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CHECK report for MethPed on tokay1

This page was generated on 2020-04-15 12:26:14 -0400 (Wed, 15 Apr 2020).

Package 1015/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MethPed 1.14.0
Helena Carén
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/MethPed
Branch: RELEASE_3_10
Last Commit: bb7d62d
Last Changed Date: 2019-10-29 13:09:34 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MethPed
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethPed.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings MethPed_1.14.0.tar.gz
StartedAt: 2020-04-15 04:37:59 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:45:48 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 468.4 seconds
RetCode: 0
Status:  OK  
CheckDir: MethPed.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethPed.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings MethPed_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/MethPed.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.14.0'
* 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 or elapsed time > 5s
                  user system elapsed
MethPed         123.67   0.42  124.10
plot.methped     46.46   0.12   46.57
probeMis         39.36   0.16   39.52
summary.methped  33.03   0.16   33.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
MethPed         85.09   0.44   85.54
plot.methped    29.76   0.14   29.91
summary.methped 28.15   0.11   28.27
probeMis        26.66   0.09   26.75
* 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-3.10-bioc/meat/MethPed.Rcheck/00check.log'
for details.



Installation output

MethPed.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/MethPed_1.14.0.tar.gz && rm -rf MethPed.buildbin-libdir && mkdir MethPed.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MethPed.buildbin-libdir MethPed_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL MethPed_1.14.0.zip && rm MethPed_1.14.0.tar.gz MethPed_1.14.0.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 9147k  100 9147k    0     0  59.8M      0 --:--:-- --:--:-- --:--:-- 61.1M

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_1.14.0.zip
* DONE (MethPed)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'MethPed' successfully unpacked and MD5 sums checked

Tests output


Example timings

MethPed.Rcheck/examples_i386/MethPed-Ex.timings

nameusersystemelapsed
MethPed123.67 0.42124.10
MethPed_900probes000
MethPed_sample2.200.112.32
checkNA2.420.112.53
plot.methped46.46 0.1246.57
probeMis39.36 0.1639.52
summary.methped33.03 0.1633.19

MethPed.Rcheck/examples_x64/MethPed-Ex.timings

nameusersystemelapsed
MethPed85.09 0.4485.54
MethPed_900probes0.020.000.01
MethPed_sample2.320.082.39
checkNA1.700.081.78
plot.methped29.76 0.1429.91
probeMis26.66 0.0926.75
summary.methped28.15 0.1128.27