Bernd Fischer
| Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021) |
| URL: https://git.bioconductor.org/packages/HD2013SGI |
| Branch: master |
| Last Commit: 8971f18 |
| Last Changed Date: 2020-10-27 10:01:22 -0500 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.13 experimental data |
|
This page was generated on 2021-01-14 15:59:08 -0500 (Thu, 14 Jan 2021).
| TO THE DEVELOPERS/MAINTAINERS OF THE HD2013SGI PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 163/385 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
| HD2013SGI 1.31.0 Bernd Fischer
| malbec2 | Linux (Ubuntu 20.04.1 LTS) / x86_64 | OK | OK | OK | | |||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | [ OK ] |
| Package: HD2013SGI |
| Version: 1.31.0 |
| Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HD2013SGI.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings HD2013SGI_1.31.0.tar.gz |
| StartedAt: 2021-01-14 11:22:31 -0500 (Thu, 14 Jan 2021) |
| EndedAt: 2021-01-14 11:26:30 -0500 (Thu, 14 Jan 2021) |
| EllapsedTime: 239.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: HD2013SGI.Rcheck |
| Warnings: 0 |
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### Running command:
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### D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HD2013SGI.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings HD2013SGI_1.31.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/HD2013SGI.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HD2013SGI/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HD2013SGI' version '1.31.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'RColorBrewer', 'gplots', 'geneplotter', 'splots', 'limma', 'vcd',
'LSD', 'EBImage'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'HD2013SGI' can be installed ... OK
* checking installed package size ... NOTE
installed size is 525.3Mb
sub-directories of 1Mb or more:
data 524.1Mb
* 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:
'EBImage' 'LSD' 'RColorBrewer' 'geneplotter' 'gplots' 'limma'
'splots' 'vcd'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'humanReadableNames'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
HD2013SGIHeatmapHuman: no visible global function definition for 'unit'
HD2013SGIHeatmapHuman: no visible global function definition for
'pushViewport'
HD2013SGIHeatmapHuman: no visible global function definition for
'viewport'
HD2013SGIHeatmapHuman: no visible global function definition for
'grid.layout'
HD2013SGIHeatmapHuman: no visible global function definition for
'grid.rect'
HD2013SGIHeatmapHuman: no visible global function definition for
'grid.raster'
HD2013SGIHeatmapHuman: no visible global function definition for
'popViewport'
HD2013SGIHeatmapHuman: no visible global function definition for
'grid.text'
HD2013SGIHeatmapHuman: no visible global function definition for 'gpar'
HD2013SGImaineffects: no visible binding for global variable 'median'
HD2013SGImaineffects : <anonymous>: no visible binding for global
variable 'median'
HD2013SGImaineffects: no visible global function definition for
'median'
HD2013SGIorderDim: no visible global function definition for 'cor'
HD2013SGIorderDim: no visible global function definition for 'hclust'
HD2013SGIorderDim: no visible global function definition for 'as.dist'
HD2013SGIselectByStability: no visible global function definition for
'lm'
HD2013SGIselectByStability : <anonymous>: no visible global function
definition for 'cor'
plotExampleInteractions: no visible binding for global variable 'sd'
plotExampleInteractions: no visible global function definition for
'par'
plotExampleInteractions: no visible global function definition for
'barplot'
plotExampleInteractions: no visible global function definition for
'abline'
plotExampleInteractions: no visible global function definition for
'points'
plotExampleInteractions: no visible global function definition for
'text'
plotExampleSingleGeneEffects: no visible global function definition for
'mad'
plotExampleSingleGeneEffects: no visible global function definition for
'par'
plotExampleSingleGeneEffects: no visible global function definition for
'barplot'
plotExampleSingleGeneEffects: no visible global function definition for
'abline'
plotExampleSingleGeneEffects: no visible global function definition for
'points'
Undefined global functions or variables:
abline as.dist barplot cor gpar grid.layout grid.raster grid.rect
grid.text hclust lm mad median par points popViewport pushViewport sd
text unit viewport
Consider adding
importFrom("graphics", "abline", "barplot", "par", "points", "text")
importFrom("stats", "as.dist", "cor", "hclust", "lm", "mad", "median",
"sd")
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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
featuresPerWell 37.88 0.50 38.37
datamatrixfull 8.43 0.11 8.57
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
featuresPerWell 29.35 0.45 29.81
datamatrixfull 6.60 0.11 6.71
* 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: 4 NOTEs
See
'D:/biocbuild/bbs-3.13-data-experiment/meat/HD2013SGI.Rcheck/00check.log'
for details.
HD2013SGI.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/HD2013SGI_1.31.0.tar.gz && rm -rf HD2013SGI.buildbin-libdir && mkdir HD2013SGI.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HD2013SGI.buildbin-libdir HD2013SGI_1.31.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL HD2013SGI_1.31.0.zip && rm HD2013SGI_1.31.0.tar.gz HD2013SGI_1.31.0.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
10 524M 10 54.2M 0 0 61.6M 0 0:00:08 --:--:-- 0:00:08 61.6M
30 524M 30 157M 0 0 85.1M 0 0:00:06 0:00:01 0:00:05 85.1M
48 524M 48 255M 0 0 78.8M 0 0:00:06 0:00:03 0:00:03 78.8M
62 524M 62 327M 0 0 84.8M 0 0:00:06 0:00:03 0:00:03 84.8M
83 524M 83 438M 0 0 90.3M 0 0:00:05 0:00:04 0:00:01 90.3M
100 524M 100 524M 0 0 92.9M 0 0:00:05 0:00:05 --:--:-- 98.7M
install for i386
* installing *source* package 'HD2013SGI' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'HD2013SGI'
finding HTML links ... done
HD2013SGI-package html
REDIRECT:topic HD2013SGI-package -> HD2013SGI-package.html [ SUCCESS ]
REDIRECT:topic HD2013SGI -> HD2013SGI-package.html [ SUCCESS ]
HD2013SGIHeatmapHuman html
REDIRECT:topic HD2013SGIHeatmapHuman -> HD2013SGIHeatmapHuman.html [ SUCCESS ]
HD2013SGImaineffects html
REDIRECT:topic HD2013SGImaineffects -> HD2013SGImaineffects.html [ SUCCESS ]
HD2013SGIorderDim html
REDIRECT:topic HD2013SGIorderDim -> HD2013SGIorderDim.html [ SUCCESS ]
HD2013SGIselectByStability html
REDIRECT:topic HD2013SGIselectByStability -> HD2013SGIselectByStability.html [ SUCCESS ]
Interactions html
REDIRECT:topic Interactions -> Interactions.html [ SUCCESS ]
QueryAnnotation html
REDIRECT:topic QueryAnnotation -> QueryAnnotation.html [ SUCCESS ]
TargetAnnotation html
REDIRECT:topic TargetAnnotation -> TargetAnnotation.html [ SUCCESS ]
datamatrix html
REDIRECT:topic datamatrix -> datamatrix.html [ SUCCESS ]
datamatrixfull html
REDIRECT:topic datamatrixfull -> datamatrixfull.html [ SUCCESS ]
featuresPerWell html
REDIRECT:topic featuresPerWell -> featuresPerWell.html [ SUCCESS ]
mainEffects html
REDIRECT:topic mainEffects -> mainEffects.html [ SUCCESS ]
nrOfInteractionsPerTarget html
REDIRECT:topic nrOfInteractionsPerTarget -> nrOfInteractionsPerTarget.html [ SUCCESS ]
stabilitySelection html
REDIRECT:topic stabilitySelection -> stabilitySelection.html [ SUCCESS ]
** 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 'HD2013SGI' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HD2013SGI' as HD2013SGI_1.31.0.zip
* DONE (HD2013SGI)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'HD2013SGI' successfully unpacked and MD5 sums checked
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HD2013SGI.Rcheck/examples_i386/HD2013SGI-Ex.timings
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HD2013SGI.Rcheck/examples_x64/HD2013SGI-Ex.timings
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