BioC 3.1: CHECK report for microRNA on zin2

Package: microRNA

Version: 1.26.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings microRNA_1.26.0.tar.gz

StartedAt: 2015-10-09 03:32:00 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:33:05 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 64.7 seconds

RetCode: 0

Status:  OK

CheckDir: microRNA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings microRNA_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/microRNA.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 ‘microRNA/DESCRIPTION’ ... OK
* this is package ‘microRNA’ version ‘1.26.0’
* 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 ... [6s/6s] 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 ... [9s/9s] OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/microRNA.Rcheck/00check.log’
for details.

* installing *source* package ‘microRNA’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (microRNA)

name	user	system	elapsed
RNA2DNA	0	0	0
get_selfhyb_subseq	0.002	0.000	0.002
hsSeqs	0.018	0.000	0.018
hsTargets	0.629	0.007	0.638
matchSeeds	3.329	0.012	3.345
mmSeqs	0.001	0.000	0.002
mmTargets	1.721	0.028	1.750
s3utr	0.004	0.000	0.005
seedRegions	0.002	0.000	0.003