Laurent Gatto
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/yaqcaffy |
| Branch: RELEASE_3_7 |
| Last Commit: 0c78f8f |
| Last Changed Date: 2018-04-30 10:35:08 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:33:36 -0400 (Wed, 17 Oct 2018).
| Package 1557/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| yaqcaffy 1.40.0 Laurent Gatto
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: yaqcaffy |
| Version: 1.40.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:yaqcaffy.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings yaqcaffy_1.40.0.tar.gz |
| StartedAt: 2018-10-17 05:28:06 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 05:33:00 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 293.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: yaqcaffy.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:yaqcaffy.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings yaqcaffy_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/yaqcaffy.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.40.0'
* 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 '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'
.mergeAffyBatchObjects: no visible global function definition for
'data'
.mergeAffyBatchObjects: no visible binding for global variable 'refA'
.mergeAffyBatchObjects: no visible binding for global variable 'refB'
.mergeAffyBatchObjects: no visible binding for global variable 'refC'
.mergeAffyBatchObjects: no visible binding for global variable 'refD'
.plotBioQC: no visible global function definition for 'boxplot'
.plotBioQC: no visible global function definition for 'text'
.plotBioQC: no visible global function definition for 'sd'
.plotBioQC: no visible global function definition for 'legend'
.plotSfs: no visible global function definition for 'dotchart'
.plotSfs: no visible global function definition for 'abline'
.plotSfs: no visible global function definition for 'mtext'
.plotSfs: no visible global function definition for 'sd'
.plotSpikesQC: no visible global function definition for 'boxplot'
.plotSpikesQC: no visible global function definition for 'text'
.plotSpikesQC: no visible global function definition for 'sd'
.plotSpikesQC: no visible global function definition for 'legend'
.plotdata: no visible global function definition for 'boxplot'
.plotdata: no visible global function definition for 'text'
.plotdata: no visible global function definition for 'abline'
.plotdata: no visible global function definition for 'qnorm'
.plotdata: no visible global function definition for 'sd'
.plotdata: no visible global function definition for 'mtext'
.plotdiag: no visible global function definition for 'abline'
.plotrectangle: no visible global function definition for 'sd'
.plotrectangle: no visible global function definition for 'qnorm'
.plotrectangle: no visible global function definition for 'rect'
.plotrectangle: no visible global function definition for 'segments'
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'
getOutliers: no visible global function definition for 'qnorm'
getOutliers: no visible global function definition for 'sd'
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'
reprodPlot: no visible global function definition for 'par'
reprodPlot: no visible global function definition for 'text'
reprodPlot: no visible global function definition for 'smoothScatter'
reprodPlot: no visible global function definition for 'mtext'
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.plot.all: no visible global function definition for 'par'
yaqc.plot.all: no visible global function definition for 'layout'
yaqc.plot.part: no visible global function definition for 'layout'
yaqc.summary: no visible global function definition for 'xtable'
Undefined global functions or variables:
abline boxplot cdfName cleancdfname data dotchart experimentData
exprs featureNames gcrma layout legend mas5 mtext package.version par
qnorm rect refA refB refC refD rma sampleNames sd segments
smoothScatter tclVar tclvalue text tk2button tk2notebook tk2notetab
tkdestroy tkframe tkgrid tklabel tkmessageBox tkpack tktoplevel
tkwm.title ttkcombobox xtable
Consider adding
importFrom("graphics", "abline", "boxplot", "dotchart", "layout",
"legend", "mtext", "par", "rect", "segments",
"smoothScatter", "text")
importFrom("stats", "qnorm", "sd")
importFrom("utils", "data")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getOutliers 23.12 1.49 44.66
getQCRatios 6.19 0.31 7.03
getAllInt 5.92 0.48 6.40
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getOutliers 19.07 0.51 19.57
getAllInt 6.23 0.22 6.46
* 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:/Users/biocbuild/bbs-3.7-bioc/meat/yaqcaffy.Rcheck/00check.log'
for details.
yaqcaffy.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/yaqcaffy_1.40.0.tar.gz && rm -rf yaqcaffy.buildbin-libdir && mkdir yaqcaffy.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=yaqcaffy.buildbin-libdir yaqcaffy_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL yaqcaffy_1.40.0.zip && rm yaqcaffy_1.40.0.tar.gz yaqcaffy_1.40.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'yaqcaffy' ...
** R
** byte-compile and prepare package for lazy loading
Creating a generic function for 'identical' from package 'base' in package 'yaqcaffy'
** help
*** installing help indices
converting help for package 'yaqcaffy'
finding HTML links ... done
YAQCStats-class html
finding level-2 HTML links ... done
YaqcControlProbes-class html
getAllInt html
getBioProbes html
getOutliers html
getQCRatios html
getRatioProbes html
getSpikeProbes html
probeSelectionInterface html
reprodPlot html
yaqc.affy html
yaqc.plot html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'yaqcaffy' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'yaqcaffy' as yaqcaffy_1.40.0.zip
* DONE (yaqcaffy)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'yaqcaffy' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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yaqcaffy.Rcheck/examples_i386/yaqcaffy-Ex.timings
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yaqcaffy.Rcheck/examples_x64/yaqcaffy-Ex.timings
|