BioC 3.2: CHECK report for rCGH on linux1.bioconductor.org

Package: rCGH

Version: 1.0.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings rCGH_1.0.0.tar.gz

StartedAt: 2015-10-20 07:43:23 -0400 (Tue, 20 Oct 2015)

EndedAt: 2015-10-20 07:51:06 -0400 (Tue, 20 Oct 2015)

EllapsedTime: 462.9 seconds

RetCode: 0

Status:  OK

CheckDir: rCGH.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings rCGH_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/rCGH.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.0.0’
* 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 ... [24s/24s] OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [231s/231s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
byGeneTable  24.909  0.200  25.126
multiplot    23.723  0.131  23.888
plotDensity  21.747  0.132  21.903
rCGH-package 21.034  0.109  21.154
view         20.644  0.184  20.846
plotLOH      20.473  0.168  20.671
plotProfile  20.267  0.144  20.443
EMnormalize  20.217  0.117  20.369
recenter     19.042  0.119  19.184
segmentCGH   18.819  0.128  18.962
adjustSignal  6.741  0.069   6.810
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [39s/40s]
 [40s/40s] 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
  ‘/home/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	0.569	0.080	0.650
EMnormalize	20.217	0.117	20.369
adjustSignal	6.741	0.069	6.810
byGeneTable	24.909	0.200	25.126
geneDB	0.026	0.000	0.026
hg19	0.002	0.000	0.003
multiplot	23.723	0.131	23.888
plotDensity	21.747	0.132	21.903
plotLOH	20.473	0.168	20.671
plotProfile	20.267	0.144	20.443
rCGH-Agilent-class	0.001	0.000	0.001
rCGH-SNP6-class	0.000	0.000	0.001
rCGH-class	0.001	0.000	0.000
rCGH-cytoScan-class	0.001	0.000	0.001
rCGH-package	21.034	0.109	21.154
readAffyCytoScan	0.376	0.040	0.417
readAffySNP6	0.366	0.056	0.423
readAgilent	0.599	0.064	0.663
recenter	19.042	0.119	19.184
segmentCGH	18.819	0.128	18.962
setInfo	0.670	0.036	0.706
view	20.644	0.184	20.846