sigsquared 1.2.0
UnJin Lee
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/sigsquared | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf sigsquared.buildbin-libdir sigsquared.Rcheck && mkdir sigsquared.buildbin-libdir sigsquared.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sigsquared.buildbin-libdir sigsquared_1.2.0.tar.gz >sigsquared.Rcheck\00install.out 2>&1 && cp sigsquared.Rcheck\00install.out sigsquared-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=sigsquared.buildbin-libdir --install="check:sigsquared-install.out" --force-multiarch --no-vignettes --timings sigsquared_1.2.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/sigsquared.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.2.0'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 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 'mcparallel'
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
definition for 'mccollect'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [19s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
analysisPipeline 16.61 0 16.62
** running examples for arch 'x64' ... [29s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
analysisPipeline 24.83 0.03 24.88
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [4s]
[5s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [5s]
[6s] 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
'D:/biocbld/bbs-3.2-bioc/meat/sigsquared.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'sigsquared' ...
** R
** data
** inst
** preparing 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
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'sigsquared' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sigsquared' as sigsquared_1.2.0.zip
* DONE (sigsquared)