BioC 2.14: CHECK report for sRAP on petty

Package: sRAP

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch sRAP_1.4.2.tar.gz

StartedAt: 2014-10-08 00:18:29 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:25:32 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 423.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: sRAP.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch sRAP_1.4.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/sRAP.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sRAP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sRAP’ version ‘1.4.2’
* 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 ‘sRAP’ can be installed ... [3s/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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
RNA.bdfunc.fc: no visible binding for global variable
  ‘bdfunc.enrichment.human’
RNA.bdfunc.fc: no visible binding for global variable
  ‘bdfunc.enrichment.mouse’
RNA.bdfunc.signal: no visible binding for global variable
  ‘bdfunc.enrichment.human’
RNA.bdfunc.signal: no visible binding for global variable
  ‘bdfunc.enrichment.mouse’
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                              old_size new_size compress
  bdfunc.enrichment.human.rda    1.3Mb    951Kb    bzip2
  bdfunc.enrichment.mouse.rda     31Kb     26Kb       xz
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
  ‘sRAP.bbl’
Please remove them from your package.
* checking examples ... [358s/371s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
RNA.bdfunc.signal 252.946 15.786 278.759
RNA.bdfunc.fc      35.817  2.871  39.884
RNA.deg            31.930  2.749  36.226
RNA.qc              6.289  1.097   7.644
RNA.norm            6.133  1.115   7.306
* 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/sRAP.Rcheck/00check.log’
for details.

* installing *source* package ‘sRAP’ ...
** 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 (sRAP)

name	user	system	elapsed
RNA.bdfunc.fc	35.817	2.871	39.884
RNA.bdfunc.signal	252.946	15.786	278.759
RNA.deg	31.930	2.749	36.226
RNA.norm	6.133	1.115	7.306
RNA.prepare.input	0.034	0.016	0.053
RNA.qc	6.289	1.097	7.644