BioC 3.0: CHECK report for MSnID on perceval

Package: MSnID

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSnID_1.0.1.tar.gz

StartedAt: 2015-04-10 04:11:32 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 04:19:29 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 476.6 seconds

RetCode: 0

Status:  OK

CheckDir: MSnID.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 --no-multiarch MSnID_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/MSnID.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSnID/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSnID’ version ‘1.0.1’
* 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 ‘MSnID’ can be installed ... [26s/29s] 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/26s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [193s/196s]
 [194s/197s] OK
* 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

* installing *source* package ‘MSnID’ ...
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘update’ from package ‘stats’ in package ‘MSnID’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSnID)

name	user	system	elapsed
MSnID-class	0.001	0.001	0.001
MSnIDFilter-class	1.246	0.034	1.788
accessions	0.500	0.019	0.645
apply_filter	1.164	0.048	2.025
assess_missed_cleavages	0.628	0.034	0.662
assess_termini	0.639	0.035	0.674
correct_peak_selection	0.138	0.033	0.199
data	0.104	0.006	0.111
evaluate_filter	0.337	0.040	0.378
id_quality	0.515	0.033	0.550
mass_measurement_error	0.100	0.010	0.126
optimize_filter	2.995	1.072	3.199
peptides	0.106	0.014	0.120
psms	0.502	0.023	0.525
read_mzIDs	0.001	0.000	0.000
recalibrate	0.163	0.044	0.233