BioC 3.5: CHECK report for REMP on veracruz2

Package: REMP

Version: 1.0.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings REMP_1.0.7.tar.gz

StartedAt: 2017-10-18 08:08:32 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 08:34:12 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 1540.2 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_1.0.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/REMP.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.0.7’
* 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’
plot,REMProduct-missing: no visible binding for global variable ‘xlim’
Undefined global functions or variables:
  main xlab xlim
* 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
GRannot   12.384  0.615  15.234
remp      10.111  0.364  10.511
initREMP   7.600  0.614   9.506
grooMethy  6.815  0.399   9.002
fetchRMSK  6.363  0.551   8.093
findRECpG  5.518  0.100   5.778
* 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	12.384	0.615	15.234
REMParcel-class	0.002	0.000	0.002
REMProduct-class	0.002	0.001	0.003
fetchRMSK	6.363	0.551	8.093
fetchRefSeqGene	3.222	0.164	4.429
findRECpG	5.518	0.100	5.778
getBackend	0.157	0.017	0.178
getGM12878	2.661	0.363	3.113
grooMethy	6.815	0.399	9.002
initREMP	7.600	0.614	9.506
options	0.003	0.001	0.004
remp	10.111	0.364	10.511