| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:29 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
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To the developers/maintainers of the Dune package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Dune.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 550/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Dune 1.6.0 (landing page) Hector Roux de Bezieux
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Dune |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Dune.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Dune_1.6.0.tar.gz |
| StartedAt: 2022-04-12 18:56:31 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 19:04:32 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 480.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Dune.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Dune.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Dune_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Dune.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Dune/DESCRIPTION' ... OK
* this is package 'Dune' version '1.6.0'
* package encoding: UTF-8
* 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 'Dune' 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
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.metricTrend: no visible binding for global variable '.'
.metricTrend: no visible binding for global variable 'step'
.metricTrend: no visible binding for global variable 'change'
.metricTrend: no visible binding for global variable 'value'
.plotMetric: no visible binding for global variable 'label2'
.plotMetric: no visible binding for global variable 'metric'
.plotMetric: no visible binding for global variable 'label1'
ARIImp : f: no visible binding for global variable 'cells'
ConfusionEvolution : <anonymous>: no visible binding for global
variable 'Freq'
ConfusionEvolution : <anonymous>: no visible binding for global
variable 'total_x'
ConfusionEvolution : <anonymous>: no visible binding for global
variable 'total_y'
ConfusionEvolution: no visible binding for global variable 'overlap'
ConfusionEvolution: no visible binding for global variable 'Freq'
ConfusionEvolution: no visible binding for global variable 'step'
ConfusionPlot: no visible binding for global variable 'Freq'
ConfusionPlot: no visible binding for global variable 'total_x'
ConfusionPlot: no visible binding for global variable 'total_y'
ConfusionPlot: no visible binding for global variable 'overlap'
NMIImp : f: no visible binding for global variable 'cells'
intermediateMat: no visible binding for global variable 'cells'
plotPrePost: no visible binding for global variable 'Nb'
Undefined global functions or variables:
. Freq Nb cells change label1 label2 metric overlap step total_x
total_y value
Consider adding
importFrom("stats", "step")
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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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
Dune 6.25 0 6.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Dune 7.28 0 7.28
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/Dune.Rcheck/00check.log'
for details.
Dune.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Dune_1.6.0.tar.gz && rm -rf Dune.buildbin-libdir && mkdir Dune.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Dune.buildbin-libdir Dune_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Dune_1.6.0.zip && rm Dune_1.6.0.tar.gz Dune_1.6.0.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
24 3895k 24 952k 0 0 963k 0 0:00:04 --:--:-- 0:00:04 963k
72 3895k 72 2840k 0 0 1410k 0 0:00:02 0:00:02 --:--:-- 1411k
100 3895k 100 3895k 0 0 1606k 0 0:00:02 0:00:02 --:--:-- 1607k
install for i386
* installing *source* package 'Dune' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Dune'
finding HTML links ... done
ARIImp html
ARIs html
ARItrend html
finding level-2 HTML links ... done
ConfusionEvolution html
ConfusionPlot html
Dune html
NMIImp html
NMIs html
NMItrend html
clusMat html
clusterConversion html
dot-adjustedRandIndex html
functionTracking html
intermediateMat html
nuclei html
plotARIs html
plotNMIs html
plotPrePost html
whenToStop 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 'Dune' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Dune' as Dune_1.6.0.zip
* DONE (Dune)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'Dune' successfully unpacked and MD5 sums checked
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Dune.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Dune)
Dune now uses the Normalized Mutual Informationinstead of the adjusted Rand Index. You can restore the old option bysetting metric'ARI' in the Dune function.
>
> test_check("Dune")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 452 ]
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 452 ]
>
> proc.time()
user system elapsed
73.09 0.79 73.95
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Dune.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Dune)
Dune now uses the Normalized Mutual Informationinstead of the adjusted Rand Index. You can restore the old option bysetting metric'ARI' in the Dune function.
>
> test_check("Dune")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 452 ]
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 452 ]
>
> proc.time()
user system elapsed
80.06 0.65 80.84
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Dune.Rcheck/examples_i386/Dune-Ex.timings
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Dune.Rcheck/examples_x64/Dune-Ex.timings
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