Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-07-24 12:05:50 -0400 (Sat, 24 Jul 2021).

CHECK results for combi on riesling1

To the developers/maintainers of the combi package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/combi.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 357/2008HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
combi 1.5.0  (landing page)
Joris Meys
Snapshot Date: 2021-07-23 14:50:08 -0400 (Fri, 23 Jul 2021)
URL: https://git.bioconductor.org/packages/combi
Branch: master
Last Commit: 9f97750
Last Changed Date: 2021-05-19 12:50:35 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: combi
Version: 1.5.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:combi.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings combi_1.5.0.tar.gz
StartedAt: 2021-07-23 23:52:59 -0400 (Fri, 23 Jul 2021)
EndedAt: 2021-07-23 23:59:05 -0400 (Fri, 23 Jul 2021)
EllapsedTime: 366.5 seconds
RetCode: 0
Status:   OK  
CheckDir: combi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:combi.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings combi_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/combi.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'combi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'combi' version '1.5.0'
* 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 'combi' 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 ... NOTE
Foreign function call to a different package:
  .C("spline_value", ..., PACKAGE = "cobs")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
addLink: no visible binding for global variable 'species'
convPlot: no visible binding for global variable 'Iteration'
convPlot: no visible binding for global variable 'Value'
convPlot: no visible binding for global variable 'Variable'
convPlot: no visible binding for global variable 'Colour'
inflPlot: no visible binding for global variable 'h'
inflPlot: no visible binding for global variable 'LatentVariable'
inflPlot: no visible binding for global variable 'value'
Undefined global functions or variables:
  Colour Iteration LatentVariable Value Variable h species value
* 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' ... 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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/combi.Rcheck/00check.log'
for details.



Installation output

combi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/combi_1.5.0.tar.gz && rm -rf combi.buildbin-libdir && mkdir combi.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=combi.buildbin-libdir combi_1.5.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL combi_1.5.0.zip && rm combi_1.5.0.tar.gz combi_1.5.0.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 1097k  100 1097k    0     0  4477k      0 --:--:-- --:--:-- --:--:-- 4496k

install for i386

* installing *source* package 'combi' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'combi'
    finding HTML links ... done
    addLink                                 html  
    arrayMult                               html  
    buildCentMat                            html  
    buildCompMat                            html  
    buildConfMat                            html  
    buildCovMat                             html  
    buildEmptyJac                           html  
    buildMarginalOffset                     html  
    buildMu                                 html  
    buildMuMargins                          html  
    buildOffsetModel                        html  
    checkAlias                              html  
    checkMeanVarTrend                       html  
    checkMonotonicity                       html  
    combi                                   html  
    convPlot                                html  
    deriv2LagrangianFeatures                html  
    deriv2LagrangianLatentVars              html  
    deriv2LagrangianLatentVarsConstr        html  
    derivLagrangianFeatures                 html  
    derivLagrangianLatentVars               html  
    derivLagrangianLatentVarsConstr         html  
    estFeatureParameters                    html  
    estIndepModel                           html  
    estLatentVars                           html  
    estMeanVarTrend                         html  
    estOff                                  html  
    extractCoords                           html  
    extractData                             html  
    extractMat                              html  
    filterConfounders                       html  
    getInflLatentVar                        html  
    gramSchmidtOrth                         html  
    indentPlot                              html  
    inflPlot                                html  
    influence.combi                         html  
    jacConfounders                          html  
    jacConfoundersComp                      html  
    jacFeatures                             html  
    jacLatentVars                           html  
    jacLatentVarsConstr                     html  
    plot.combi                              html  
    polyHorner                              html  
    predictSpline                           html  
    prepareJacMat                           html  
    prepareJacMatComp                       html  
    prepareScoreMat                         html  
    print.combi                             html  
    quasiJacIndep                           html  
    quasiScoreIndep                         html  
    rowMultiply                             html  
    scaleCoords                             html  
    scoreConfounders                        html  
    scoreConfoundersComp                    html  
    scoreFeatureParams                      html  
    scoreLatentVars                         html  
    seqM                                    html  
    trimOnConfounders                       html  
    zhangMetabo                             html  
    zhangMetavars                           html  
    zhangMicrobio                           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 'combi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'combi' as combi_1.5.0.zip
* DONE (combi)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'combi' successfully unpacked and MD5 sums checked

Tests output

combi.Rcheck/tests_i386/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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(combi)
> test_check("combi")
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
  37.26    0.51   37.78 

combi.Rcheck/tests_x64/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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(combi)
> test_check("combi")
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
  35.68    0.56   36.23 

Example timings

combi.Rcheck/examples_i386/combi-Ex.timings

nameusersystemelapsed
addLink0.270.050.32
checkMeanVarTrend3.610.023.62
combi0.010.000.02
convPlot0.470.030.50
extractCoords0.030.010.04
extractData0.030.000.03
inflPlot0.610.020.63
plot.combi1.560.011.58
print.combi0.040.000.03

combi.Rcheck/examples_x64/combi-Ex.timings

nameusersystemelapsed
addLink0.300.050.34
checkMeanVarTrend3.170.023.19
combi0.020.000.01
convPlot0.510.000.52
extractCoords0.050.000.05
extractData0.020.000.01
inflPlot0.620.000.63
plot.combi1.660.001.65
print.combi0.010.000.02