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BioC 3.2: CHECK report for coRNAi on oaxaca

This page was generated on 2016-04-23 10:24:45 -0700 (Sat, 23 Apr 2016).

Package 228/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coRNAi 1.20.0
Elin Axelsson
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/coRNAi
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: coRNAi
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings coRNAi_1.20.0.tar.gz
StartedAt: 2016-04-22 23:12:23 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:15:08 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 165.4 seconds
RetCode: 0
Status:  OK 
CheckDir: coRNAi.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings coRNAi_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/coRNAi.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘coRNAi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coRNAi’ version ‘1.20.0’
* 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 ‘coRNAi’ can be installed ... [16s/16s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘cellHTS2’ ‘limma’ ‘locfit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘moMatrix’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BoxPlotShorth: no visible binding for global variable ‘shorth’
MainFitPlot: no visible global function definition for ‘locfit’
MainFitPlot: no visible global function definition for ‘lfknots’
cellHTS2df: no visible global function definition for ‘fData’
cellHTS2df: no visible global function definition for ‘Data’
df2lmFit: no visible global function definition for ‘lmFit’
estpart: no visible binding for global variable ‘shorth’
interactiontable: no visible global function definition for ‘topTable’
interactiontable: no visible global function definition for ‘eBayes’
* 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 ... [20s/20s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
cortestmatrices 6.136  0.117   6.256
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/coRNAi.Rcheck/00check.log’
for details.


coRNAi.Rcheck/00install.out:

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

coRNAi.Rcheck/coRNAi-Ex.timings:

nameusersystemelapsed
BoxPlotShorth0.1270.0130.140
InteractGraph000
InteractLevelPlot0.2330.0110.245
MainFitPlot0.0200.0010.021
PlotHeatmap0.1810.0120.194
Pplot0.0050.0010.005
cellHTS2df0.0680.0080.076
cortestmatrices6.1360.1176.256
data2graph0.0010.0000.000
df2array0.0550.0060.061
df2fitmatrix0.1400.0090.149
df2lmFit0.1420.0120.154
estmodel0.1050.0070.111
faultyscreen0.0600.0050.066
interactiontable0.0190.0010.019
key0.0030.0010.003
repplots3.9600.2084.221
rlmmain0.1380.0140.155
screen1_raw0.0140.0050.019
screen2_raw0.1320.0070.140
signalplots0.1210.0080.145
tt2matrix0.0030.0000.003
updateDf0.1220.0080.130
weightDf0.0820.0050.088