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CHECK report for RCM on tokay2

This page was generated on 2020-10-17 11:57:34 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE RCM PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1435/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCM 1.4.0
Joris Meys
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/RCM
Branch: RELEASE_3_11
Last Commit: 9436a06
Last Changed Date: 2020-04-27 15:22:26 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: RCM
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCM.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings RCM_1.4.0.tar.gz
StartedAt: 2020-10-17 07:21:07 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:28:11 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 424.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RCM.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RCM.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings RCM_1.4.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/RCM.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 'RCM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RCM' 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 'RCM' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:

  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
plotRespFun       18.66   0.18   19.18
addOrthProjection 10.44   0.00   10.44
extractCoord      10.36   0.00   10.36
plot.RCM          10.23   0.04   10.27
inertia            9.55   0.07    9.73
liks               9.61   0.00    9.61
RCM                9.24   0.09    9.33
RCM_NB             8.08   0.02    8.09
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:

  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
plotRespFun       17.00   0.01   17.14
plot.RCM           9.46   0.02    9.49
addOrthProjection  9.42   0.02    9.43
inertia            9.12   0.00    9.13
extractCoord       9.08   0.00    9.09
RCM                8.42   0.06    8.48
liks               7.38   0.00    7.37
RCM_NB             6.34   0.00    6.36
* 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: 2 WARNINGs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/RCM.Rcheck/00check.log'
for details.

Installation output

RCM.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/RCM_1.4.0.tar.gz && rm -rf RCM.buildbin-libdir && mkdir RCM.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RCM.buildbin-libdir RCM_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL RCM_1.4.0.zip && rm RCM_1.4.0.tar.gz RCM_1.4.0.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
  0 2721k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2721k  100 2721k    0     0  14.4M      0 --:--:-- --:--:-- --:--:-- 14.9M

install for i386

* installing *source* package 'RCM' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RCM'
    finding HTML links ... done
    JacCol_constr                           html  
    JacCol_constr_noLab                     html  
    LR_nb                                   html  
    LR_nb_Jac                               html  
    NBalphaInfl                             html  
    NBcolInfl                               html  
    NBjacobianAbunds                        html  
    NBjacobianCol                           html  
    NBjacobianColNP                         html  
    NBjacobianLibSizes                      html  
    NBjacobianPsi                           html  
    NBjacobianRow                           html  
    NBpsiInfl                               html  
    NBrowInfl                               html  
    RCM                                     html  
    RCM_NB                                  html  
    Zeller                                  html  
    addOrthProjection                       html  
    arrayprod                               html  
    buildCentMat                            html  
    buildConfMat                            html  
    buildConfMat.character                  html  
    buildConfMat.data.frame                 html  
    buildCovMat                             html  
    buildDesign                             html  
    dLR_nb                                  html  
    dNBabunds                               html  
    dNBlibSizes                             html  
    dNBllcol                                html  
    dNBllcolNP                              html  
    dNBllcol_constr                         html  
    dNBllcol_constr_noLab                   html  
    dNBllrow                                html  
    dNBpsis                                 html  
    deviances                               html  
    ellipseCoord                            html  
    estDisp                                 html  
    estNBparams                             html  
    estNBparamsNoLab                        html  
    estNPresp                               html  
    extractCoord                            html  
    extractE                                html  
    filterConfounders                       html  
    getDevMat                               html  
    getDevianceRes                          html  
    getInflCol                              html  
    getInflRow                              html  
    getInt                                  html  
    getLogLik                               html  
    getModelMat                             html  
    getRowMat                               html  
    heq_nb                                  html  
    heq_nb_jac                              html  
    indentPlot                              html  
    inertia                                 html  
    liks                                    html  
    plot.RCM                                html  
    plotRespFun                             html  
    residualPlot                            html  
    respFunJacMat                           html  
    respFunScoreMat                         html  
    rowMultiply                             html  
    seq_k                                   html  
    trimOnConfounders                       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 'RCM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RCM' as RCM_1.4.0.zip
* DONE (RCM)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'RCM' successfully unpacked and MD5 sums checked

Tests output

RCM.Rcheck/tests_i386/testthat.Rout


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(RCM)
> 
> test_check("RCM")
== testthat results  ===========================================================
[ OK: 12 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  15.40    0.93   16.32

RCM.Rcheck/tests_x64/testthat.Rout


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(RCM)
> 
> test_check("RCM")
== testthat results  ===========================================================
[ OK: 12 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  16.56    0.40   16.95

Example timings

RCM.Rcheck/examples_i386/RCM-Ex.timings

nameusersystemelapsed
RCM9.240.099.33
RCM_NB8.080.028.09
addOrthProjection10.44 0.0010.44
extractCoord10.36 0.0010.36
inertia9.550.079.73
liks9.610.009.61
plot.RCM10.23 0.0410.27
plotRespFun18.66 0.1819.18
residualPlot4.250.084.33

RCM.Rcheck/examples_x64/RCM-Ex.timings

nameusersystemelapsed
RCM8.420.068.48
RCM_NB6.340.006.36
addOrthProjection9.420.029.43
extractCoord9.080.009.09
inertia9.120.009.13
liks7.380.007.37
plot.RCM9.460.029.49
plotRespFun17.00 0.0117.14
residualPlot4.360.024.37