Package: REMP

Version: 1.8.2

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:REMP.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings REMP_1.8.2.tar.gz

StartedAt: 2019-10-16 04:26:16 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:35:13 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 536.9 seconds

RetCode: 0

Status:  OK

CheckDir: REMP.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:REMP.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings REMP_1.8.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/REMP.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.2’
* package encoding: UTF-8
* 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
  ‘IlluminaHumanMethylationEPICanno.ilm10b2.hg19’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
initREMP: no visible binding for global variable
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
initREMP: no visible binding for global variable
  ‘IlluminaHumanMethylationEPICanno.ilm10b2.hg19’
remprofile: no visible binding for global variable
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
remprofile: no visible binding for global variable
  ‘IlluminaHumanMethylationEPICanno.ilm10b2.hg19’
Undefined global functions or variables:
  IlluminaHumanMethylation450kanno.ilmn12.hg19
  IlluminaHumanMethylationEPICanno.ilm10b2.hg19
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
remp            14.388  1.048  22.887
fetchRMSK       14.482  0.493  42.584
GRannot         11.423  0.264  14.502
rempTemplate     9.570  0.520  18.587
remprofile       8.968  0.360  13.846
initREMP         6.687  0.435   9.468
getGM12878       5.984  0.303   9.342
fetchRefSeqGene  4.751  0.124  15.745
grooMethy        3.291  0.116  46.261
findRECpG        1.007  0.172   6.347
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/REMP.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL REMP
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘REMP’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (REMP)

name	user	system	elapsed
GRannot	11.423	0.264	14.502
REMParcel-class	0.001	0.000	0.001
REMProduct-class	0.000	0.001	0.001
fetchRMSK	14.482	0.493	42.584
fetchRefSeqGene	4.751	0.124	15.745
findRECpG	1.007	0.172	6.347
getBackend	2.111	0.633	3.626
getGM12878	5.984	0.303	9.342
grooMethy	3.291	0.116	46.261
initREMP	6.687	0.435	9.468
options	0.002	0.000	0.002
remp	14.388	1.048	22.887
rempTemplate	9.570	0.520	18.587
remprofile	8.968	0.360	13.846