BioC 3.2: CHECK report for microRNA on oaxaca

Package: microRNA

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings microRNA_1.28.0.tar.gz

StartedAt: 2016-04-23 02:08:36 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:09:56 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 80.0 seconds

RetCode: 0

Status:  OK

CheckDir: microRNA.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 microRNA_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/microRNA.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘microRNA/DESCRIPTION’ ... OK
* this is package ‘microRNA’ version ‘1.28.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘Rlibstree’
* 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 ‘microRNA’ can be installed ... [7s/7s] OK
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data      5.4Mb
    extdata   2.0Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biostrings’
A package should be listed in only one of these fields.
* 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 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 examples ... [12s/12s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
matchSeeds 5.149  0.126    5.29
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/microRNA.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
RNA2DNA	0.001	0.000	0.001
get_selfhyb_subseq	0.004	0.000	0.004
hsSeqs	0.022	0.003	0.025
hsTargets	0.700	0.032	0.733
matchSeeds	5.149	0.126	5.290
mmSeqs	0.003	0.000	0.004
mmTargets	2.112	0.038	2.157
s3utr	0.005	0.015	0.021
seedRegions	0.004	0.001	0.005