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BioC 3.6: CHECK report for rCGH on malbec1

This page was generated on 2017-08-16 13:23:28 -0400 (Wed, 16 Aug 2017).

Package 1091/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rCGH 1.7.0
Frederic Commo
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rCGH
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rCGH
Version: 1.7.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings rCGH_1.7.0.tar.gz
StartedAt: 2017-08-16 01:46:12 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:52:03 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 351.5 seconds
RetCode: 0
Status:  OK 
CheckDir: rCGH.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings rCGH_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/rCGH.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.7.0’
* 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 ‘rCGH’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      2.8Mb
    extdata   1.2Mb
* 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 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  12.280  0.196  12.587
multiplot    12.040  0.292  12.347
plotProfile   9.928  0.216  10.160
rCGH-package  8.060  0.236   8.313
plotLOH       6.972  0.152   7.130
EMnormalize   6.792  0.080   6.883
plotDensity   6.672  0.168   6.847
view          6.544  0.152   6.719
recenter      6.508  0.148   6.670
adjustSignal  6.440  0.192   6.642
segmentCGH    6.040  0.124   6.187
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/rCGH.Rcheck/00check.log’
for details.


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
AllAccessors0.7840.0680.852
EMnormalize6.7920.0806.883
adjustSignal6.4400.1926.642
byGeneTable12.280 0.19612.587
hg180.0040.0000.003
hg190.0040.0000.003
hg380.0040.0000.003
multiplot12.040 0.29212.347
plotDensity6.6720.1686.847
plotLOH6.9720.1527.130
plotProfile 9.928 0.21610.160
rCGH-Agilent-class0.0040.0000.001
rCGH-SNP6-class0.0000.0000.001
rCGH-class0.0000.0000.001
rCGH-cytoScan-class000
rCGH-generic-class0.0000.0000.001
rCGH-oncoScan-class000
rCGH-package8.0600.2368.313
readAffyCytoScan0.4880.0360.523
readAffyOncoScan0.0400.0000.038
readAffySNP60.5080.0640.573
readAgilent0.8960.0720.967
readGeneric0.0080.0040.011
recenter6.5080.1486.670
segmentCGH6.0400.1246.187
setInfo0.5000.0480.551
view6.5440.1526.719