Package: REMP

Version: 1.10.1

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:REMP.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings REMP_1.10.1.tar.gz

StartedAt: 2020-04-15 04:34:24 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:43:19 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 535.5 seconds

RetCode: 0

Status:  OK

CheckDir: REMP.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:REMP.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings REMP_1.10.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/REMP.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.10.1’
* 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            22.876  1.296  26.592
fetchRMSK       17.248  0.456  20.233
rempTemplate    14.560  0.528  17.802
remprofile      14.532  0.388  17.560
GRannot         12.560  0.296  15.783
initREMP        10.508  0.472  15.780
fetchRefSeqGene  7.300  0.116   9.158
getGM12878       7.088  0.252   7.889
grooMethy        4.144  0.124   6.799
* 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-3.10-bioc/meat/REMP.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL REMP
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* installing to library ‘/home/biocbuild/bbs-3.10-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	12.560	0.296	15.783
REMParcel-class	0.004	0.000	0.001
REMProduct-class	0.000	0.000	0.001
fetchRMSK	17.248	0.456	20.233
fetchRefSeqGene	7.300	0.116	9.158
findRECpG	1.872	0.196	2.161
getBackend	2.560	0.856	3.687
getGM12878	7.088	0.252	7.889
grooMethy	4.144	0.124	6.799
initREMP	10.508	0.472	15.780
options	0.000	0.000	0.002
remp	22.876	1.296	26.592
rempTemplate	14.560	0.528	17.802
remprofile	14.532	0.388	17.560