BioC 3.2: CHECK report for RiboProfiling on perceval

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: 2015-10-20 11:18:18 -0400 (Tue, 20 Oct 2015)

EndedAt: 2015-10-20 11:33:48 -0400 (Tue, 20 Oct 2015)

EllapsedTime: 929.3 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 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [35s/35s] 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 ... [450s/450s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
countShiftReads   92.208  5.550  97.788
countsPlot        85.239  5.088  90.357
riboSeqFromBAM    71.990  2.916  75.014
codonInfo         68.965  2.241  71.218
orfRelativePos    38.233  2.432  40.673
aroundPromoter    16.798  1.013  17.814
plotSummarizedCov 13.989  1.043  15.032
readStartCov      10.923  1.101  12.028
histMatchLength    4.796  0.355   5.155
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [129s/130s]
 [130s/130s] 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	16.798	1.013	17.814
codonInfo	68.965	2.241	71.218
codonPCA	2.011	0.069	2.084
countShiftReads	92.208	5.550	97.788
countsPlot	85.239	5.088	90.357
histMatchLength	4.796	0.355	5.155
orfRelativePos	38.233	2.432	40.673
plotSummarizedCov	13.989	1.043	15.032
printPCA	2.220	0.049	2.270
readStartCov	10.923	1.101	12.028
readsToReadStart	4.392	0.353	4.747
riboSeqFromBAM	71.990	2.916	75.014