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BioC 3.3: CHECK report for mirIntegrator on linux2.bioconductor.org

This page was generated on 2015-10-27 12:12:58 -0400 (Tue, 27 Oct 2015).

Package 651/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mirIntegrator 1.1.0
Diana Diaz
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mirIntegrator
Last Changed Rev: 109592 / Revision: 109948
Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015)
linux2.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows2.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: mirIntegrator
Version: 1.1.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings mirIntegrator_1.1.0.tar.gz
StartedAt: 2015-10-27 05:51:46 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 05:53:51 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 124.7 seconds
RetCode: 0
Status:  OK 
CheckDir: mirIntegrator.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings mirIntegrator_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/mirIntegrator.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.1.0’
* 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 ‘mirIntegrator’ can be installed ... [8s/8s] 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’
Undefined global functions or variables:
  x 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [20s/20s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
pathways2pdf 6.977  0.059   7.058
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [7s/7s]
 [7s/7s] 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-3.3-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_mRNA0.1880.0030.192
GSE43592_miRNA0.0120.0000.012
augmented_pathways1.0800.0121.092
integrate_mir3.4930.0083.502
kegg_pathways0.2370.0030.241
mirTarBase0.0610.0000.062
names_pathways0.0020.0000.002
pathways2pdf6.9770.0597.058
plot_augmented_pathway1.8600.0201.879
plot_change0.8280.0120.841
smallest_pathway0.4560.0000.457