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BioC 3.1: CHECK report for MSnID on zin2

This page was generated on 2015-10-09 09:26:25 -0700 (Fri, 09 Oct 2015).

Package 634/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSnID 1.2.0
Vlad Petyuk
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/MSnID
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: MSnID
Version: 1.2.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings MSnID_1.2.0.tar.gz
StartedAt: 2015-10-09 03:49:27 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 03:52:16 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 168.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: MSnID.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings MSnID_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-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 ‘1.2.0’
* 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 ‘MSnID’ can be installed ... [11s/11s] WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘data.table::melt’ when loading ‘MSnID’
  Warning: replacing previous import by ‘data.table::dcast’ when loading ‘MSnID’
See ‘/home/biocbuild/bbs-3.1-bioc/meat/MSnID.Rcheck/00install.out’ for details.
* 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 ... WARNING
Codoc mismatches from documentation object 'optimize_filter':
optimize_filter
  Code: function(filterObj, msnidObj, fdr.max, method, level, n.iter,
                 mc.cores = NULL)
  Docs: function(filterObj, msnidObj, fdr.max, method, level, n.iter)
  Argument names in code not in docs:
    mc.cores

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'optimize_filter':
  ‘mc.cores’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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’ [57s/57s]
 [57s/58s] 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: 3 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.1-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
Warning: replacing previous import by ‘data.table::melt’ when loading ‘MSnID’
Warning: replacing previous import by ‘data.table::dcast’ when loading ‘MSnID’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Warning: replacing previous import by ‘data.table::melt’ when loading ‘MSnID’
Warning: replacing previous import by ‘data.table::dcast’ when loading ‘MSnID’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (MSnID)

MSnID.Rcheck/MSnID-Ex.timings:

nameusersystemelapsed
MSnID-class0.0010.0000.001
MSnIDFilter-class0.4610.0040.468
accessions0.2600.0000.261
apply_filter0.3620.0160.378
assess_missed_cleavages0.1840.0000.184
assess_termini0.1960.0000.200
correct_peak_selection0.2800.0000.283
data0.0950.0080.103
evaluate_filter0.4000.0000.399
id_quality0.0980.0000.098
mass_measurement_error0.090.000.09
optimize_filter1.6300.0281.785
peptides0.080.000.08
psms0.0890.0000.088
read_mzIDs0.0000.0000.001
recalibrate0.0980.0000.098