rCGH 1.0.2
Frederic Commo
| 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/rCGH | | Last Changed Rev: 110002 / Revision: 116712 | | Last Changed Date: 2015-10-27 12:41:32 -0700 (Tue, 27 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rCGH_1.0.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/rCGH.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.0.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘rCGH’ can be installed ... [32s/35s] WARNING
Found the following significant warnings:
Warning: replacing previous import ‘aCGH::heatmap’ by ‘stats::heatmap’ when loading ‘rCGH’
See ‘/Users/biocbuild/bbs-3.2-bioc/meat/rCGH.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 5.2Mb
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [157s/160s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
byGeneTable 17.902 0.242 18.791
multiplot 14.908 0.107 15.442
plotProfile 14.231 0.091 14.344
rCGH-package 13.932 0.117 14.083
plotLOH 12.952 0.076 13.040
recenter 12.762 0.069 12.863
segmentCGH 12.556 0.058 12.632
view 12.329 0.061 12.417
EMnormalize 11.428 0.072 11.509
plotDensity 11.367 0.062 11.442
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [34s/34s]
[34s/34s] 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 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/rCGH.Rcheck/00check.log’
for details.
* installing *source* package ‘rCGH’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘aCGH::heatmap’ by ‘stats::heatmap’ when loading ‘rCGH’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘aCGH::heatmap’ by ‘stats::heatmap’ when loading ‘rCGH’
* DONE (rCGH)