aroma.light 3.0.0
Henrik Bengtsson
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/aroma.light | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings aroma.light_3.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/aroma.light.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘aroma.light/DESCRIPTION’ ... OK
* this is package ‘aroma.light’ version ‘3.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘aroma.light’ can be installed ... [1s/1s] 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
* 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 ... [28s/28s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
normalizeCurveFit 11.797 0.023 11.853
normalizeAffine 11.479 0.028 11.514
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘backtransformAffine.matrix.R’ [0s/0s]
Running ‘backtransformPrincipalCurve.matrix.R’ [1s/1s]
Running ‘callNaiveGenotypes.R’ [1s/1s]
Running ‘distanceBetweenLines.R’ [0s/0s]
Running ‘findPeaksAndValleys.R’ [0s/0s]
Running ‘fitPrincipalCurve.matrix.R’ [1s/1s]
Running ‘fitXYCurve.matrix.R’ [0s/0s]
Running ‘iwpca.matrix.R’ [0s/0s]
Running ‘likelihood.smooth.spline.R’ [0s/0s]
Running ‘medianPolish.matrix.R’ [0s/0s]
Running ‘normalizeAffine.matrix.R’ [4s/4s]
Running ‘normalizeAverage.list.R’ [0s/0s]
Running ‘normalizeAverage.matrix.R’ [0s/0s]
Running ‘normalizeCurveFit.matrix.R’ [12s/12s]
Running ‘normalizeDifferencesToAverage.R’ [0s/0s]
Running ‘normalizeFragmentLength-ex1.R’ [1s/1s]
Running ‘normalizeFragmentLength-ex2.R’ [1s/1s]
Running ‘normalizeQuantileRank.list.R’ [0s/0s]
Running ‘normalizeQuantileRank.matrix.R’ [0s/0s]
Running ‘normalizeQuantileSpline.matrix.R’ [1s/1s]
Running ‘normalizeTumorBoost,flavors.R’ [1s/1s]
Running ‘normalizeTumorBoost.R’ [1s/1s]
Running ‘robustSmoothSpline.R’ [0s/0s]
Running ‘rowAverages.matrix.R’ [0s/0s]
Running ‘sampleCorrelations.matrix.R’ [1s/1s]
Running ‘sampleTuples.R’ [0s/0s]
Running ‘wpca.matrix.R’ [0s/0s]
Running ‘wpca2.matrix.R’ [0s/0s]
[30s/30s] OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.2-bioc/meat/aroma.light.Rcheck/00check.log’
for details.