Back to Multiple platform build/check report for BioC 3.12
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

CHECK report for MethPed on tokay1

This page was generated on 2021-05-06 12:32:12 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the MethPed package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1067/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MethPed 1.18.0  (landing page)
Helena Carén
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/MethPed
Branch: RELEASE_3_12
Last Commit: 311faed
Last Changed Date: 2020-10-27 11:11:53 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: MethPed
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethPed.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MethPed_1.18.0.tar.gz
StartedAt: 2021-05-06 04:30:05 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:36:53 -0400 (Thu, 06 May 2021)
EllapsedTime: 408.0 seconds
RetCode: 0
Status:   OK   
CheckDir: MethPed.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethPed.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MethPed_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MethPed.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MethPed/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethPed' 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 'MethPed' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    data   6.7Mb
* 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 ... OK
* 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 ... NOTE
  Note: found 3 marked Latin-1 strings
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... 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
MethPed         94.36   0.55   94.92
plot.methped    33.93   0.14   34.13
probeMis        33.70   0.14   33.84
summary.methped 27.03   0.13   27.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
MethPed         77.26   0.34   77.63
summary.methped 30.77   0.13   30.89
plot.methped    25.67   0.14   25.81
probeMis        24.68   0.11   24.80
* 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-3.12-bioc/meat/MethPed.Rcheck/00check.log'
for details.



Installation output

MethPed.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/MethPed_1.18.0.tar.gz && rm -rf MethPed.buildbin-libdir && mkdir MethPed.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MethPed.buildbin-libdir MethPed_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL MethPed_1.18.0.zip && rm MethPed_1.18.0.tar.gz MethPed_1.18.0.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 9147k  100 9147k    0     0  68.9M      0 --:--:-- --:--:-- --:--:-- 69.7M

install for i386

* installing *source* package 'MethPed' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MethPed'
    finding HTML links ... done
    MethPed                                 html  
    MethPed_900probes                       html  
    MethPed_sample                          html  
    checkNA                                 html  
    plot.methped                            html  
    probeMis                                html  
    summary.methped                         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 'MethPed' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MethPed' as MethPed_1.18.0.zip
* DONE (MethPed)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'MethPed' successfully unpacked and MD5 sums checked

Tests output


Example timings

MethPed.Rcheck/examples_i386/MethPed-Ex.timings

nameusersystemelapsed
MethPed94.36 0.5594.92
MethPed_900probes000
MethPed_sample1.860.011.87
checkNA1.920.031.95
plot.methped33.93 0.1434.13
probeMis33.70 0.1433.84
summary.methped27.03 0.1327.16

MethPed.Rcheck/examples_x64/MethPed-Ex.timings

nameusersystemelapsed
MethPed77.26 0.3477.63
MethPed_900probes000
MethPed_sample1.540.021.56
checkNA1.660.061.72
plot.methped25.67 0.1425.81
probeMis24.68 0.1124.80
summary.methped30.77 0.1330.89