Multiple platform build/check report for BioC 3.11

Package: pmp

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pmp.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pmp_1.0.0.tar.gz

StartedAt: 2020-10-17 06:58:36 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 07:03:19 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 282.9 seconds

RetCode: 0

Status: OK

CheckDir: pmp.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pmp.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pmp_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/pmp.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.0.0'
* 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 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/pmp_1.0.0.tar.gz && rm -rf pmp.buildbin-libdir && mkdir pmp.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pmp.buildbin-libdir pmp_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL pmp_1.0.0.zip && rm pmp_1.0.0.tar.gz pmp_1.0.0.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 1708k  100 1708k    0     0  5800k      0 --:--:-- --:--:-- --:--:-- 5951k

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_1.0.0.zip
* DONE (pmp)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'pmp' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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>
== testthat results  ===========================================================
[ OK: 85 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  15.15    0.87   16.18


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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>
== testthat results  ===========================================================
[ OK: 85 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  18.87    0.54   19.46

name	user	system	elapsed
QCRSC	0.25	0.04	0.30
filter_peaks_by_blank	0.19	0.03	0.22
filter_peaks_by_fraction	1.29	0.11	1.41
filter_peaks_by_rsd	0.05	0.00	0.04
filter_samples_by_mv	0.03	0.00	0.04
glog_plot_optimised_lambda	0.92	0.03	0.95
glog_transformation	0.33	0.00	0.33
mv_imputation	0.16	0.00	0.15
normalise_to_sum	0.03	0.00	0.03
pqn_normalisation	0.20	0.00	0.21
processing_history	0.13	0.00	0.12
remove_peaks	0.01	0.00	0.02
sbc_plot	0.52	0.00	0.51

name	user	system	elapsed
QCRSC	1.06	0.00	1.07
filter_peaks_by_blank	0.14	0.00	0.14
filter_peaks_by_fraction	1.26	0.08	1.35
filter_peaks_by_rsd	0.04	0.00	0.03
filter_samples_by_mv	0.01	0.00	0.01
glog_plot_optimised_lambda	0.69	0.02	0.71
glog_transformation	1.03	0.03	1.06
mv_imputation	0.12	0.00	0.12
normalise_to_sum	0.04	0.00	0.03
pqn_normalisation	0.17	0.00	0.18
processing_history	0.08	0.00	0.07
remove_peaks	0.01	0.00	0.02
sbc_plot	0.41	0.00	0.41

CHECK report for pmp on tokay2

Summary

Command output

Installation output

Tests output

Example timings