BioC 3.2: CHECK report for rCGH on oaxaca

Package: rCGH

Version: 0.99.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rCGH_0.99.7.tar.gz

StartedAt: 2015-08-24 03:08:07 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:16:19 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 492.9 seconds

RetCode: 0

Status:  OK

CheckDir: rCGH.Rcheck

Warnings: 0

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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_0.99.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/rCGH.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘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 for sufficient/correct file permissions ... OK
* checking whether package ‘rCGH’ can be installed ... [38s/40s] OK
* 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 ... [170s/175s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
byGeneTable  19.381  0.228  19.995
multiplot    16.124  0.119  17.794
rCGH-package 15.488  0.111  16.014
plotProfile  15.238  0.089  15.523
plotLOH      14.454  0.100  14.883
recenter     14.159  0.066  14.449
segmentCGH   13.397  0.052  13.525
view         13.110  0.058  13.189
EMnormalize  12.702  0.066  13.956
plotDensity  12.530  0.060  12.733
adjustSignal  4.943  0.026   5.314
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [37s/37s]
 [37s/37s] 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
  ‘/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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rCGH)

name	user	system	elapsed
AllAccessors	1.316	0.027	1.345
EMnormalize	12.702	0.066	13.956
adjustSignal	4.943	0.026	5.314
byGeneTable	19.381	0.228	19.995
geneDB	0.058	0.001	0.060
hg19	0.005	0.001	0.006
multiplot	16.124	0.119	17.794
plotDensity	12.530	0.060	12.733
plotLOH	14.454	0.100	14.883
plotProfile	15.238	0.089	15.523
rCGH-Agilent-class	0.001	0.001	0.001
rCGH-SNP6-class	0.001	0.000	0.001
rCGH-class	0.001	0.000	0.001
rCGH-cytoScan-class	0.001	0.001	0.002
rCGH-package	15.488	0.111	16.014
readAffyCytoScan	0.952	0.005	0.958
readAffySNP6	1.359	0.007	1.371
readAgilent	1.217	0.012	1.239
recenter	14.159	0.066	14.449
segmentCGH	13.397	0.052	13.525
setInfo	0.907	0.005	0.914
view	13.110	0.058	13.189