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This page was generated on 2022-01-26 13:06:55 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for missMethyl on tokay2


To the developers/maintainers of the missMethyl package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/missMethyl.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 1173/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
missMethyl 1.28.0  (landing page)
Belinda Phipson
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/missMethyl
git_branch: RELEASE_3_14
git_last_commit: 6a36aee
git_last_commit_date: 2021-10-26 12:14:52 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: missMethyl
Version: 1.28.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:missMethyl.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings missMethyl_1.28.0.tar.gz
StartedAt: 2022-01-25 23:07:00 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 23:37:04 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 1803.2 seconds
RetCode: 0
Status:   OK  
CheckDir: missMethyl.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:missMethyl.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings missMethyl_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/missMethyl.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 'missMethyl/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'missMethyl' version '1.28.0'
* 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 'missMethyl' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
goregion: no visible global function definition for 'seqlevelsStyle<-'
Undefined global functions or variables:
  seqlevelsStyle<-
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
SWAN               32.86   3.77   36.63
RUVadj             30.82   5.33   39.03
RUVfit             26.88   1.62   28.50
getAdj             26.47   1.56   28.03
topRUV             24.55   2.45   27.01
topGSA             21.11   1.88   23.03
densityByProbeType 13.81   1.80   15.62
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
RUVadj             29.81   1.64   31.47
SWAN               24.78   2.34   27.13
topRUV             21.22   1.27   22.50
RUVfit             18.51   1.16   19.67
getAdj             17.95   1.16   19.12
topGSA             16.77   0.86   17.63
densityByProbeType 10.48   1.37   11.86
* 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/missMethyl.Rcheck/00check.log'
for details.



Installation output

missMethyl.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/missMethyl_1.28.0.tar.gz && rm -rf missMethyl.buildbin-libdir && mkdir missMethyl.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=missMethyl.buildbin-libdir missMethyl_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL missMethyl_1.28.0.zip && rm missMethyl_1.28.0.tar.gz missMethyl_1.28.0.zip
###
##############################################################################
##############################################################################


  % 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 73866  100 73866    0     0   398k      0 --:--:-- --:--:-- --:--:--  400k

install for i386

* installing *source* package 'missMethyl' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'missMethyl'
    finding HTML links ... done
    RUVadj                                  html  
    finding level-2 HTML links ... done

    RUVfit                                  html  
    SWAN                                    html  
    contrasts.varFit                        html  
    densityByProbeType                      html  
    getAdj                                  html  
    getINCs                                 html  
    getLeveneResiduals                      html  
    getMappedEntrezIDs                      html  
    gometh                                  html  
    goregion                                html  
    gsameth                                 html  
    gsaregion                               html  
    gsaseq                                  html  
    missMethyl-package                      html  
    topGSA                                  html  
    topRUV                                  html  
    topVar                                  html  
    varFit                                  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 'missMethyl' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'missMethyl' as missMethyl_1.28.0.zip
* DONE (missMethyl)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'missMethyl' successfully unpacked and MD5 sums checked

Tests output


Example timings

missMethyl.Rcheck/examples_i386/missMethyl-Ex.timings

nameusersystemelapsed
RUVadj30.82 5.3339.03
RUVfit26.88 1.6228.50
SWAN32.86 3.7736.63
contrasts.varFit0.030.010.05
densityByProbeType13.81 1.8015.62
getAdj26.47 1.5628.03
getINCs0.160.030.19
getLeveneResiduals0.010.000.02
getMappedEntrezIDs000
gometh000
goregion000
gsameth000
gsaregion000
gsaseq000
topGSA21.11 1.8823.03
topRUV24.55 2.4527.01
topVar0.020.020.03
varFit0.010.000.02

missMethyl.Rcheck/examples_x64/missMethyl-Ex.timings

nameusersystemelapsed
RUVadj29.81 1.6431.47
RUVfit18.51 1.1619.67
SWAN24.78 2.3427.13
contrasts.varFit0.050.000.05
densityByProbeType10.48 1.3711.86
getAdj17.95 1.1619.12
getINCs0.220.000.22
getLeveneResiduals000
getMappedEntrezIDs000
gometh000
goregion000
gsameth000
gsaregion000
gsaseq000
topGSA16.77 0.8617.63
topRUV21.22 1.2722.50
topVar000
varFit0.020.000.02