BioC 3.3: CHECK report for RiboProfiling on linux2.bioconductor.org

Package: RiboProfiling

Version: 1.1.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings RiboProfiling_1.1.0.tar.gz

StartedAt: 2015-10-27 07:30:16 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:40:36 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 620.5 seconds

RetCode: 0

Status:  OK

CheckDir: RiboProfiling.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings RiboProfiling_1.1.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/RiboProfiling.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.1.0’
* 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 ... [19s/19s] 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 ... NOTE
Missing or unexported object: ‘GenomicFeatures::makeTranscriptDbFromUCSC’
* 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 ... [320s/320s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
countShiftReads   69.661  1.534  71.361
countsPlot        63.990  0.748  64.821
riboSeqFromBAM    61.444  0.200  61.823
codonInfo         38.377  0.164  38.666
orfRelativePos    32.000  0.136  32.250
aroundPromoter    11.628  0.168  11.826
plotSummarizedCov 11.135  0.012  11.162
readStartCov       7.916  0.012   7.945
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [95s/95s]
 [95s/95s] 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: 2 NOTEs
See
  ‘/home/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	11.628	0.168	11.826
codonInfo	38.377	0.164	38.666
codonPCA	1.4	0.0	1.4
countShiftReads	69.661	1.534	71.361
countsPlot	63.990	0.748	64.821
histMatchLength	4.762	0.008	4.785
orfRelativePos	32.000	0.136	32.250
plotSummarizedCov	11.135	0.012	11.162
printPCA	1.552	0.000	1.553
readStartCov	7.916	0.012	7.945
readsToReadStart	2.894	0.000	2.921
riboSeqFromBAM	61.444	0.200	61.823