Joris Meys
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/combi |
| Branch: RELEASE_3_12 |
| Last Commit: 9a2a1d2 |
| Last Changed Date: 2020-10-27 11:54:37 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:30:27 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the combi package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 355/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| combi 1.2.0 (landing page) Joris Meys
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: combi |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:combi.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings combi_1.2.0.tar.gz |
| StartedAt: 2021-05-06 01:40:11 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 01:55:07 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 896.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: combi.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:combi.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings combi_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/combi.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.2.0'
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
checkMeanVarTrend 7.85 0.17 8.22
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
checkMeanVarTrend 7.33 0.02 7.45
* 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
'C:/Users/biocbuild/bbs-3.12-bioc/meat/combi.Rcheck/00check.log'
for details.
combi.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/combi_1.2.0.tar.gz && rm -rf combi.buildbin-libdir && mkdir combi.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=combi.buildbin-libdir combi_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL combi_1.2.0.zip && rm combi_1.2.0.tar.gz combi_1.2.0.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
1 1097k 1 11435 0 0 17550 0 0:01:04 --:--:-- 0:01:04 17565
100 1097k 100 1097k 0 0 883k 0 0:00:01 0:00:01 --:--:-- 884k
install for i386
* installing *source* package 'combi' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning in .recacheSubclasses(def@className, def, env) :
undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** 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
Warning in .recacheSubclasses(def@className, def, env) :
undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** testing if installed package can be loaded from final location
Warning in .recacheSubclasses(def@className, def, env) :
undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** 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
Warning in .recacheSubclasses(def@className, def, env) :
undefined subclass "numericVector" of class "Mnumeric"; definition not updated
* MD5 sums
packaged installation of 'combi' as combi_1.2.0.zip
* DONE (combi)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'combi' successfully unpacked and MD5 sums checked
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combi.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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)
Warning message:
In .recacheSubclasses(def@className, def, env) :
undefined subclass "numericVector" of class "Mnumeric"; definition not updated
> test_check("combi")
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 15 ]
>
> proc.time()
user system elapsed
409.64 4.28 414.00
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combi.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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)
Warning message:
In .recacheSubclasses(def@className, def, env) :
undefined subclass "numericVector" of class "Mnumeric"; definition not updated
> test_check("combi")
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 15 ]
>
> proc.time()
user system elapsed
69.68 0.65 70.37
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combi.Rcheck/examples_i386/combi-Ex.timings
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combi.Rcheck/examples_x64/combi-Ex.timings
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