BioC 3.0: CHECK report for proBAMr on perceval

Package: proBAMr

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch proBAMr_1.0.1.tar.gz

StartedAt: 2015-04-10 05:00:42 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 05:06:41 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 359.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: proBAMr.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch proBAMr_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/proBAMr.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘proBAMr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proBAMr’ version ‘1.0.1’
* 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 ‘proBAMr’ can be installed ... [31s/31s] OK
* checking installed package size ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [20s/20s] WARNING
Found the following significant warnings:

  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [20s/21s]
 [21s/21s] 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

WARNING: There was 1 warning.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/proBAMr.Rcheck/00check.log’
for details.

* installing *source* package ‘proBAMr’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (proBAMr)

name	user	system	elapsed
PSMtab2SAM	1.292	0.020	1.315
PrepareAnnotationGENCODE	2.238	0.111	2.366