BioC 2.13: CHECK report for PAPi on moscato1

Package: PAPi

Version: 1.2.0

Command: rm -rf PAPi.buildbin-libdir && mkdir PAPi.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PAPi.buildbin-libdir PAPi_1.2.0.tar.gz >PAPi-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=PAPi.buildbin-libdir --install="check:PAPi-install.out" --force-multiarch --no-vignettes --timings PAPi_1.2.0.tar.gz && mv PAPi.buildbin-libdir/* PAPi.Rcheck/ && rmdir PAPi.buildbin-libdir

StartedAt: 2014-04-05 05:41:28 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 05:43:54 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 146.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: PAPi.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/PAPi.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PAPi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PAPi' 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 whether package 'PAPi' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 '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 ...
** running examples for arch 'i386' ... [6s] OK
** running examples for arch 'x64' ... [5s] 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
  'D:/biocbld/bbs-2.13-bioc/meat/PAPi.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'PAPi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PAPi' as PAPi_1.2.0.zip
* DONE (PAPi)

name	user	system	elapsed
PAPi-package	0.01	0.00	0.01
addKeggCodes	0.03	0.00	0.03
buildDatabase	0	0	0
keggLibrary	0.03	0.02	0.05
metabolomicsData	0.10	0.01	0.13
papi	0.02	0.00	0.01
papiData	0.02	0.00	0.02
papiHtest	0.03	0.00	0.03
papiLine	0	0	0
papiResults	0.02	0.00	0.02

name	user	system	elapsed
PAPi-package	0.13	0.00	0.12
addKeggCodes	0.02	0.00	0.01
buildDatabase	0	0	0
keggLibrary	0.01	0.01	0.04
metabolomicsData	0.02	0.00	0.02
papi	0.01	0.00	0.01
papiData	0.02	0.00	0.02
papiHtest	0.17	0.00	0.17
papiLine	0	0	0
papiResults	0	0	0