Dharmesh D. Bhuva
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/dcanr |
| Branch: RELEASE_3_9 |
| Last Commit: 0adcc26 |
| Last Changed Date: 2019-05-02 11:54:15 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:44:11 -0400 (Wed, 16 Oct 2019).
| Package 391/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| dcanr 1.0.0 Dharmesh D. Bhuva
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: dcanr |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dcanr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings dcanr_1.0.0.tar.gz |
| StartedAt: 2019-10-16 03:04:12 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:05:59 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 107.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: dcanr.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dcanr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings dcanr_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/dcanr.Rcheck' * using R version 3.6.1 (2019-07-05) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'dcanr/DESCRIPTION' ... OK * this is package 'dcanr' version '1.0.0' * 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 'dcanr' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ...It is recommended to use 'given' instead of 'middle'. 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 ... NOTE ftgi.score: no visible binding for global variable 'i' ftgi.score: no visible binding for global variable 'j' Undefined global functions or variables: i j * 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: 1 NOTE See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/dcanr.Rcheck/00check.log' for details.
dcanr.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/dcanr_1.0.0.tar.gz && rm -rf dcanr.buildbin-libdir && mkdir dcanr.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dcanr.buildbin-libdir dcanr_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL dcanr_1.0.0.zip && rm dcanr_1.0.0.tar.gz dcanr_1.0.0.zip
###
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install for i386
* installing *source* package 'dcanr' ...
** using staged installation
It is recommended to use 'given' instead of 'middle'.
It is recommended to use 'given' instead of 'middle'.
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'dcScore' with signature '"Matrix","ANY","ANY"': no definition for class "Matrix"
in method for 'dcScore' with signature '"ExpressionSet","ANY","ANY"': no definition for class "ExpressionSet"
in method for 'dcScore' with signature '"SummarizedExperiment","ANY","ANY"': no definition for class "SummarizedExperiment"
in method for 'dcScore' with signature '"DGEList","ANY","ANY"': no definition for class "DGEList"
** help
*** installing help indices
converting help for package 'dcanr'
finding HTML links ... done
cor.pairs html
dcAdjust html
dcEvaluate html
dcMethods html
dcNetwork html
dcPipeline html
dcScore html
dcTest html
dcanr-package html
getSimData html
mi.ap html
perfMethods html
performanceMeasure html
plotSimNetwork html
sim102 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 'dcanr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dcanr' as dcanr_1.0.0.zip
* DONE (dcanr)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'dcanr' successfully unpacked and MD5 sums checked
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dcanr.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(dcanr)
>
> test_check("dcanr")
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.0699999999999985
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.00999999999999979
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.0199999999999996
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.0200000000000014
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.0100000000000016
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.00999999999999979
== testthat results ===========================================================
[ OK: 171 | SKIPPED: 0 | WARNINGS: 299 | FAILED: 0 ]
>
> proc.time()
user system elapsed
14.32 0.90 15.64
|
dcanr.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(dcanr)
>
> test_check("dcanr")
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.00999999999999801
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.0100000000000016
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.0199999999999996
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.0199999999999996
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.00999999999999801
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.0100000000000016
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287
Estimating optimal shrinkage intensity lambda (correlation matrix): 1
Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.0100000000000016
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1
Iteration: 2
One-Stepper Time: 0.0100000000000016
== testthat results ===========================================================
[ OK: 171 | SKIPPED: 0 | WARNINGS: 299 | FAILED: 0 ]
>
> proc.time()
user system elapsed
19.57 0.67 20.46
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dcanr.Rcheck/examples_i386/dcanr-Ex.timings
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dcanr.Rcheck/examples_x64/dcanr-Ex.timings
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