BioC 3.5: CHECK report for REMP on toluca2

Package: REMP

Version: 0.99.25

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings REMP_0.99.25.tar.gz

StartedAt: 2017-04-23 08:53:06 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 09:18:38 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 1531.3 seconds

RetCode: 0

Status:  OK

CheckDir: REMP.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 REMP_0.99.25.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/REMP.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘REMP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘REMP’ version ‘0.99.25’
* 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 ‘REMP’ can be installed ... 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 ... NOTE
plot,REMProduct-missing: no visible binding for global variable ‘main’
plot,REMProduct-missing: no visible binding for global variable ‘xlab’
Undefined global functions or variables:
  main xlab
* 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 ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
remp            19.802  0.464  20.795
GRannot         18.306  0.971  20.096
initREMP        10.260  0.766  12.003
grooMethy        9.205  0.583  12.381
fetchRMSK        8.678  0.697  11.247
fetchRefSeqGene  4.389  0.464   7.120
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/REMP.Rcheck/00check.log’
for details.

* installing *source* package ‘REMP’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (REMP)

name	user	system	elapsed
GRannot	18.306	0.971	20.096
REMParcel-class	0.001	0.000	0.002
REMProduct-class	0.003	0.000	0.003
fetchRMSK	8.678	0.697	11.247
fetchRefSeqGene	4.389	0.464	7.120
findRECpG	4.066	0.038	4.167
getBackend	0.083	0.007	0.090
getGM12878	3.214	0.426	3.685
grooMethy	9.205	0.583	12.381
initREMP	10.260	0.766	12.003
options	0.003	0.001	0.004
remp	19.802	0.464	20.795