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BioC 3.2: CHECK report for rCGH on moscato1

This page was generated on 2015-08-20 13:24:24 -0700 (Thu, 20 Aug 2015).

Package 825/1069HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rCGH 0.99.7
Frederic Commo
Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rCGH
Last Changed Rev: 106975 / Revision: 107602
Last Changed Date: 2015-08-01 09:35:29 -0700 (Sat, 01 Aug 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 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  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: rCGH
Version: 0.99.7
Command: rm -rf rCGH.buildbin-libdir rCGH.Rcheck && mkdir rCGH.buildbin-libdir rCGH.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rCGH.buildbin-libdir rCGH_0.99.7.tar.gz >rCGH.Rcheck\00install.out 2>&1 && cp rCGH.Rcheck\00install.out rCGH-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=rCGH.buildbin-libdir --install="check:rCGH-install.out" --force-multiarch --no-vignettes --timings rCGH_0.99.7.tar.gz
StartedAt: 2015-08-20 09:19:49 -0700 (Thu, 20 Aug 2015)
EndedAt: 2015-08-20 09:42:35 -0700 (Thu, 20 Aug 2015)
EllapsedTime: 1366.3 seconds
RetCode: 0
Status:  OK  
CheckDir: rCGH.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf rCGH.buildbin-libdir rCGH.Rcheck && mkdir rCGH.buildbin-libdir rCGH.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rCGH.buildbin-libdir rCGH_0.99.7.tar.gz >rCGH.Rcheck\00install.out 2>&1 && cp rCGH.Rcheck\00install.out rCGH-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=rCGH.buildbin-libdir --install="check:rCGH-install.out" --force-multiarch --no-vignettes --timings rCGH_0.99.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/rCGH.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rCGH/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rCGH' version '0.99.7'
* 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 whether package 'rCGH' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [403s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
byGeneTable  42.32   0.27   43.77
multiplot    39.97   0.26   40.23
plotProfile  39.17   0.21   39.37
rCGH-package 39.11   0.09   39.20
recenter     38.39   0.21   38.60
plotLOH      36.50   0.18   36.77
segmentCGH   35.02   0.12   35.14
EMnormalize  33.77   0.16   33.95
view         33.01   0.12   33.15
plotDensity  30.95   0.16   31.11
adjustSignal 11.79   0.03   11.82
** running examples for arch 'x64' ... [397s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
byGeneTable  43.20   0.19   43.38
plotProfile  39.87   0.17   40.14
multiplot    38.88   0.15   39.10
rCGH-package 38.84   0.17   39.03
plotLOH      38.02   0.11   38.13
segmentCGH   34.96   0.20   35.16
recenter     35.00   0.16   35.18
view         34.28   0.13   34.41
plotDensity  32.21   0.13   32.47
EMnormalize  30.13   0.14   30.28
adjustSignal 10.92   0.08   11.00
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [57s]
 [57s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [83s]
 [84s] 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
  'D:/biocbld/bbs-3.2-bioc/meat/rCGH.Rcheck/00check.log'
for details.


rCGH.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'rCGH' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rCGH' as rCGH_0.99.7.zip
* DONE (rCGH)

rCGH.Rcheck/examples_i386/rCGH-Ex.timings:

nameusersystemelapsed
AllAccessors1.830.202.03
EMnormalize33.77 0.1633.95
adjustSignal11.79 0.0311.82
byGeneTable42.32 0.2743.77
geneDB0.030.000.03
hg19000
multiplot39.97 0.2640.23
plotDensity30.95 0.1631.11
plotLOH36.50 0.1836.77
plotProfile39.17 0.2139.37
rCGH-Agilent-class0.020.000.02
rCGH-SNP6-class000
rCGH-class000
rCGH-cytoScan-class000
rCGH-package39.11 0.0939.20
readAffyCytoScan1.010.131.14
readAffySNP61.410.311.71
readAgilent1.730.262.00
recenter38.39 0.2138.60
segmentCGH35.02 0.1235.14
setInfo1.140.191.33
view33.01 0.1233.15

rCGH.Rcheck/examples_x64/rCGH-Ex.timings:

nameusersystemelapsed
AllAccessors0.990.191.18
EMnormalize30.13 0.1430.28
adjustSignal10.92 0.0811.00
byGeneTable43.20 0.1943.38
geneDB0.050.000.05
hg190.010.000.01
multiplot38.88 0.1539.10
plotDensity32.21 0.1332.47
plotLOH38.02 0.1138.13
plotProfile39.87 0.1740.14
rCGH-Agilent-class000
rCGH-SNP6-class000
rCGH-class000
rCGH-cytoScan-class000
rCGH-package38.84 0.1739.03
readAffyCytoScan1.140.171.31
readAffySNP60.950.311.26
readAgilent1.740.251.98
recenter35.00 0.1635.18
segmentCGH34.96 0.2035.16
setInfo0.630.170.80
view34.28 0.1334.41