Nima Hejazi
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/biotmle |
| Branch: RELEASE_3_12 |
| Last Commit: a54105e |
| Last Changed Date: 2021-02-08 21:10:16 -0400 (Mon, 08 Feb 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:30:03 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the biotmle package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 189/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biotmle 1.14.0 (landing page) Nima Hejazi
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: biotmle |
| Version: 1.14.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biotmle.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings biotmle_1.14.0.tar.gz |
| StartedAt: 2021-05-06 00:56:20 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 01:01:53 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 332.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: biotmle.Rcheck |
| Warnings: 2 |
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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:biotmle.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings biotmle_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/biotmle.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 'biotmle/DESCRIPTION' ... OK
* this is package 'biotmle' version '1.14.0'
* 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 'biotmle' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEvWQkA/R.INSTALL1ec45de31b48/biotmle/man/biomarkertmle.Rd:52: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEvWQkA/R.INSTALL1ec45de31b48/biotmle/man/biomarkertmle.Rd:54: file link 'DoparParam' in package 'BiocParallel' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/biotmle.Rcheck/00install.out' for details.
* 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 ... WARNING
Codoc mismatches from documentation object 'biomarkertmle':
biomarkertmle
Code: function(se, varInt, normalized = TRUE, ngscounts = FALSE,
parallel = TRUE, bppar_type = NULL, future_param =
NULL, bppar_debug = FALSE, cv_folds = 1, g_lib =
c("SL.mean", "SL.glm", "SL.bayesglm", "SL.glmnet"),
Q_lib = c("SL.mean", "SL.bayesglm", "SL.earth",
"SL.ranger"), ...)
Docs: function(se, varInt, normalized = TRUE, ngscounts = FALSE,
parallel = TRUE, bppar_type = NULL, future_param =
NULL, bppar_debug = FALSE, cv_folds = 1, g_lib =
c("SL.mean", "SL.glm", "SL.bayesglm", "SL.glmnet"),
Q_lib = c("SL.mean", "SL.bayesglm", "SL.earth",
"SL.xgboost"), ...)
Mismatches in argument default values:
Name: 'Q_lib' Code: c("SL.mean", "SL.bayesglm", "SL.earth", "SL.ranger") Docs: c("SL.mean", "SL.bayesglm", "SL.earth", "SL.xgboost")
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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
bioTMLE-class 1.73 0.05 7.77
** 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 WARNINGs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/biotmle.Rcheck/00check.log'
for details.
biotmle.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/biotmle_1.14.0.tar.gz && rm -rf biotmle.buildbin-libdir && mkdir biotmle.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biotmle.buildbin-libdir biotmle_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL biotmle_1.14.0.zip && rm biotmle_1.14.0.tar.gz biotmle_1.14.0.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 287k 100 287k 0 0 9417k 0 --:--:-- --:--:-- --:--:-- 9896k
install for i386
* installing *source* package 'biotmle' ...
** using staged installation
** R
** 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 'biotmle'
finding HTML links ... done
bioTMLE-class html
biomarkertmle html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEvWQkA/R.INSTALL1ec45de31b48/biotmle/man/biomarkertmle.Rd:52: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEvWQkA/R.INSTALL1ec45de31b48/biotmle/man/biomarkertmle.Rd:54: file link 'DoparParam' in package 'BiocParallel' does not exist and so has been treated as a topic
data.frame_OR_EList-class html
eif html
exp_biomarkertmle html
heatmap_ic html
modtest_ic html
plot.bioTMLE html
rnaseq_ic html
toptable html
volcano_ic 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 'biotmle' ...
** 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 'biotmle' as biotmle_1.14.0.zip
* DONE (biotmle)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'biotmle' successfully unpacked and MD5 sums checked
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biotmle.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(biotmle)
biotmle v1.14.0: Targeted Learning with Moderated Statistics for Biomarker Discovery
Warning message:
In .recacheSubclasses(def@className, def, env) :
undefined subclass "numericVector" of class "Mnumeric"; definition not updated
>
> test_check("biotmle")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 13 ]
>
> proc.time()
user system elapsed
22.29 1.29 23.85
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biotmle.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(biotmle)
biotmle v1.14.0: Targeted Learning with Moderated Statistics for Biomarker Discovery
Warning message:
In .recacheSubclasses(def@className, def, env) :
undefined subclass "numericVector" of class "Mnumeric"; definition not updated
>
> test_check("biotmle")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 13 ]
>
> proc.time()
user system elapsed
25.92 0.81 31.48
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biotmle.Rcheck/examples_i386/biotmle-Ex.timings
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biotmle.Rcheck/examples_x64/biotmle-Ex.timings
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