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BioC 3.2: CHECK report for MSnID on zin1

This page was generated on 2015-08-24 10:50:09 -0700 (Mon, 24 Aug 2015).

Package 658/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnID 1.3.1
Vlad Petyuk
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnID
Last Changed Rev: 104337 / Revision: 107696
Last Changed Date: 2015-05-28 14:02:34 -0700 (Thu, 28 May 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MSnID
Version: 1.3.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MSnID_1.3.1.tar.gz
StartedAt: 2015-08-24 02:00:12 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 02:02:59 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 166.6 seconds
RetCode: 0
Status:  OK 
CheckDir: MSnID.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MSnID_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/MSnID.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 ‘MSnID/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSnID’ version ‘1.3.1’
* 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 ... [11s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... [9s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [56s/57s]
 [56s/57s] 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

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/MSnID.Rcheck/00check.log’
for details.


MSnID.Rcheck/00install.out:

* 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)

MSnID.Rcheck/MSnID-Ex.timings:

nameusersystemelapsed
MSnID-class0.0000.0000.001
MSnIDFilter-class0.4560.0040.460
accessions0.2470.0080.256
apply_filter0.2150.0000.217
assess_missed_cleavages0.1670.0000.167
assess_termini0.3470.0000.347
correct_peak_selection0.0920.0000.092
data0.0860.0000.086
evaluate_filter0.2020.0000.202
id_quality0.0870.0000.087
mass_measurement_error0.2490.0040.253
optimize_filter1.4160.0201.555
peptides0.0780.0000.077
psms0.0830.0000.082
read_mzIDs0.0000.0000.001
recalibrate0.0940.0000.093