BioC 3.3: CHECK report for RiboProfiling on morelia

Package: RiboProfiling

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RiboProfiling_1.1.0.tar.gz

StartedAt: 2015-10-22 10:32:39 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 10:41:59 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 560.7 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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/RiboProfiling.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.1.0’
* 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 ... [17s/17s] 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 ... [270s/281s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
countShiftReads   55.541  2.942  61.102
countsPlot        53.172  3.037  57.703
riboSeqFromBAM    48.114  1.924  50.374
codonInfo         31.322  1.341  32.899
orfRelativePos    24.495  1.741  26.406
aroundPromoter    10.600  0.595  11.267
plotSummarizedCov  9.220  0.601   9.855
readStartCov       6.676  0.557   7.269
codonPCA           1.380  0.036   6.734
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [89s/90s]
 [89s/90s] 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-3.3-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	10.600	0.595	11.267
codonInfo	31.322	1.341	32.899
codonPCA	1.380	0.036	6.734
countShiftReads	55.541	2.942	61.102
countsPlot	53.172	3.037	57.703
histMatchLength	3.004	0.141	3.172
orfRelativePos	24.495	1.741	26.406
plotSummarizedCov	9.220	0.601	9.855
printPCA	1.404	0.030	1.444
readStartCov	6.676	0.557	7.269
readsToReadStart	2.462	0.188	2.658
riboSeqFromBAM	48.114	1.924	50.374