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BioC 3.3: CHECK report for rCGH on moscato2

This page was generated on 2016-10-13 12:54:13 -0700 (Thu, 13 Oct 2016).

Package 941/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rCGH 1.2.2
Frederic Commo
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/rCGH
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
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
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: 1.2.2
Command: rm -rf rCGH.buildbin-libdir rCGH.Rcheck && mkdir rCGH.buildbin-libdir rCGH.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rCGH.buildbin-libdir rCGH_1.2.2.tar.gz >rCGH.Rcheck\00install.out 2>&1 && cp rCGH.Rcheck\00install.out rCGH-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=rCGH.buildbin-libdir --install="check:rCGH-install.out" --force-multiarch --no-vignettes --timings rCGH_1.2.2.tar.gz
StartedAt: 2016-10-13 07:57:14 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 08:17:57 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 1242.8 seconds
RetCode: 0
Status:  OK  
CheckDir: rCGH.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf rCGH.buildbin-libdir rCGH.Rcheck && mkdir rCGH.buildbin-libdir rCGH.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rCGH.buildbin-libdir rCGH_1.2.2.tar.gz >rCGH.Rcheck\00install.out 2>&1 && cp rCGH.Rcheck\00install.out rCGH-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=rCGH.buildbin-libdir --install="check:rCGH-install.out" --force-multiarch --no-vignettes --timings rCGH_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/rCGH.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.2.2'
* 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 ... 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
* 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' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
multiplot    39.35   0.08   39.43
plotProfile  38.90   0.20   39.13
rCGH-package 36.53   0.14   36.68
byGeneTable  36.34   0.18   47.19
recenter     34.25   0.19   34.46
plotLOH      33.99   0.08   34.07
plotDensity  31.40   0.19   31.59
EMnormalize  30.80   0.11   30.90
segmentCGH   29.80   0.12   29.92
view         28.94   0.13   29.08
adjustSignal 13.49   0.17   13.67
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
byGeneTable  37.52   0.25   37.77
plotProfile  34.36   0.26   34.64
rCGH-package 32.72   0.23   33.62
view         32.57   0.12   32.71
recenter     31.61   0.13   31.73
multiplot    31.30   0.21   31.71
segmentCGH   31.25   0.20   31.45
plotLOH      29.63   0.08   29.70
EMnormalize  27.10   0.14   28.38
plotDensity  25.37   0.14   25.52
adjustSignal 10.37   0.15   10.53
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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:


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_1.2.2.zip
* DONE (rCGH)

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

nameusersystemelapsed
AllAccessors1.980.242.22
EMnormalize30.80 0.1130.90
adjustSignal13.49 0.1713.67
byGeneTable36.34 0.1847.19
hg180.010.000.01
hg19000
hg38000
multiplot39.35 0.0839.43
plotDensity31.40 0.1931.59
plotLOH33.99 0.0834.07
plotProfile38.90 0.2039.13
rCGH-Agilent-class000
rCGH-SNP6-class000
rCGH-class000
rCGH-cytoScan-class000
rCGH-generic-class000
rCGH-package36.53 0.1436.68
readAffyCytoScan0.860.110.97
readAffySNP60.970.281.24
readAgilent1.480.231.74
readGeneric0.020.020.03
recenter34.25 0.1934.46
segmentCGH29.80 0.1229.92
setInfo0.980.111.09
view28.94 0.1329.08

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

nameusersystemelapsed
AllAccessors1.420.171.59
EMnormalize27.10 0.1428.38
adjustSignal10.37 0.1510.53
byGeneTable37.52 0.2537.77
hg18000
hg19000
hg380.020.000.02
multiplot31.30 0.2131.71
plotDensity25.37 0.1425.52
plotLOH29.63 0.0829.70
plotProfile34.36 0.2634.64
rCGH-Agilent-class000
rCGH-SNP6-class000
rCGH-class000
rCGH-cytoScan-class000
rCGH-generic-class0.010.000.02
rCGH-package32.72 0.2333.62
readAffyCytoScan0.980.151.12
readAffySNP60.800.341.14
readAgilent1.320.341.67
readGeneric0.030.000.03
recenter31.61 0.1331.73
segmentCGH31.25 0.2031.45
setInfo1.160.141.30
view32.57 0.1232.71