BioC 3.0: CHECK report for COHCAP on perceval

Package: COHCAP

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch COHCAP_1.4.0.tar.gz

StartedAt: 2015-04-10 00:12:03 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:13:44 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 100.5 seconds

RetCode: 0

Status:  OK

CheckDir: COHCAP.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 --no-multiarch COHCAP_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/COHCAP.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘COHCAP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COHCAP’ version ‘1.4.0’
* 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 ‘COHCAP’ can be installed ... [1s/5s] OK
* checking installed package size ... OK
* 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 ... NOTE
COHCAP.annotate: no visible binding for global variable
  ‘COHCAP.450k.UCSC’
COHCAP.annotate: no visible binding for global variable
  ‘COHCAP.450k.HMM’
COHCAP.annotate: no visible binding for global variable ‘COHCAP.27k’
COHCAP.avg.by.site: no visible binding for global variable
  ‘integrate.folder’
COHCAP.integrate.avg.by.island: no visible binding for global variable
  ‘na.rm’
cor.test.est: no visible binding for global variable ‘na.rm’
cor.test.pvalue: no visible binding for global variable ‘na.rm’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [36s/63s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
COHCAP.integrate.avg.by.island 5.944  0.596  11.779
COHCAP.avg.by.island           5.579  0.460  10.461
COHCAP.integrate.avg.by.site   5.433  0.507   9.541
COHCAP.avg.by.site             4.743  0.396   7.074
COHCAP.site                    4.640  0.297   6.341
COHCAP.annotate                4.089  0.233  11.201
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/COHCAP.Rcheck/00check.log’
for details.

* installing *source* package ‘COHCAP’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (COHCAP)

name	user	system	elapsed
COHCAP.BSSeq.preprocess	0.036	0.050	1.441
COHCAP.annotate	4.089	0.233	11.201
COHCAP.avg.by.island	5.579	0.460	10.461
COHCAP.avg.by.site	4.743	0.396	7.074
COHCAP.integrate.avg.by.island	5.944	0.596	11.779
COHCAP.integrate.avg.by.site	5.433	0.507	9.541
COHCAP.qc	2.154	0.143	4.166
COHCAP.site	4.640	0.297	6.341