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BioC 3.1: CHECK report for copynumber on petty

This page was generated on 2015-10-09 09:35:38 -0700 (Fri, 09 Oct 2015).

Package 212/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
copynumber 1.8.0
Gro Nilsen
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/copynumber
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: copynumber
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings copynumber_1.8.0.tar.gz
StartedAt: 2015-10-08 22:19:03 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 22:23:30 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 266.7 seconds
RetCode: 0
Status:  OK 
CheckDir: copynumber.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings copynumber_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/copynumber.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘copynumber/DESCRIPTION’ ... OK
* this is package ‘copynumber’ version ‘1.8.0’
* 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 ‘copynumber’ can be installed ... [12s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
Package in Depends field not imported from: ‘BiocGenerics’
  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 ... 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 R/sysdata.rda ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [107s/110s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plotCircle       16.515  0.466  17.108
plotFreq          8.738  0.158   8.905
plotHeatmap       7.986  0.188   8.187
subsetSegments    7.353  0.179   7.552
getGRangesFormat  7.284  0.178   7.468
callAberrations   6.984  0.193   7.182
plotAberration    6.845  0.147   6.995
plotGenome        5.543  0.104   5.700
plotAllele        5.233  0.123   8.663
* 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
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/copynumber.Rcheck/00check.log’
for details.


copynumber.Rcheck/00install.out:

* installing *source* package ‘copynumber’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (copynumber)

copynumber.Rcheck/copynumber-Ex.timings:

nameusersystemelapsed
SNPdata0.0340.0050.039
aspcf4.0510.1154.168
callAberrations6.9840.1937.182
getGRangesFormat7.2840.1787.468
imputeMissing4.1580.0754.235
interpolate.pcf1.2590.0241.283
lymphoma0.0010.0000.001
micma0.0020.0010.001
multipcf0.9320.0160.949
pcf1.3610.0261.388
pcfPlain0.4010.0060.408
plotAberration6.8450.1476.995
plotAllele5.2330.1238.663
plotChrom3.9570.0584.024
plotCircle16.515 0.46617.108
plotFreq8.7380.1588.905
plotGamma3.1570.0373.196
plotGenome5.5430.1045.700
plotHeatmap7.9860.1888.187
plotSample4.6110.0974.717
selectSegments1.9000.0071.910
subsetData0.0100.0000.011
subsetSegments7.3530.1797.552
winsorize0.3350.0070.342