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BioC 3.2: CHECK report for mirIntegrator on zin1

This page was generated on 2015-08-24 10:50:39 -0700 (Mon, 24 Aug 2015).

Package 629/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mirIntegrator 0.99.5
Diana Diaz
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mirIntegrator
Last Changed Rev: 104760 / Revision: 107696
Last Changed Date: 2015-06-09 14:33:49 -0700 (Tue, 09 Jun 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: mirIntegrator
Version: 0.99.5
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings mirIntegrator_0.99.5.tar.gz
StartedAt: 2015-08-24 01:43:28 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 01:45:32 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 124.4 seconds
RetCode: 0
Status:  OK 
CheckDir: mirIntegrator.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings mirIntegrator_0.99.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/mirIntegrator.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 ‘mirIntegrator/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mirIntegrator’ version ‘0.99.5’
* 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 ‘mirIntegrator’ can be installed ... [9s/9s] 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 ... NOTE
plotLines: no visible binding for global variable ‘x’
plotLines: no visible binding for global variable ‘y’
* 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 ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
pathways2pdf 6.118   0.04   6.155
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [8s/8s]
 [8s/8s] 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/mirIntegrator.Rcheck/00check.log’
for details.


mirIntegrator.Rcheck/00install.out:

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

mirIntegrator.Rcheck/mirIntegrator-Ex.timings:

nameusersystemelapsed
GSE43592_mRNA0.1310.0000.131
GSE43592_miRNA0.010.000.01
augmented_pathways0.7260.0040.729
integrate_mir3.1920.0043.194
kegg_pathways0.2030.0000.203
mirTarBase0.0690.0040.070
names_pathways0.0010.0000.003
pathways2pdf6.1180.0406.155
plot_augmented_pathway2.0850.0232.132
plot_change0.9730.0040.978
smallest_pathway0.4550.0040.459