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BioC 3.2: CHECK report for MergeMaid on zin1

This page was generated on 2015-08-24 10:46:57 -0700 (Mon, 24 Aug 2015).

Package 593/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MergeMaid 2.41.0
Xiaogang Zhong
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MergeMaid
Last Changed Rev: 102594 / Revision: 107696
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MergeMaid
Version: 2.41.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MergeMaid_2.41.0.tar.gz
StartedAt: 2015-08-24 01:26:12 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 01:27:23 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 71.3 seconds
RetCode: 0
Status:  OK 
CheckDir: MergeMaid.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MergeMaid_2.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/MergeMaid.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 ‘MergeMaid/DESCRIPTION’ ... OK
* this is package ‘MergeMaid’ version ‘2.41.0’
* 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 ‘MergeMaid’ can be installed ... [2s/2s] 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘MASS’ ‘methods’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.fdr.mergeCor: no visible global function definition for ‘.getnull’
.mergemodel: no visible global function definition for ‘coxph’
maxintcor: no visible global function definition for ‘ginv’
* 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 ... [47s/47s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
intcorDens               22.701  0.092  22.795
class.mergeExpressionSet  9.508  0.004   9.513
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/MergeMaid.Rcheck/00check.log’
for details.


MergeMaid.Rcheck/00install.out:

* installing *source* package ‘MergeMaid’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘MergeMaid’
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘MergeMaid’
Creating a generic function for ‘summary’ from package ‘base’ in package ‘MergeMaid’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MergeMaid)

MergeMaid.Rcheck/MergeMaid-Ex.timings:

nameusersystemelapsed
class.mergeCoeff1.0750.0091.083
class.mergeCor3.3770.0073.443
class.mergeExpressionSet9.5080.0049.513
intCor4.4960.0044.497
intcorDens22.701 0.09222.795
intersection0.160.000.16
mergeExprs3.4200.0003.418
modelOutcome1.6960.0001.695