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BioC 3.4: CHECK report for rCGH on zin1

This page was generated on 2016-09-21 03:40:02 -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: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings rCGH_1.3.3.tar.gz
StartedAt: 2016-09-20 11:18:27 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 11:27:29 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 541.8 seconds
RetCode: 0
Status:  OK 
CheckDir: rCGH.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings rCGH_1.3.3.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/rCGH.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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
byGeneTable  33.936  0.132  34.130
plotProfile  32.420  0.148  32.575
multiplot    32.300  0.224  32.527
plotLOH      29.648  0.136  29.784
rCGH-package 29.540  0.160  29.714
EMnormalize  29.184  0.112  29.297
view         28.904  0.124  29.033
plotDensity  28.752  0.120  28.876
recenter     28.528  0.108  28.641
segmentCGH   15.064  0.152  15.215
adjustSignal 14.340  0.104  14.449
* 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
AllAccessors1.0760.0681.143
EMnormalize29.184 0.11229.297
adjustSignal14.340 0.10414.449
byGeneTable33.936 0.13234.130
hg180.0040.0000.003
hg190.0040.0000.003
hg380.0040.0000.003
multiplot32.300 0.22432.527
plotDensity28.752 0.12028.876
plotLOH29.648 0.13629.784
plotProfile32.420 0.14832.575
rCGH-Agilent-class0.0000.0000.002
rCGH-SNP6-class0.0000.0000.001
rCGH-class0.0040.0000.000
rCGH-cytoScan-class0.0000.0000.001
rCGH-generic-class000
rCGH-oncoScan-class0.0000.0000.001
rCGH-package29.540 0.16029.714
readAffyCytoScan0.7800.0840.867
readAffyOncoScan0.0280.0080.039
readAffySNP60.4520.1040.555
readAgilent0.6680.0760.746
readGeneric0.0120.0000.012
recenter28.528 0.10828.641
segmentCGH15.064 0.15215.215
setInfo0.500.040.54
view28.904 0.12429.033