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BioC 3.4: CHECK report for SWATH2stats on morelia

This page was generated on 2016-09-21 03:54:56 -0700 (Wed, 21 Sep 2016).

Package 1182/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SWATH2stats 1.3.10
Peter Blattmann
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SWATH2stats
Last Changed Rev: 119907 / Revision: 121152
Last Changed Date: 2016-08-05 06:48:27 -0700 (Fri, 05 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SWATH2stats
Version: 1.3.10
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SWATH2stats_1.3.10.tar.gz
StartedAt: 2016-09-20 13:42:50 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 13:43:42 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 52.6 seconds
RetCode: 0
Status:  OK 
CheckDir: SWATH2stats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SWATH2stats_1.3.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/SWATH2stats.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SWATH2stats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SWATH2stats’ version ‘1.3.10’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘imsbInfer’
* 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 ‘SWATH2stats’ can be installed ... 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 ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 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
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/SWATH2stats.Rcheck/00check.log’
for details.


SWATH2stats.Rcheck/00install.out:

* installing *source* package ‘SWATH2stats’ ...
** 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 (SWATH2stats)

SWATH2stats.Rcheck/SWATH2stats-Ex.timings:

nameusersystemelapsed
assess_decoy_rate0.2350.0040.239
assess_fdr_byrun0.3780.0070.384
assess_fdr_overall0.4580.0070.466
convert4MSstats0.7300.0190.749
convert4aLFQ0.7120.0230.736
convert4mapDIA0.7610.0170.779
convert4pythonscript0.2490.0050.254
count_analytes0.2750.0040.279
disaggregate0.7310.0180.749
filter_all_peptides0.3120.0020.314
filter_mscore_all0.3220.0030.325
filter_mscore_fdr0.6130.0340.647
filter_on_max_peptides0.3990.0030.401
filter_on_min_peptides0.3980.0080.407
filter_proteotypic_peptides0.3500.0040.354
import_data0.5270.0250.551
mscore4assayfdr0.6660.0120.679
mscore4pepfdr0.4900.0030.494
mscore4protfdr0.5900.0170.609
plot.fdr_cube0.4520.0050.460
plot.fdr_table0.2550.0030.259
plot_correlation_between_samples0.4260.0040.431
plot_variation0.8410.0220.864
plot_variation_vs_total0.5660.0120.578
reduce_OpenSWATH_output0.2270.0020.229
sample_annotation0.3730.0020.376
transform_MSstats_OpenSWATH0.0070.0010.007
write_matrix_peptides0.4790.0140.495
write_matrix_proteins0.2840.0020.286