Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:16 -0400 (Fri, 15 Oct 2021).

CHECK results for pmp on tokay2

To the developers/maintainers of the pmp package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pmp.git to
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raw results

Package 1408/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pmp 1.4.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/pmp
git_branch: RELEASE_3_13
git_last_commit: e0310dc
git_last_commit_date: 2021-05-19 12:48:58 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: pmp
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pmp.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings pmp_1.4.0.tar.gz
StartedAt: 2021-10-15 03:31:38 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 03:35:44 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 245.7 seconds
RetCode: 0
Status:   OK  
CheckDir: pmp.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pmp.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings pmp_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/pmp.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pmp/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pmp' version '1.4.0'
* 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 'pmp' 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 ... 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 ... OK
* checking LazyData ... OK
* 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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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: OK


Installation output

pmp.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/pmp_1.4.0.tar.gz && rm -rf pmp.buildbin-libdir && mkdir pmp.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pmp.buildbin-libdir pmp_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL pmp_1.4.0.zip && rm pmp_1.4.0.tar.gz pmp_1.4.0.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 1708k  100 1708k    0     0  1831k      0 --:--:-- --:--:-- --:--:-- 1833k

install for i386

* installing *source* package 'pmp' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pmp'
    finding HTML links ... done
    MTBLS79                                 html  
    QCRSC                                   html  
    filter_peaks_by_blank                   html  
    filter_peaks_by_fraction                html  
    filter_peaks_by_rsd                     html  
    filter_samples_by_mv                    html  
    glog_plot_optimised_lambda              html  
    glog_transformation                     html  
    mv_imputation                           html  
    normalise_to_sum                        html  
    pqn_normalisation                       html  
    processing_history                      html  
    remove_peaks                            html  
    sbc_plot                                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 'pmp' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pmp' as pmp_1.4.0.zip
* DONE (pmp)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'pmp' successfully unpacked and MD5 sums checked

Tests output

pmp.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(pmp)
> 
> test_check("pmp")
  missForest iteration 1 in progress...done!
  missForest iteration 2 in progress...done!
      NRMSE 
0.003724107 
<simpleError in qcData[id, ]: incorrect number of dimensions>
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 90 ]
> 
> proc.time()
   user  system elapsed 
  17.21    1.01   18.21 

pmp.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(pmp)
> 
> test_check("pmp")
  missForest iteration 1 in progress...done!
  missForest iteration 2 in progress...done!
      NRMSE 
0.003724107 
<simpleError in qcData[id, ]: incorrect number of dimensions>
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 90 ]
> 
> proc.time()
   user  system elapsed 
  17.06    0.39   17.43 

Example timings

pmp.Rcheck/examples_i386/pmp-Ex.timings

nameusersystemelapsed
QCRSC0.250.010.26
filter_peaks_by_blank0.120.000.13
filter_peaks_by_fraction1.140.131.26
filter_peaks_by_rsd0.030.000.03
filter_samples_by_mv0.030.000.03
glog_plot_optimised_lambda0.750.020.77
glog_transformation0.330.000.33
mv_imputation0.140.000.14
normalise_to_sum0.030.000.03
pqn_normalisation0.170.000.17
processing_history0.080.000.07
remove_peaks0.020.000.02
sbc_plot0.930.000.94

pmp.Rcheck/examples_x64/pmp-Ex.timings

nameusersystemelapsed
QCRSC0.760.000.76
filter_peaks_by_blank0.140.000.14
filter_peaks_by_fraction1.620.071.69
filter_peaks_by_rsd0.050.000.05
filter_samples_by_mv0.030.000.03
glog_plot_optimised_lambda0.820.030.86
glog_transformation1.150.001.14
mv_imputation0.140.010.16
normalise_to_sum0.030.000.03
pqn_normalisation0.220.000.22
processing_history0.110.000.11
remove_peaks0.010.000.01
sbc_plot0.580.000.58