BioC 2.14: CHECK report for msmsTests on zin2

Package: msmsTests

Version: 1.2.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings msmsTests_1.2.0.tar.gz

StartedAt: 2014-10-08 01:19:20 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:22:30 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 189.6 seconds

RetCode: 0

Status:  OK

CheckDir: msmsTests.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings msmsTests_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/msmsTests.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.2.0’
* 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 ... [12s/13s] 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
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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [63s/71s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
res.volcanoplot 11.817  0.320  14.494
msms.glm.qlll   11.520  0.328  12.220
test.results    11.168  0.348  15.039
msms.glm.pois   10.733  0.328  11.385
pval.by.fc       9.493  0.292  10.214
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.14-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	1.116	0.016	1.206
msms.glm.pois	10.733	0.328	11.385
msms.glm.qlll	11.520	0.328	12.220
msms.spk	0.008	0.000	0.009
pval.by.fc	9.493	0.292	10.214
res.volcanoplot	11.817	0.320	14.494
test.results	11.168	0.348	15.039