BioC 3.1: CHECK report for maSigPro on moscato2
This page was generated on 2015-10-09 09:27:33 -0700 (Fri, 09 Oct 2015).
maSigPro 1.40.0 Maria Jose Nueda
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/maSigPro | Last Changed Rev: 102591 / Revision: 109384 | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK |  |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |  |
Summary
Package: maSigPro
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Version: 1.40.0
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Command: rm -rf maSigPro.buildbin-libdir maSigPro.Rcheck && mkdir maSigPro.buildbin-libdir maSigPro.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=maSigPro.buildbin-libdir maSigPro_1.40.0.tar.gz >maSigPro.Rcheck\00install.out 2>&1 && cp maSigPro.Rcheck\00install.out maSigPro-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=maSigPro.buildbin-libdir --install="check:maSigPro-install.out" --force-multiarch --no-vignettes --timings maSigPro_1.40.0.tar.gz
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StartedAt: 2015-10-09 03:24:53 -0700 (Fri, 09 Oct 2015)
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EndedAt: 2015-10-09 03:26:42 -0700 (Fri, 09 Oct 2015)
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EllapsedTime: 109.3 seconds
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RetCode: 0
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Status: OK
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CheckDir: maSigPro.Rcheck
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Warnings: 0
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Command output
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###
### Running command:
###
### rm -rf maSigPro.buildbin-libdir maSigPro.Rcheck && mkdir maSigPro.buildbin-libdir maSigPro.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=maSigPro.buildbin-libdir maSigPro_1.40.0.tar.gz >maSigPro.Rcheck\00install.out 2>&1 && cp maSigPro.Rcheck\00install.out maSigPro-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=maSigPro.buildbin-libdir --install="check:maSigPro-install.out" --force-multiarch --no-vignettes --timings maSigPro_1.40.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/maSigPro.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'maSigPro/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'maSigPro' version '1.40.0'
* 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 'maSigPro' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'Biobase' 'stats' 'MASS'
A package should be listed in only one of these fields.
* 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
Namespace in Imports field not imported from: 'utils'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
see.genes: warning in mfuzz(signif, c = k, m = m): partial argument
match of 'c' to 'centers'
* 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' ... [20s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
T.fit 6.69 0.03 6.72
maSigPro 4.83 0.02 5.23
** running examples for arch 'x64' ... [26s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
T.fit 8.68 0.01 8.68
maSigPro 6.07 0.01 6.16
* 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
'E:/biocbld/bbs-3.1-bioc/meat/maSigPro.Rcheck/00check.log'
for details.
maSigPro.Rcheck/00install.out:
install for i386
* installing *source* package 'maSigPro' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'maSigPro' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'maSigPro' as maSigPro_1.40.0.zip
* DONE (maSigPro)
maSigPro.Rcheck/examples_i386/maSigPro-Ex.timings:
name | user | system | elapsed
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NBdata | 0.05 | 0.00 | 0.05 |
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NBdesign | 0 | 0 | 0 |
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PlotGroups | 0.02 | 0.00 | 0.01 |
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PlotProfiles | 0.02 | 0.00 | 0.02 |
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T.fit | 6.69 | 0.03 | 6.72 |
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average.rows | 0 | 0 | 0 |
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data.abiotic | 0 | 0 | 0 |
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edesign.OD | 0 | 0 | 0 |
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edesign.abiotic | 0 | 0 | 0 |
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edesignCT | 0 | 0 | 0 |
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edesignDR | 0.00 | 0.02 | 0.01 |
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get.siggenes | 3.19 | 0.01 | 3.20 |
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i.rank | 0 | 0 | 0 |
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maSigPro | 4.83 | 0.02 | 5.23 |
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maSigProUsersGuide | 0 | 0 | 0 |
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make.design.matrix | 0 | 0 | 0 |
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p.vector | 1.93 | 0.00 | 1.94 |
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position | 0 | 0 | 0 |
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reg.coeffs | 0 | 0 | 0 |
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see.genes | 0.75 | 0.19 | 0.93 |
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stepback | 0.03 | 0.00 | 0.03 |
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stepfor | 0.13 | 0.00 | 0.13 |
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suma2Venn | 0.00 | 0.01 | 0.01 |
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two.ways.stepback | 0.09 | 0.00 | 0.10 |
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two.ways.stepfor | 0.13 | 0.00 | 0.12 |
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maSigPro.Rcheck/examples_x64/maSigPro-Ex.timings:
name | user | system | elapsed
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NBdata | 0.01 | 0.01 | 0.03 |
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NBdesign | 0.00 | 0.02 | 0.01 |
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PlotGroups | 0.01 | 0.00 | 0.02 |
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PlotProfiles | 0.00 | 0.02 | 0.02 |
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T.fit | 8.68 | 0.01 | 8.68 |
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average.rows | 0.01 | 0.00 | 0.02 |
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data.abiotic | 0 | 0 | 0 |
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edesign.OD | 0 | 0 | 0 |
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edesign.abiotic | 0.01 | 0.00 | 0.01 |
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edesignCT | 0 | 0 | 0 |
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edesignDR | 0.02 | 0.00 | 0.02 |
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get.siggenes | 4.66 | 0.02 | 4.68 |
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i.rank | 0 | 0 | 0 |
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maSigPro | 6.07 | 0.01 | 6.16 |
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maSigProUsersGuide | 0 | 0 | 0 |
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make.design.matrix | 0.00 | 0.02 | 0.01 |
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p.vector | 2.64 | 0.01 | 2.66 |
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position | 0 | 0 | 0 |
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reg.coeffs | 0 | 0 | 0 |
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see.genes | 1.08 | 0.14 | 1.21 |
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stepback | 0.03 | 0.00 | 0.03 |
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stepfor | 0.14 | 0.00 | 0.14 |
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suma2Venn | 0 | 0 | 0 |
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two.ways.stepback | 0.14 | 0.00 | 0.14 |
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two.ways.stepfor | 0.24 | 0.00 | 0.23 |
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