BioC 3.3: CHECK report for yaqcaffy on windows2.bioconductor.org
This page was generated on 2015-10-27 12:14:21 -0400 (Tue, 27 Oct 2015).
yaqcaffy 1.31.0
Laurent Gatto
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/yaqcaffy | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
Summary
| Package: yaqcaffy
|
| Version: 1.31.0
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| Command: rm -rf yaqcaffy.buildbin-libdir yaqcaffy.Rcheck && mkdir yaqcaffy.buildbin-libdir yaqcaffy.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=yaqcaffy.buildbin-libdir yaqcaffy_1.31.0.tar.gz >yaqcaffy.Rcheck\00install.out 2>&1 && cp yaqcaffy.Rcheck\00install.out yaqcaffy-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=yaqcaffy.buildbin-libdir --install="check:yaqcaffy-install.out" --force-multiarch --no-vignettes --timings yaqcaffy_1.31.0.tar.gz
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| StartedAt: 2015-10-27 06:56:45 -0400 (Tue, 27 Oct 2015)
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| EndedAt: 2015-10-27 06:59:53 -0400 (Tue, 27 Oct 2015)
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| EllapsedTime: 188.2 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: yaqcaffy.Rcheck
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| Warnings: 0
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Command output
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###
### Running command:
###
### rm -rf yaqcaffy.buildbin-libdir yaqcaffy.Rcheck && mkdir yaqcaffy.buildbin-libdir yaqcaffy.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=yaqcaffy.buildbin-libdir yaqcaffy_1.31.0.tar.gz >yaqcaffy.Rcheck\00install.out 2>&1 && cp yaqcaffy.Rcheck\00install.out yaqcaffy-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=yaqcaffy.buildbin-libdir --install="check:yaqcaffy-install.out" --force-multiarch --no-vignettes --timings yaqcaffy_1.31.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/yaqcaffy.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'yaqcaffy/DESCRIPTION' ... OK
* this is package 'yaqcaffy' version '1.31.0'
* 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 'yaqcaffy' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... 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 ... NOTE
'library' or 'require' calls in package code:
'MAQCsubsetAFX' 'tcltk' 'tcltk2' 'xtable'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: 'simpleaffy:::.bg.stats'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.isHgu133plus2: no visible global function definition for 'cdfName'
getBio: no visible global function definition for 'featureNames'
getDeg: no visible global function definition for 'cleancdfname'
getDeg: no visible global function definition for 'cdfName'
getDeg: no visible global function definition for 'featureNames'
getQcdefData: no visible global function definition for 'cleancdfname'
getSpk: no visible global function definition for 'featureNames'
probeSelectionInterface: no visible global function definition for
'tkmessageBox'
probeSelectionInterface: no visible global function definition for
'tktoplevel'
probeSelectionInterface: no visible global function definition for
'tkframe'
probeSelectionInterface: no visible global function definition for
'tkwm.title'
probeSelectionInterface: no visible global function definition for
'tk2notebook'
probeSelectionInterface: no visible global function definition for
'tkpack'
probeSelectionInterface: no visible global function definition for
'tk2notetab'
probeSelectionInterface: no visible global function definition for
'featureNames'
probeSelectionInterface: no visible global function definition for
'tclVar'
probeSelectionInterface: no visible global function definition for
'ttkcombobox'
probeSelectionInterface: no visible global function definition for
'tklabel'
probeSelectionInterface: no visible global function definition for
'tk2button'
probeSelectionInterface : <anonymous>: no visible global function
definition for 'tclvalue'
probeSelectionInterface : <anonymous>: no visible global function
definition for 'tkdestroy'
probeSelectionInterface: no visible global function definition for
'tkgrid'
reprodPlot: no visible global function definition for 'exprs'
reprodPlot: no visible global function definition for 'gcrma'
reprodPlot: no visible global function definition for 'mas5'
reprodPlot: no visible global function definition for 'rma'
reprodPlot: no visible global function definition for 'sampleNames'
yaqc.affy.affybatch: no visible global function definition for
'package.version'
yaqc.affy.affybatch: no visible global function definition for
'experimentData'
yaqc.affy.affybatch : <anonymous>: no visible global function
definition for 'exprs'
yaqc.affy.affybatch: no visible global function definition for
'sampleNames'
yaqc.affy.exprSet: no visible global function definition for
'package.version'
yaqc.affy.exprSet : <anonymous>: no visible global function definition
for 'exprs'
yaqc.summary: no visible global function definition for 'xtable'
Undefined global functions or variables:
cdfName cleancdfname experimentData exprs featureNames gcrma mas5
package.version rma sampleNames tclVar tclvalue tk2button tk2notebook
tk2notetab tkdestroy tkframe tkgrid tklabel tkmessageBox tkpack
tktoplevel tkwm.title ttkcombobox xtable
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [44s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getOutliers 19.10 0.74 19.97
getAllInt 5.82 0.18 6.04
** running examples for arch 'x64' ... [46s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getOutliers 20.61 0.37 20.98
getAllInt 6.29 0.17 6.47
* 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: 2 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/yaqcaffy.Rcheck/00check.log'
for details.
yaqcaffy.Rcheck/00install.out:
install for i386
* installing *source* package 'yaqcaffy' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'summary' from package 'base' in package 'yaqcaffy'
Creating a generic function for 'merge' from package 'base' in package 'yaqcaffy'
Creating a generic function for 'identical' from package 'base' in package 'yaqcaffy'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'yaqcaffy' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'yaqcaffy' as yaqcaffy_1.31.0.zip
* DONE (yaqcaffy)
yaqcaffy.Rcheck/examples_i386/yaqcaffy-Ex.timings:
| name | user | system | elapsed
|
| YaqcControlProbes-class | 0 | 0 | 0 |
|
| getAllInt | 5.82 | 0.18 | 6.04 |
|
| getBioProbes | 0.34 | 0.01 | 0.36 |
|
| getOutliers | 19.10 | 0.74 | 19.97 |
|
| getQCRatios | 4.61 | 0.26 | 4.87 |
|
| getRatioProbes | 0.47 | 0.03 | 0.50 |
|
| getSpikeProbes | 0.55 | 0.02 | 0.56 |
|
| probeSelectionInterface | 0 | 0 | 0 |
|
| reprodPlot | 0 | 0 | 0 |
|
| yaqc.affy | 4.40 | 0.06 | 4.47 |
|
| yaqc.plot | 4.66 | 0.00 | 4.66 |
|
yaqcaffy.Rcheck/examples_x64/yaqcaffy-Ex.timings:
| name | user | system | elapsed
|
| YaqcControlProbes-class | 0 | 0 | 0 |
|
| getAllInt | 6.29 | 0.17 | 6.47 |
|
| getBioProbes | 0.33 | 0.02 | 0.35 |
|
| getOutliers | 20.61 | 0.37 | 20.98 |
|
| getQCRatios | 4.61 | 0.08 | 4.69 |
|
| getRatioProbes | 0.55 | 0.00 | 0.54 |
|
| getSpikeProbes | 0.50 | 0.03 | 0.54 |
|
| probeSelectionInterface | 0 | 0 | 0 |
|
| reprodPlot | 0 | 0 | 0 |
|
| yaqc.affy | 4.60 | 0.14 | 4.74 |
|
| yaqc.plot | 4.26 | 0.08 | 4.34 |
|