinomMV	0.002	0.000	0.003
rowVars	0.001	0.000	0.000
sSeq-package	111.959	0.092	112.044
sim	0.394	0.000	0.394