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This page was generated on 2021-12-01 17:18:02 -0500 (Wed, 01 Dec 2021).

CHECK results for REMP on tokay2

To the developers/maintainers of the REMP package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/REMP.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1577/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
REMP 1.18.0  (landing page)
Yinan Zheng
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/REMP
git_branch: RELEASE_3_14
git_last_commit: 3164bd7
git_last_commit_date: 2021-10-26 12:32:57 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: REMP
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:REMP.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings REMP_1.18.0.tar.gz
StartedAt: 2021-12-01 04:14:05 -0500 (Wed, 01 Dec 2021)
EndedAt: 2021-12-01 04:25:03 -0500 (Wed, 01 Dec 2021)
EllapsedTime: 657.6 seconds
RetCode: 0
Status:   OK  
CheckDir: REMP.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:REMP.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings REMP_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/REMP.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'REMP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'REMP' version '1.18.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
remp            21.07   1.73   22.22
fetchRMSK       18.17   0.77   21.00
rempTemplate    14.61   0.77   14.98
GRannot         12.21   1.50   15.37
remprofile      11.94   0.81   12.56
initREMP        11.74   0.77   13.00
fetchRefSeqGene  7.91   1.42    9.83
getGM12878       6.21   0.26    6.93
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
remp            21.37   1.17   22.09
fetchRMSK       15.28   0.64   16.45
remprofile      13.64   0.78   14.27
rempTemplate    12.52   0.97   13.55
GRannot         12.56   0.90   14.69
initREMP        11.16   0.64   12.31
fetchRefSeqGene  7.67   0.52    8.77
* 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/REMP.Rcheck/00check.log'
for details.



Installation output

REMP.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/REMP_1.18.0.tar.gz && rm -rf REMP.buildbin-libdir && mkdir REMP.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=REMP.buildbin-libdir REMP_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL REMP_1.18.0.zip && rm REMP_1.18.0.tar.gz REMP_1.18.0.zip
###
##############################################################################
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 78082  100 78082    0     0   483k      0 --:--:-- --:--:-- --:--:--  485k

install for i386

* 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
  converting help for package 'REMP'
    finding HTML links ... done
    Alu.hg19.demo                           html  
    finding level-2 HTML links ... done

    Alu.hg38.demo                           html  
    GRannot                                 html  
    REMP-package                            html  
    REMParcel-class                         html  
    REMProduct-class                        html  
    fetchRMSK                               html  
    fetchRefSeqGene                         html  
    findRECpG                               html  
    getBackend                              html  
    getGM12878                              html  
    grooMethy                               html  
    initREMP                                html  
    options                                 html  
    remp                                    html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/REMP.buildbin-libdir/00LOCK-REMP/00new/REMP/help/remp.html
    rempTemplate                            html  
    remprofile                              html  
** 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

install for x64

* installing *source* package 'REMP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'REMP' as REMP_1.18.0.zip
* DONE (REMP)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'REMP' successfully unpacked and MD5 sums checked

Tests output


Example timings

REMP.Rcheck/examples_i386/REMP-Ex.timings

nameusersystemelapsed
GRannot12.21 1.5015.37
REMParcel-class000
REMProduct-class000
fetchRMSK18.17 0.7721.00
fetchRefSeqGene7.911.429.83
findRECpG1.360.251.70
getBackend1.330.021.34
getGM128786.210.266.93
grooMethy2.910.334.43
initREMP11.74 0.7713.00
options000
remp21.07 1.7322.22
rempTemplate14.61 0.7714.98
remprofile11.94 0.8112.56

REMP.Rcheck/examples_x64/REMP-Ex.timings

nameusersystemelapsed
GRannot12.56 0.9014.69
REMParcel-class000
REMProduct-class000
fetchRMSK15.28 0.6416.45
fetchRefSeqGene7.670.528.77
findRECpG2.330.062.39
getBackend1.230.001.23
getGM128783.840.224.06
grooMethy2.990.474.74
initREMP11.16 0.6412.31
options000
remp21.37 1.1722.09
rempTemplate12.52 0.9713.55
remprofile13.64 0.7814.27