BioC 2.14: CHECK report for pathifier on zin2

Package: pathifier

Version: 1.2.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings pathifier_1.2.0.tar.gz

StartedAt: 2014-10-08 01:41:04 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:41:51 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 46.7 seconds

RetCode: 0

Status:  OK

CheckDir: pathifier.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings pathifier_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/pathifier.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 ‘pathifier/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathifier’ 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 ‘pathifier’ can be installed ... [1s/1s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [34s/34s] OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
pathifier-package              16.973  0.004  17.012
quantify_pathways_deregulation 16.789  0.008  16.864
* 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

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

name	user	system	elapsed
KEGG	0.020	0.000	0.019
Sheffer	0.024	0.000	0.060
pathifier-package	16.973	0.004	17.012
quantify_pathways_deregulation	16.789	0.008	16.864