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) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
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 1435/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RCM 1.4.0 Joris Meys
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| 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 |
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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.
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
|
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
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RCM.Rcheck/examples_i386/RCM-Ex.timings
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RCM.Rcheck/examples_x64/RCM-Ex.timings
|