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BioC 3.4: CHECK report for rCGH on morelia

This page was generated on 2016-09-21 03:54:39 -0700 (Wed, 21 Sep 2016).

Package 984/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rCGH 1.3.3
Frederic Commo
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rCGH
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 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
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: rCGH
Version: 1.3.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rCGH_1.3.3.tar.gz
StartedAt: 2016-09-20 11:57:21 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 12:03:52 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 391.3 seconds
RetCode: 0
Status:  OK 
CheckDir: rCGH.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 rCGH_1.3.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/rCGH.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rCGH/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rCGH’ version ‘1.3.3’
* 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 ‘rCGH’ can be installed ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
multiplot    16.200  0.192  16.407
byGeneTable  14.859  0.251  17.966
plotProfile  14.271  0.136  14.443
plotDensity  11.126  0.061  11.203
plotLOH      10.964  0.061  11.043
rCGH-package 10.500  0.056  10.569
recenter      9.850  0.037   9.933
EMnormalize   9.090  0.051   9.146
view          9.058  0.027   9.093
segmentCGH    7.064  0.035   7.105
adjustSignal  6.407  0.029   6.441
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: OK

rCGH.Rcheck/00install.out:

* installing *source* package ‘rCGH’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rCGH)

rCGH.Rcheck/rCGH-Ex.timings:

nameusersystemelapsed
AllAccessors1.3090.0161.325
EMnormalize9.0900.0519.146
adjustSignal6.4070.0296.441
byGeneTable14.859 0.25117.966
hg180.0050.0010.005
hg190.0040.0010.005
hg380.0030.0000.004
multiplot16.200 0.19216.407
plotDensity11.126 0.06111.203
plotLOH10.964 0.06111.043
plotProfile14.271 0.13614.443
rCGH-Agilent-class0.0010.0000.001
rCGH-SNP6-class0.0000.0000.001
rCGH-class0.0010.0000.000
rCGH-cytoScan-class0.0000.0000.001
rCGH-generic-class0.0010.0000.001
rCGH-oncoScan-class0.0010.0000.001
rCGH-package10.500 0.05610.569
readAffyCytoScan1.1810.0061.188
readAffyOncoScan0.0300.0010.030
readAffySNP60.7520.0070.759
readAgilent0.9600.0070.968
readGeneric0.0100.0010.010
recenter9.8500.0379.933
segmentCGH7.0640.0357.105
setInfo0.5540.0020.557
view9.0580.0279.093