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BioC 2.14: CHECK report for PAPi on zin2

This page was generated on 2014-10-08 08:49:57 -0700 (Wed, 08 Oct 2014).

Package 565/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PAPi 1.4.0
Raphael Aggio
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/PAPi
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: PAPi
Version: 1.4.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings PAPi_1.4.0.tar.gz
StartedAt: 2014-10-08 01:40:37 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 01:41:50 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 73.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: PAPi.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings PAPi_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/PAPi.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 ‘PAPi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PAPi’ version ‘1.4.0’
* 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 ‘PAPi’ can be installed ... [7s/7s] 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 ... WARNING
Codoc mismatches from documentation object 'papiHtest':
papiHtest
  Code: function(inputData, signif.level = 0.05, log.transform = TRUE,
                 save = TRUE, folder, StatTest, output, adjust.pValue =
                 TRUE, method = "bonferroni")
  Docs: function(inputData, signif.level = 0.05, log.transform = FALSE,
                 save = TRUE, folder, StatTest, output, adjust.pValue =
                 TRUE, method = "bonferroni")
  Mismatches in argument default values:
    Name: 'log.transform' Code: TRUE Docs: FALSE

Codoc mismatches from documentation object 'papiLine':
papiLine
  Code: function(inputData, relative = TRUE, save = FALSE, folder,
                 output = "papi_graph", setRef.cond = FALSE, Ref.cond,
                 color = "auto", cex.xlab, cex.ylab = 1, position.ylab,
                 margins = c(25, 8, 2, 2), yscale, dot.size = 1.5,
                 legend.position, cex.legend = 1, graphWidth = 3000,
                 graphHeight = 2000, graph.bg = "transparent",
                 graph.res = 300)
  Docs: function(inputData, relative = TRUE, save = TRUE, folder,
                 output = "papi_graph", setRef.cond = FALSE, Ref.cond,
                 color = "auto", cex.xlab, cex.ylab = 1, position.ylab,
                 margins = c(25, 8, 2, 2), yscale, dot.size = 1.5,
                 legend.position, cex.legend = 1, graphWidth = 3000,
                 graphHeight = 2000, graph.bg = "transparent",
                 graph.res = 300)
  Mismatches in argument default values:
    Name: 'save' Code: FALSE Docs: TRUE

* 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 ... [3s/3s] 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

WARNING: There was 1 warning.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/PAPi.Rcheck/00check.log’
for details.

PAPi.Rcheck/00install.out:

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

PAPi.Rcheck/PAPi-Ex.timings:

nameusersystemelapsed
PAPi-package0.0040.0000.003
addKeggCodes0.0120.0000.009
buildDatabase0.0000.0000.001
keggLibrary0.0240.0000.021
metabolomicsData0.0040.0000.004
papi0.0000.0000.001
papiData0.0040.0000.004
papiHtest0.020.000.02
papiLine0.1040.0000.106
papiResults0.0040.0000.005