BioC 3.2: CHECK report for RiboProfiling on oaxaca

Package: RiboProfiling

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RiboProfiling_1.0.0.tar.gz

StartedAt: 2015-10-27 07:18:30 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:30:04 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 693.6 seconds

RetCode: 0

Status:  OK

CheckDir: RiboProfiling.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 RiboProfiling_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/RiboProfiling.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 ‘RiboProfiling/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RiboProfiling’ 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 ‘RiboProfiling’ can be installed ... [27s/27s] OK
* checking installed package size ... NOTE
  installed size is 10.4Mb
  sub-directories of 1Mb or more:
    data      2.9Mb
    extdata   6.9Mb
* 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 ... [322s/326s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
countShiftReads   65.946  3.633  69.613
countsPlot        61.593  3.903  65.527
riboSeqFromBAM    57.670  2.331  60.055
codonInfo         37.729  1.329  39.078
orfRelativePos    27.063  2.316  29.395
aroundPromoter    12.269  0.574  12.854
plotSummarizedCov 11.585  0.753  12.345
readStartCov       9.315  0.709  10.030
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [94s/94s]
 [94s/94s] 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/RiboProfiling.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
aroundPromoter	12.269	0.574	12.854
codonInfo	37.729	1.329	39.078
codonPCA	1.389	0.093	4.524
countShiftReads	65.946	3.633	69.613
countsPlot	61.593	3.903	65.527
histMatchLength	3.815	0.189	4.010
orfRelativePos	27.063	2.316	29.395
plotSummarizedCov	11.585	0.753	12.345
printPCA	1.725	0.034	1.767
readStartCov	9.315	0.709	10.030
readsToReadStart	3.401	0.238	3.641
riboSeqFromBAM	57.670	2.331	60.055