Florian Hahne
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/prada |
| Branch: master |
| Last Commit: 5a2d974 |
| Last Changed Date: 2019-01-04 10:41:32 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:53:52 -0400 (Tue, 09 Apr 2019).
| Package 1215/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| prada 1.59.1 Florian Hahne
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: prada |
| Version: 1.59.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:prada.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings prada_1.59.1.tar.gz |
| StartedAt: 2019-04-09 05:01:59 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 05:03:14 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 74.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: prada.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:prada.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings prada_1.59.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/prada.Rcheck' * using R Under development (unstable) (2019-03-09 r76216) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'prada/DESCRIPTION' ... OK * this is package 'prada' version '1.59.1' * 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 'prada' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMnpapD/R.INSTALL135821ab3f49/prada/man/cytoSet-class.Rd:88: file link 'phenoData-class' in package 'Biobase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMnpapD/R.INSTALL135821ab3f49/prada/man/readCytoSet.Rd:11: file link 'dir' in package 'base' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/prada.Rcheck/00install.out' for details. * 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' 'grid' 'methods' 'RColorBrewer' 'rrcov' 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 'library' or 'require' call to 'tcltk' in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE analysePlate: no visible binding for global variable 'dat' gatePoints: no visible binding for global variable 'prev' killProgress: no visible binding for global variable '.tkprogress.canceled' killProgress: no visible global function definition for 'tkdestroy' killProgress: no visible binding for global variable '.tkprogress.window' progress: no visible global function definition for 'tktoplevel' progress: no visible global function definition for 'tclVar' progress: no visible global function definition for 'tkwm.geometry' progress: no visible binding for global variable '.tkprogress.window' progress: no visible global function definition for 'tkwm.title' progress: no visible global function definition for 'tkconfigure' progress: no visible global function definition for 'tkframe' progress: no visible global function definition for 'tkfont.create' progress: no visible binding for '<<-' assignment to '.tkprogress.labelText' progress: no visible binding for global variable '.tkprogress.labelText' progress: no visible global function definition for 'tclvalue<-' progress: no visible global function definition for 'tklabel' progress: no visible global function definition for 'tclvalue' progress: no visible global function definition for 'tkgrid' progress: no visible global function definition for 'tclRequire' progress: no visible global function definition for 'tkwidget' progress: no visible binding for global variable '.tkprogress.iterator' progress: no visible binding for global variable '.tkprogress.fallbackIterator' progress: no visible global function definition for 'tkbind' progress : <anonymous>: no visible binding for '<<-' assignment to '.tkprogress.canceled' updateProgress: no visible binding for '<<-' assignment to '.tkprogress.iterator' updateProgress: no visible binding for global variable '.tkprogress.iterator' updateProgress: no visible global function definition for 'tclvalue<-' updateProgress: no visible binding for '<<-' assignment to '.tkprogress.fallbackIterator' updateProgress: no visible binding for global variable '.tkprogress.fallbackIterator' updateProgress: no visible binding for '<<-' assignment to '.tkprogress.labelText' updateProgress: no visible binding for global variable '.tkprogress.labelText' updateProgress: no visible global function definition for 'tcl' Undefined global functions or variables: .tkprogress.canceled .tkprogress.fallbackIterator .tkprogress.iterator .tkprogress.labelText .tkprogress.window dat prev tcl tclRequire tclVar tclvalue tclvalue<- tkbind tkconfigure tkdestroy tkfont.create tkframe tkgrid tklabel tktoplevel tkwidget tkwm.geometry tkwm.title * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/prada/libs/i386/prada.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/prada/libs/x64/prada.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... 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: 1 WARNING, 4 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/prada.Rcheck/00check.log' for details.
prada.Rcheck/00install.out
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/prada_1.59.1.tar.gz && rm -rf prada.buildbin-libdir && mkdir prada.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=prada.buildbin-libdir prada_1.59.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL prada_1.59.1.zip && rm prada_1.59.1.tar.gz prada_1.59.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'prada' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c inPolygon.c -o inPolygon.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o prada.dll tmp.def inPolygon.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/prada.buildbin-libdir/00LOCK-prada/00new/prada/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'prada'
finding HTML links ... done
analysePlate html
as.all html
barploterrbar html
combineFrames html
csApply html
cytoFrame-class html
cytoSet-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMnpapD/R.INSTALL135821ab3f49/prada/man/cytoSet-class.Rd:88: file link 'phenoData-class' in package 'Biobase' does not exist and so has been treated as a topic
data-cytoFrame html
data-cytoSet html
devDims html
devRes html
fitNorm2 html
gate-class html
gateSet-class html
getAlphaNumeric html
getPradaPar html
new-internal html
plotNorm2 html
plotPlate html
readCytoSet html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMnpapD/R.INSTALL135821ab3f49/prada/man/readCytoSet.Rd:11: file link 'dir' in package 'base' does not exist and so has been treated as a topic
readFCS html
readFCSaux html
removeCensored html
tcltkProgress html
threePanelPlot html
thresholds html
touchFCS html
vpLocation html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'prada' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c inPolygon.c -o inPolygon.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o prada.dll tmp.def inPolygon.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/prada.buildbin-libdir/prada/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'prada' as prada_1.59.1.zip
* DONE (prada)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'prada' successfully unpacked and MD5 sums checked
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prada.Rcheck/examples_i386/prada-Ex.timings
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prada.Rcheck/examples_x64/prada-Ex.timings
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