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CHECK report for REMP on malbec2

This page was generated on 2020-10-17 11:55:33 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE REMP PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1463/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
REMP 1.12.0
Yinan Zheng
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/REMP
Branch: RELEASE_3_11
Last Commit: 392ce3a
Last Changed Date: 2020-04-27 15:05:16 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: REMP
Version: 1.12.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:REMP.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings REMP_1.12.0.tar.gz
StartedAt: 2020-10-17 04:39:34 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:48:12 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 518.1 seconds
RetCode: 0
Status:  OK 
CheckDir: REMP.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:REMP.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings REMP_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/REMP.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.12.0’
* 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 (user + system) or elapsed time > 5s
                  user system elapsed
remp            21.321  1.565  22.632
fetchRMSK       15.462  0.376  16.197
rempTemplate    13.074  0.511  14.966
remprofile      12.163  0.426  12.760
GRannot         11.656  0.344  13.257
initREMP         9.966  0.381  10.552
getGM12878       6.151  0.292   6.807
fetchRefSeqGene  6.229  0.112   6.561
grooMethy        3.475  0.113   8.477
* 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-3.11-bioc/meat/REMP.Rcheck/00check.log’
for details.



Installation output

REMP.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL REMP
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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)

Tests output


Example timings

REMP.Rcheck/REMP-Ex.timings

nameusersystemelapsed
GRannot11.656 0.34413.257
REMParcel-class000
REMProduct-class0.0020.0000.002
fetchRMSK15.462 0.37616.197
fetchRefSeqGene6.2290.1126.561
findRECpG1.4570.2131.669
getBackend2.8330.8533.699
getGM128786.1510.2926.807
grooMethy3.4750.1138.477
initREMP 9.966 0.38110.552
options0.0020.0000.002
remp21.321 1.56522.632
rempTemplate13.074 0.51114.966
remprofile12.163 0.42612.760