Ilyess Rachedi
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/conclus |
| git_branch: RELEASE_3_14 |
| git_last_commit: 4f3d751 |
| git_last_commit_date: 2022-04-08 16:47:00 -0400 (Fri, 08 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:22 -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 | ||||
|
To the developers/maintainers of the conclus package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/conclus.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 382/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| conclus 1.2.4 (landing page) Ilyess Rachedi
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: conclus |
| Version: 1.2.4 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:conclus.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings conclus_1.2.4.tar.gz |
| StartedAt: 2022-04-12 17:48:07 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 18:08:36 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 1228.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: conclus.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:conclus.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings conclus_1.2.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/conclus.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 'conclus/DESCRIPTION' ... OK
* this is package 'conclus' version '1.2.4'
* 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 'conclus' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 (user + system) or elapsed time > 5s
user system elapsed
runCONCLUS 19.48 0.28 99.75
addClustering-scRNAseq 11.44 0.64 49.70
retrieveGenesInfo-scRNAseq 9.92 0.14 60.19
normaliseCountMatrix-scRNAseq 9.28 0.05 23.13
retrieveFromGEO 8.68 0.58 9.53
testClustering-scRNAseq 1.00 0.02 16.79
clusterCellsInternal-scRNAseq 0.37 0.06 14.46
runDBSCAN-scRNAseq 0.28 0.01 14.69
generateTSNECoordinates-scRNAseq 0.20 0.00 18.99
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runCONCLUS 20.83 0.17 93.86
addClustering-scRNAseq 9.98 0.45 28.21
retrieveFromGEO 9.98 0.19 10.17
retrieveGenesInfo-scRNAseq 9.58 0.14 21.69
normaliseCountMatrix-scRNAseq 7.31 0.06 20.86
testClustering-scRNAseq 1.00 0.04 19.94
runDBSCAN-scRNAseq 0.50 0.01 17.01
clusterCellsInternal-scRNAseq 0.33 0.03 16.45
generateTSNECoordinates-scRNAseq 0.25 0.00 22.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-all.R'
OK
** running tests for arch 'x64' ...
Running 'test-all.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: OK
conclus.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/conclus_1.2.4.tar.gz && rm -rf conclus.buildbin-libdir && mkdir conclus.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=conclus.buildbin-libdir conclus_1.2.4.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL conclus_1.2.4.zip && rm conclus_1.2.4.tar.gz conclus_1.2.4.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
0 1448k 0 5187 0 0 62930 0 0:00:23 --:--:-- 0:00:23 63256
91 1448k 91 1318k 0 0 1220k 0 0:00:01 0:00:01 --:--:-- 1220k
100 1448k 100 1448k 0 0 1255k 0 0:00:01 0:00:01 --:--:-- 1255k
install for i386
* installing *source* package 'conclus' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'conclus'
finding HTML links ... done
Dbscan-class html
Tsne-class html
addClustering-scRNAseq html
calculateClustersSimilarity-scRNAseq html
clusterCellsInternal-scRNAseq html
conclusCacheClear html
constructors html
exportResults-scRNAseq html
generateTSNECoordinates-scRNAseq html
getters html
loadDataOrMatrix html
normaliseCountMatrix-scRNAseq html
plotCellHeatmap html
plotCellSimilarity-scRNAseq html
plotClusteredTSNE-scRNAseq html
plotClustersSimilarity html
plotGeneExpression-scRNAseq html
rankGenes-scRNAseq html
retrieveFromGEO html
retrieveGenesInfo-scRNAseq html
retrieveTableClustersCells-scRNAseq html
retrieveTopClustersMarkers-scRNAseq html
runCONCLUS html
runDBSCAN-scRNAseq html
scRNAseq-class html
setters html
testClustering-scRNAseq 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 'conclus' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'conclus' as conclus_1.2.4.zip
* DONE (conclus)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'conclus' successfully unpacked and MD5 sums checked
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conclus.Rcheck/tests_i386/test-all.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("conclus")
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> test_check("conclus")
Min. 1st Qu. Median Mean 3rd Qu. Max.
1 1 1 1 1 1
The following matrix shows how many times a number of clusters 'k' has been found among the dbscan solutions :
1 2 3 4 5
Number of clusters k : 1 2 3 4 5
Count : 56 10 10 4 4
Statistics about number of clusters 'k' among dbscan solutions:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1.00 1.00 1.00 1.69 2.00 5.00
Suggested clusters number to use in clusterCellsInternal() : clusterNumber=1.[ FAIL 0 | WARN 0 | SKIP 0 | PASS 278 ]
>
> proc.time()
user system elapsed
59.28 1.98 144.82
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conclus.Rcheck/tests_x64/test-all.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("conclus")
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> test_check("conclus")
Min. 1st Qu. Median Mean 3rd Qu. Max.
1 1 1 1 1 1
The following matrix shows how many times a number of clusters 'k' has been found among the dbscan solutions :
1 2 3 4 5
Number of clusters k : 1 2 3 4 5
Count : 56 10 10 4 4
Statistics about number of clusters 'k' among dbscan solutions:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1.00 1.00 1.00 1.69 2.00 5.00
Suggested clusters number to use in clusterCellsInternal() : clusterNumber=1.[ FAIL 0 | WARN 0 | SKIP 0 | PASS 278 ]
>
> proc.time()
user system elapsed
50.57 1.56 145.25
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conclus.Rcheck/examples_i386/conclus-Ex.timings
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conclus.Rcheck/examples_x64/conclus-Ex.timings
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