BioC 3.2: CHECK report for msmsTests on oaxaca

Package: msmsTests

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings msmsTests_1.7.0.tar.gz

StartedAt: 2015-08-24 02:05:17 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 02:08:31 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 193.9 seconds

RetCode: 0

Status:  OK

CheckDir: msmsTests.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 msmsTests_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/msmsTests.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 ‘msmsTests/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘msmsTests’ version ‘1.7.0’
* 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 ‘msmsTests’ can be installed ... [14s/15s] 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘MSnbase’ ‘msmsEDA’
  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
msms.edgeR: no visible global function definition for ‘exprs’
msms.edgeR: no visible global function definition for ‘pData’
msms.glm.pois: no visible global function definition for ‘exprs’
msms.glm.pois: no visible global function definition for ‘pData’
msms.glm.qlll: no visible global function definition for ‘exprs’
msms.glm.qlll: no visible global function definition for ‘pData’
test.results: no visible global function definition for ‘exprs’
* 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 ... [66s/67s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
test.results    12.469  0.027  12.658
res.volcanoplot 12.365  0.033  12.568
msms.glm.qlll   11.775  0.023  11.885
msms.glm.pois   11.284  0.025  11.422
pval.by.fc       9.874  0.034  10.094
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘xtable’
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/msmsTests.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
msms.edgeR	0.779	0.022	0.840
msms.glm.pois	11.284	0.025	11.422
msms.glm.qlll	11.775	0.023	11.885
msms.spk	0.008	0.001	0.010
pval.by.fc	9.874	0.034	10.094
res.volcanoplot	12.365	0.033	12.568
test.results	12.469	0.027	12.658