UnJin Lee
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/sigsquared |
| git_branch: RELEASE_3_14 |
| git_last_commit: 9ef5a53 |
| git_last_commit_date: 2021-10-26 12:18:55 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:22 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the sigsquared package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sigsquared.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1795/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sigsquared 1.26.0 (landing page) UnJin Lee
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: sigsquared |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sigsquared.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings sigsquared_1.26.0.tar.gz |
| StartedAt: 2022-04-13 02:58:52 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 03:00:43 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 111.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: sigsquared.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sigsquared.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings sigsquared_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/sigsquared.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sigsquared/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sigsquared' version '1.26.0'
* 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 'sigsquared' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
GPL version 3
Standardizable: TRUE
Standardized license specification:
GPL-3
* 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 ... NOTE
Package in Depends field not imported from: 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
analysisPipeline,ExpressionSet-geneSignature: no visible binding for
global variable 'nCores'
analysisPipeline,ExpressionSet-geneSignature: no visible global
function definition for 'mcparallel'
analysisPipeline,ExpressionSet-geneSignature: no visible global
function definition for 'mccollect'
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
binding for global variable 'mc'
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
binding for global variable 'nCores'
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
global function definition for 'mcparallel'
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
global function definition for 'mccollect'
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
definition for 'new'
eJPDF,ExpressionSet-geneSignature-numeric: no visible binding for
global variable 'mc'
eJPDF,ExpressionSet-geneSignature-numeric: no visible binding for
global variable 'nCores'
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
definition for 'rnorm'
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
definition for 'mcparallel'
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
definition for 'mccollect'
genGeneDirect,matrix: no visible global function definition for 'sd'
optCF,ExpressionSet-geneSignature: no visible global function
definition for 'new'
optCF,ExpressionSet-geneSignature: no visible global function
definition for 'rnorm'
optCF,ExpressionSet-geneSignature: no visible global function
definition for 'optim'
summarizeSolnSpace,solnSpace: no visible global function definition for
'sd'
Undefined global functions or variables:
mc mccollect mcparallel nCores new optim rnorm sd
Consider adding
importFrom("methods", "new")
importFrom("stats", "optim", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
analysisPipeline 14.33 0.08 14.41
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
analysisPipeline 17.01 0.08 17.09
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/sigsquared.Rcheck/00check.log'
for details.
sigsquared.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/sigsquared_1.26.0.tar.gz && rm -rf sigsquared.buildbin-libdir && mkdir sigsquared.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sigsquared.buildbin-libdir sigsquared_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL sigsquared_1.26.0.zip && rm sigsquared_1.26.0.tar.gz sigsquared_1.26.0.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 150k 100 150k 0 0 664k 0 --:--:-- --:--:-- --:--:-- 667k
install for i386
* installing *source* package 'sigsquared' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'ensembleCostFcn' with signature 'dataSet="ExpressionSet",geneSig="geneSignature",jpdf="solnSpace"': no definition for class "solnSpace"
in method for 'getCVCuts' with signature 'cutoffResults="solnSpace"': no definition for class "solnSpace"
in method for 'summarizeCVCuts' with signature 'cutoffResults="solnSpace"': no definition for class "solnSpace"
** help
*** installing help indices
converting help for package 'sigsquared'
finding HTML links ... done
BrCa443 html
analysisPipeline html
ensembleAdjustable html
geneSignature-class html
setGeneSignature html
sigsquared 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 'sigsquared' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sigsquared' as sigsquared_1.26.0.zip
* DONE (sigsquared)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'sigsquared' successfully unpacked and MD5 sums checked
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sigsquared.Rcheck/tests_i386/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
> BiocGenerics:::testPackage("sigsquared")
RUNIT TEST PROTOCOL -- Wed Apr 13 03:00:31 2022
***********************************************
Number of test functions: 8
Number of errors: 0
Number of failures: 0
1 Test Suite :
sigsquared RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
1.89 0.14 2.01
|
sigsquared.Rcheck/tests_x64/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
> BiocGenerics:::testPackage("sigsquared")
RUNIT TEST PROTOCOL -- Wed Apr 13 03:00:34 2022
***********************************************
Number of test functions: 8
Number of errors: 0
Number of failures: 0
1 Test Suite :
sigsquared RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
2.31 0.14 2.43
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sigsquared.Rcheck/examples_i386/sigsquared-Ex.timings
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sigsquared.Rcheck/examples_x64/sigsquared-Ex.timings
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