BioC 2.13: CHECK report for sigaR on moscato1
This page was generated on 2014-04-05 09:50:36 -0700 (Sat, 05 Apr 2014).
sigaR 1.6.0
Wessel N. van Wieringen
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/sigaR | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ OK ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
Summary
| Package: sigaR
|
| Version: 1.6.0
|
| Command: rm -rf sigaR.buildbin-libdir && mkdir sigaR.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=sigaR.buildbin-libdir sigaR_1.6.0.tar.gz >sigaR-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=sigaR.buildbin-libdir --install="check:sigaR-install.out" --force-multiarch --no-vignettes --timings sigaR_1.6.0.tar.gz && mv sigaR.buildbin-libdir/* sigaR.Rcheck/ && rmdir sigaR.buildbin-libdir
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| StartedAt: 2014-04-05 06:44:00 -0700 (Sat, 05 Apr 2014)
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| EndedAt: 2014-04-05 06:53:24 -0700 (Sat, 05 Apr 2014)
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| EllapsedTime: 564.1 seconds
|
| RetCode: 0
|
| Status: OK
|
| CheckDir: sigaR.Rcheck
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| Warnings: 0
|
Command output
* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/sigaR.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sigaR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sigaR' version '1.6.0'
* 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 'sigaR' 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:
'mvtnorm' 'penalized'
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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ExpressionSet2weightedSubset: no visible binding for global variable
'sigaR'
RCMestimation : RCMmlH2: multiple local function definitions for
'tau.estimator' with different formal arguments
RCMtest: no visible binding for global variable 'sigaR'
RCMtest: no visible binding for global variable 'quadprog'
RCMtest: no visible binding for global variable 'MASS'
cghCall2maximumSubset: no visible binding for global variable 'sigaR'
cghCall2weightedSubset: no visible binding for global variable 'sigaR'
cghSeg2weightedSubset: no visible binding for global variable 'sigaR'
entropyTest: no visible binding for global variable 'sigaR'
entropyTest: no visible binding for global variable 'corpcor'
matchAnn2Ann: no visible binding for global variable 'sigaR'
matchCGHcall2ExpressionSet: no visible binding for global variable
'sigaR'
mutInfTest: no visible binding for global variable 'sigaR'
mutInfTest: no visible binding for global variable 'corpcor'
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
'sigaR.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [218s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mutInfTest 167.48 6.55 174.05
cisEffectTune 17.62 0.00 17.61
RCMtest 5.82 0.00 5.82
** running examples for arch 'x64' ... [241s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mutInfTest 181.37 5.46 186.85
cisEffectTune 25.17 0.02 25.20
RCMtest 6.16 0.02 6.17
* 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
NOTE: There were 3 notes.
See
'D:/biocbld/bbs-2.13-bioc/meat/sigaR.Rcheck/00check.log'
for details.
sigaR.Rcheck/00install.out:
install for i386
* installing *source* package 'sigaR' ...
** 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 'sigaR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sigaR' as sigaR_1.6.0.zip
* DONE (sigaR)
sigaR.Rcheck/examples_i386/sigaR-Ex.timings:
| name | user | system | elapsed
|
| CNGEheatmaps | 1.12 | 0.06 | 1.38 |
|
| ExpressionSet2order | 0.01 | 0.00 | 0.02 |
|
| ExpressionSet2subset | 0.01 | 0.00 | 0.02 |
|
| ExpressionSet2weightedSubset | 0.17 | 0.00 | 0.19 |
|
| RCMestimation | 1.16 | 0.00 | 1.15 |
|
| RCMrandom | 1.25 | 0.00 | 1.25 |
|
| RCMtest | 5.82 | 0.00 | 5.82 |
|
| cghCall2cghSeg | 0.06 | 0.00 | 0.07 |
|
| cghCall2maximumSubset | 0.36 | 0.00 | 0.35 |
|
| cghCall2order | 0.01 | 0.00 | 0.02 |
|
| cghCall2subset | 0.05 | 0.00 | 0.05 |
|
| cghCall2weightedSubset | 0.22 | 0.00 | 0.22 |
|
| cghSeg2order | 0.06 | 0.00 | 0.06 |
|
| cghSeg2subset | 0.09 | 0.00 | 0.09 |
|
| cghSeg2weightedSubset | 0.27 | 0.00 | 0.27 |
|
| cisEffectPlot | 0.1 | 0.0 | 0.1 |
|
| cisEffectTable | 1.92 | 0.00 | 1.92 |
|
| cisEffectTest | 2.32 | 0.00 | 2.33 |
|
| cisEffectTune | 17.62 | 0.00 | 17.61 |
|
| cisTest-class | 0 | 0 | 0 |
|
| entTest-class | 0.02 | 0.00 | 0.01 |
|
| entropyTest | 0.22 | 0.00 | 0.22 |
|
| expandMatching2singleIDs | 0.08 | 0.00 | 0.08 |
|
| getSegFeatures | 0.01 | 0.00 | 0.01 |
|
| hdEntropy | 0.09 | 0.00 | 0.09 |
|
| hdMI | 0.34 | 0.00 | 0.35 |
|
| matchAnn2Ann | 0.05 | 0.00 | 0.05 |
|
| matchCGHcall2ExpressionSet | 0.06 | 0.00 | 0.06 |
|
| merge2ExpressionSets | 0.07 | 0.00 | 0.06 |
|
| merge2cghCalls | 0.1 | 0.0 | 0.1 |
|
| miTest-class | 0.01 | 0.00 | 0.01 |
|
| mutInfTest | 167.48 | 6.55 | 174.05 |
|
| nBreakpoints | 0.53 | 0.00 | 0.53 |
|
| pathway1sample | 0.25 | 0.00 | 0.25 |
|
| pathway2sample | 4.39 | 0.42 | 4.81 |
|
| pathwayFit-class | 0 | 0 | 0 |
|
| pathwayPlot | 0.19 | 0.00 | 0.19 |
|
| pollackCN16 | 0.01 | 0.00 | 0.02 |
|
| pollackGE16 | 0 | 0 | 0 |
|
| profilesPlot | 0.13 | 0.00 | 0.14 |
|
| rcmFit-class | 0.01 | 0.00 | 0.01 |
|
| rcmTest-class | 0 | 0 | 0 |
|
| splitMatchingAtBreakpoints | 0.36 | 0.00 | 0.36 |
|
| uniqGenomicInfo | 0.02 | 0.00 | 0.02 |
|
sigaR.Rcheck/examples_x64/sigaR-Ex.timings:
| name | user | system | elapsed
|
| CNGEheatmaps | 1.42 | 0.04 | 1.64 |
|
| ExpressionSet2order | 0.01 | 0.00 | 0.01 |
|
| ExpressionSet2subset | 0.02 | 0.00 | 0.02 |
|
| ExpressionSet2weightedSubset | 0.24 | 0.00 | 0.24 |
|
| RCMestimation | 1.42 | 0.00 | 1.42 |
|
| RCMrandom | 1.55 | 0.00 | 1.55 |
|
| RCMtest | 6.16 | 0.02 | 6.17 |
|
| cghCall2cghSeg | 0.08 | 0.00 | 0.08 |
|
| cghCall2maximumSubset | 0.39 | 0.00 | 0.39 |
|
| cghCall2order | 0.01 | 0.00 | 0.02 |
|
| cghCall2subset | 0.06 | 0.00 | 0.06 |
|
| cghCall2weightedSubset | 0.29 | 0.00 | 0.28 |
|
| cghSeg2order | 0.08 | 0.00 | 0.07 |
|
| cghSeg2subset | 0.11 | 0.00 | 0.11 |
|
| cghSeg2weightedSubset | 0.28 | 0.00 | 0.28 |
|
| cisEffectPlot | 0.08 | 0.01 | 0.39 |
|
| cisEffectTable | 2.31 | 0.00 | 2.31 |
|
| cisEffectTest | 2.97 | 0.00 | 2.96 |
|
| cisEffectTune | 25.17 | 0.02 | 25.20 |
|
| cisTest-class | 0 | 0 | 0 |
|
| entTest-class | 0 | 0 | 0 |
|
| entropyTest | 0.2 | 0.0 | 0.2 |
|
| expandMatching2singleIDs | 0.15 | 0.01 | 0.17 |
|
| getSegFeatures | 0.02 | 0.00 | 0.01 |
|
| hdEntropy | 0.03 | 0.00 | 0.03 |
|
| hdMI | 0.37 | 0.02 | 0.39 |
|
| matchAnn2Ann | 0.08 | 0.00 | 0.08 |
|
| matchCGHcall2ExpressionSet | 0.08 | 0.00 | 0.08 |
|
| merge2ExpressionSets | 0.07 | 0.02 | 0.09 |
|
| merge2cghCalls | 0.1 | 0.0 | 0.1 |
|
| miTest-class | 0 | 0 | 0 |
|
| mutInfTest | 181.37 | 5.46 | 186.85 |
|
| nBreakpoints | 0.33 | 0.00 | 0.32 |
|
| pathway1sample | 0.19 | 0.00 | 0.19 |
|
| pathway2sample | 4.00 | 0.45 | 4.57 |
|
| pathwayFit-class | 0 | 0 | 0 |
|
| pathwayPlot | 0.20 | 0.00 | 0.21 |
|
| pollackCN16 | 0.01 | 0.00 | 0.01 |
|
| pollackGE16 | 0.00 | 0.01 | 0.02 |
|
| profilesPlot | 0.27 | 0.00 | 0.26 |
|
| rcmFit-class | 0 | 0 | 0 |
|
| rcmTest-class | 0 | 0 | 0 |
|
| splitMatchingAtBreakpoints | 0.48 | 0.02 | 0.50 |
|
| uniqGenomicInfo | 0.02 | 0.00 | 0.02 |
|