BioC 3.3: CHECK report for RiboProfiling on zin2

Package: RiboProfiling

Version: 1.2.1

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings RiboProfiling_1.2.1.tar.gz

StartedAt: 2016-05-13 06:27:57 -0700 (Fri, 13 May 2016)

EndedAt: 2016-05-13 06:38:21 -0700 (Fri, 13 May 2016)

EllapsedTime: 624.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RiboProfiling.Rcheck

Warnings: 1

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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_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/RiboProfiling.Rcheck’
* using R version 3.3.0 (2016-05-03)
* 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 ‘1.2.1’
* 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/20s] WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboProfiling’
See ‘/home/biocbuild/bbs-3.3-bioc/meat/RiboProfiling.Rcheck/00install.out’ for details.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [310s/309s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
countShiftReads   71.146  2.014  72.826
countsPlot        68.911  1.248  69.842
riboSeqFromBAM    62.521  1.130  63.361
orfRelativePos    34.828  0.245  35.020
codonInfo         24.936  0.143  25.088
aroundPromoter     9.559  0.104   9.665
plotSummarizedCov  8.242  0.153   8.361
readStartCov       6.226  0.080   6.290
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [92s/92s]
 [92s/92s] 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 WARNING, 1 NOTE
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
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboProfiling’
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboProfiling’
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
* DONE (RiboProfiling)

name	user	system	elapsed
aroundPromoter	9.559	0.104	9.665
codonInfo	24.936	0.143	25.088
codonPCA	1.365	0.041	1.393
countShiftReads	71.146	2.014	72.826
countsPlot	68.911	1.248	69.842
histMatchLength	3.267	0.016	3.281
orfRelativePos	34.828	0.245	35.020
plotSummarizedCov	8.242	0.153	8.361
printPCA	1.733	0.056	1.774
readStartCov	6.226	0.080	6.290
readsToStartOrEnd	2.758	0.008	2.764
riboSeqFromBAM	62.521	1.130	63.361