aroma.light 2.5.2
Henrik Bengtsson
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/aroma.light | | Last Changed Rev: 105052 / Revision: 107602 | | Last Changed Date: 2015-06-16 18:03:37 -0700 (Tue, 16 Jun 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf aroma.light.buildbin-libdir aroma.light.Rcheck && mkdir aroma.light.buildbin-libdir aroma.light.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=aroma.light.buildbin-libdir aroma.light_2.5.2.tar.gz >aroma.light.Rcheck\00install.out 2>&1 && cp aroma.light.Rcheck\00install.out aroma.light-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=aroma.light.buildbin-libdir --install="check:aroma.light-install.out" --force-multiarch --no-vignettes --timings aroma.light_2.5.2.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/aroma.light.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 'aroma.light/DESCRIPTION' ... OK
* this is package 'aroma.light' version '2.5.2'
* package encoding: latin1
* 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 ... NOTE
Found the following hidden files and directories:
inst/rsp/.rspPlugins
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'aroma.light' can be installed ... OK
* checking installed package size ... OK
* checking package 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
* 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 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 examples ...
** running examples for arch 'i386' ... [52s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
normalizeCurveFit 22.22 0 22.50
normalizeAffine 20.05 0 20.06
** running examples for arch 'x64' ... [53s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
normalizeAffine 20.53 0.03 21.86
normalizeCurveFit 18.78 0.02 18.86
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'backtransformAffine.matrix.R' [1s]
Running 'backtransformPrincipalCurve.matrix.R' [1s]
Running 'callNaiveGenotypes.R' [2s]
Running 'distanceBetweenLines.R' [1s]
Running 'findPeaksAndValleys.R' [1s]
Running 'fitPrincipalCurve.matrix.R' [1s]
Running 'fitXYCurve.matrix.R' [1s]
Running 'iwpca.matrix.R' [1s]
Running 'likelihood.smooth.spline.R' [1s]
Running 'medianPolish.matrix.R' [1s]
Running 'normalizeAffine.matrix.R' [6s]
Running 'normalizeCurveFit.matrix.R' [19s]
Running 'normalizeDifferencesToAverage.R' [1s]
Running 'normalizeFragmentLength-ex1.R' [1s]
Running 'normalizeFragmentLength-ex2.R' [1s]
Running 'normalizeQuantileRank.list.R' [1s]
Running 'normalizeQuantileRank.matrix.R' [1s]
Running 'normalizeQuantileSpline.matrix.R' [2s]
Running 'normalizeTumorBoost,flavors.R' [1s]
Running 'normalizeTumorBoost.R' [1s]
Running 'robustSmoothSpline.R' [1s]
Running 'sampleCorrelations.matrix.R' [1s]
Running 'sampleTuples.R' [0s]
Running 'wpca.matrix.R' [0s]
Running 'wpca2.matrix.R' [1s]
[47s] OK
** running tests for arch 'x64' ...
Running 'backtransformAffine.matrix.R' [1s]
Running 'backtransformPrincipalCurve.matrix.R' [1s]
Running 'callNaiveGenotypes.R' [2s]
Running 'distanceBetweenLines.R' [1s]
Running 'findPeaksAndValleys.R' [1s]
Running 'fitPrincipalCurve.matrix.R' [1s]
Running 'fitXYCurve.matrix.R' [1s]
Running 'iwpca.matrix.R' [0s]
Running 'likelihood.smooth.spline.R' [2s]
Running 'medianPolish.matrix.R' [1s]
Running 'normalizeAffine.matrix.R' [8s]
Running 'normalizeCurveFit.matrix.R' [20s]
Running 'normalizeDifferencesToAverage.R' [1s]
Running 'normalizeFragmentLength-ex1.R' [2s]
Running 'normalizeFragmentLength-ex2.R' [1s]
Running 'normalizeQuantileRank.list.R' [1s]
Running 'normalizeQuantileRank.matrix.R' [1s]
Running 'normalizeQuantileSpline.matrix.R' [2s]
Running 'normalizeTumorBoost,flavors.R' [4s]
Running 'normalizeTumorBoost.R' [1s]
Running 'robustSmoothSpline.R' [1s]
Running 'sampleCorrelations.matrix.R' [1s]
Running 'sampleTuples.R' [0s]
Running 'wpca.matrix.R' [0s]
Running 'wpca2.matrix.R' [2s]
[55s] OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'D:/biocbld/bbs-3.2-bioc/meat/aroma.light.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'aroma.light' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
install for x64
* installing *source* package 'aroma.light' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'aroma.light' as aroma.light_2.5.2.zip
* DONE (aroma.light)