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

Package: RiboProfiling

Version: 1.0.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RiboProfiling_1.0.0.tar.gz

StartedAt: 2015-10-27 07:30:33 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:41:19 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 645.9 seconds

RetCode: 0

Status:  OK

CheckDir: RiboProfiling.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 RiboProfiling_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/RiboProfiling.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 ‘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 ... [24s/24s] OK
* checking installed package size ... NOTE
  installed size is 10.5Mb
  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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [311s/311s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
countShiftReads   65.636  1.387  67.133
riboSeqFromBAM    59.853  0.044  59.969
countsPlot        57.976  0.160  58.174
codonInfo         41.298  0.196  41.702
orfRelativePos    30.241  0.000  30.283
aroundPromoter    14.153  0.172  14.389
plotSummarizedCov 10.388  0.000  10.407
readStartCov       7.539  0.000   7.545
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [101s/101s]
 [101s/101s] 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/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	14.153	0.172	14.389
codonInfo	41.298	0.196	41.702
codonPCA	1.330	0.036	1.379
countShiftReads	65.636	1.387	67.133
countsPlot	57.976	0.160	58.174
histMatchLength	3.701	0.004	3.705
orfRelativePos	30.241	0.000	30.283
plotSummarizedCov	10.388	0.000	10.407
printPCA	1.894	0.000	1.902
readStartCov	7.539	0.000	7.545
readsToReadStart	4.017	0.000	4.020
riboSeqFromBAM	59.853	0.044	59.969