Zhenyu Xu
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/tilingArray |
| Branch: RELEASE_3_12 |
| Last Commit: 93ea2a8 |
| Last Changed Date: 2020-10-27 10:25:35 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:33:58 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the tilingArray package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1860/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| tilingArray 1.68.0 (landing page) Zhenyu Xu
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: tilingArray |
| Version: 1.68.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tilingArray.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings tilingArray_1.68.0.tar.gz |
| StartedAt: 2021-05-06 07:31:55 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 07:35:09 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 194.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: tilingArray.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tilingArray.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings tilingArray_1.68.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/tilingArray.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'tilingArray/DESCRIPTION' ... OK
* this is package 'tilingArray' version '1.68.0'
* 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 'tilingArray' 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
Packages in Depends field not imported from:
'Biobase' 'pixmap'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.onAttach: no visible global function definition for 'addVigs2WinMenu'
comparisonPlot : myColors: no visible global function definition for
'quantile'
grid.image: no visible global function definition for 'colorRamp'
grid.image: no visible global function definition for 'rgb'
interpolateZ: no visible global function definition for 'approx'
matDensities : densXY: no visible global function definition for
'density'
myPixmap: no visible global function definition for 'pixmapGrey'
myWrite: no visible global function definition for 'write.pnm'
normalizeByReference: no visible global function definition for 'exprs'
normalizeByReference: no visible global function definition for
'quantile'
normalizeByReference: no visible global function definition for
'approxfun'
normalizeByReference: no visible global function definition for 'pdf'
normalizeByReference: no visible global function definition for
'smoothScatter'
normalizeByReference: no visible global function definition for 'lines'
normalizeByReference: no visible global function definition for
'dev.off'
normalizeByReference: no visible global function definition for
'exprs<-'
plotAlongChrom: no visible global function definition for 'colorRamp'
plotAlongChrom: no visible global function definition for 'quantile'
plotFeatures: no visible global function definition for 'listLen'
plotPenLL: no visible binding for global variable 'quantile'
plotPenLL: no visible global function definition for 'matplot'
plotPenLL: no visible global function definition for 'segments'
plotPenLL: no visible global function definition for 'legend'
plotSegmentationDots: no visible global function definition for
'quantile'
plotSegmentationHeatmap: no visible global function definition for
'colorRamp'
plotSegmentationHeatmap: no visible global function definition for
'quantile'
qcPlots: no visible global function definition for 'pData'
qcPlots: no visible global function definition for 'exprs'
qcPlots: no visible global function definition for 'png'
qcPlots: no visible global function definition for 'boxplot'
qcPlots: no visible global function definition for 'dev.off'
qcPlots: no visible global function definition for 'matplot'
qcPlots: no visible global function definition for 'jpeg'
raster.image: no visible global function definition for 'colorRamp'
raster.image: no visible global function definition for 'rgb'
readCel2eSet: no visible global function definition for 'varLabels'
segChrom: no visible global function definition for 'exprs'
plot,segmentation-ANY: no visible global function definition for 'note'
plot,segmentation-ANY: no visible global function definition for
'plot.default'
plot,segmentation-ANY: no visible global function definition for
'abline'
plot,segmentation-ANY: no visible global function definition for
'mtext'
Undefined global functions or variables:
abline addVigs2WinMenu approx approxfun boxplot colorRamp density
dev.off exprs exprs<- jpeg legend lines listLen matplot mtext note
pData pdf pixmapGrey plot.default png quantile rgb segments
smoothScatter varLabels write.pnm
Consider adding
importFrom("grDevices", "colorRamp", "dev.off", "jpeg", "pdf", "png",
"rgb")
importFrom("graphics", "abline", "boxplot", "legend", "lines",
"matplot", "mtext", "plot.default", "segments",
"smoothScatter")
importFrom("stats", "approx", "approxfun", "density", "quantile")
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 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... 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-3.12-bioc/R/library/tilingArray/libs/i386/tilingArray.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/tilingArray/libs/x64/tilingArray.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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/tilingArray.Rcheck/00check.log'
for details.
tilingArray.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/tilingArray_1.68.0.tar.gz && rm -rf tilingArray.buildbin-libdir && mkdir tilingArray.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=tilingArray.buildbin-libdir tilingArray_1.68.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL tilingArray_1.68.0.zip && rm tilingArray_1.68.0.tar.gz tilingArray_1.68.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1160k 100 1160k 0 0 2523k 0 --:--:-- --:--:-- --:--:-- 2532k
install for i386
* installing *source* package 'tilingArray' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c findsegments.c -o findsegments.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sampleStep.c -o sampleStep.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o tilingArray.dll tmp.def findsegments.o sampleStep.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/tilingArray.buildbin-libdir/00LOCK-tilingArray/00new/tilingArray/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'tilingArray'
finding HTML links ... done
PMindex html
breakpointsPretend html
class-segmentation html
comparisonPlot html
costMatrix html
findsegments html
gffSub html
normalizeByReference html
otherStrand html
plotAlongChrom html
plotAlongChromLegend html
plotFeatures html
plotSegmentationDots html
plotSegmentationHeatmap html
plotpenLL html
posMin html
qcPlots html
readCel2eSet html
sampleStep html
segChrom html
segment html
segnf html
tilingArray-package 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 'tilingArray' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c findsegments.c -o findsegments.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sampleStep.c -o sampleStep.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o tilingArray.dll tmp.def findsegments.o sampleStep.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/tilingArray.buildbin-libdir/tilingArray/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'tilingArray' as tilingArray_1.68.0.zip
* DONE (tilingArray)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'tilingArray' successfully unpacked and MD5 sums checked
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tilingArray.Rcheck/examples_i386/tilingArray-Ex.timings
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tilingArray.Rcheck/examples_x64/tilingArray-Ex.timings
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