| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-26 06:18:04 -0000 (Fri, 26 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4254 |
| 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 benchdamic package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/benchdamic.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 150/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| benchdamic 1.7.0 (landing page) Matteo Calgaro
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | TIMEOUT | |||||||||
| Package: benchdamic |
| Version: 1.7.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings benchdamic_1.7.0.tar.gz |
| StartedAt: 2023-05-26 03:47:26 -0000 (Fri, 26 May 2023) |
| EndedAt: 2023-05-26 04:27:26 -0000 (Fri, 26 May 2023) |
| EllapsedTime: 2400.1 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: benchdamic.Rcheck |
| Warnings: NA |
##############################################################################
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### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings benchdamic_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/benchdamic.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘benchdamic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘benchdamic’ version ‘1.7.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘benchdamic’ 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
* 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 loading without being on the library search path ... 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotConcordance 6.678 0.060 6.754
createConcordance 6.321 0.048 6.387
DA_DESeq2 5.364 0.411 5.792
areaCAT 5.632 0.036 5.680
plotMD 5.354 0.051 5.425
runSplits 5.214 0.051 5.276
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘intro.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ...
benchdamic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL benchdamic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘benchdamic’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (benchdamic)
benchdamic.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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(benchdamic)
>
> test_check("benchdamic")
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 292 ]
>
> proc.time()
user system elapsed
94.500 2.922 118.110
benchdamic.Rcheck/benchdamic-Ex.timings
| name | user | system | elapsed | |
| CAT | 0.006 | 0.000 | 0.006 | |
| DA_ALDEx2 | 4.189 | 0.492 | 4.846 | |
| DA_ANCOM | 2.128 | 0.136 | 2.272 | |
| DA_DESeq2 | 5.364 | 0.411 | 5.792 | |
| DA_MAST | 1.845 | 0.119 | 1.979 | |
| DA_NOISeq | 1.665 | 0.843 | 2.516 | |
| DA_Seurat | 0.950 | 0.035 | 1.007 | |
| DA_basic | 0.049 | 0.000 | 0.049 | |
| DA_corncob | 1.761 | 0.087 | 1.983 | |
| DA_dearseq | 0.076 | 0.000 | 0.078 | |
| DA_edgeR | 0.228 | 0.008 | 0.235 | |
| DA_limma | 0.088 | 0.012 | 0.101 | |
| DA_metagenomeSeq | 0.349 | 0.015 | 0.369 | |
| RMSE | 0.000 | 0.001 | 0.001 | |
| addKnowledge | 0.217 | 0.017 | 0.236 | |
| areaCAT | 5.632 | 0.036 | 5.680 | |
| checkNormalization | 0.001 | 0.000 | 0.000 | |
| createColors | 0.006 | 0.000 | 0.006 | |
| createConcordance | 6.321 | 0.048 | 6.387 | |
| createEnrichment | 0.351 | 0.000 | 0.352 | |
| createMocks | 0.003 | 0.000 | 0.003 | |
| createPositives | 1.144 | 0.016 | 1.162 | |
| createSplits | 0.038 | 0.000 | 0.038 | |
| createTIEC | 3.502 | 0.063 | 3.579 | |
| enrichmentTest | 0.164 | 0.009 | 0.173 | |
| extractDA | 0.262 | 0.007 | 0.270 | |
| extractStatistics | 0.250 | 0.017 | 0.266 | |
| fitDM | 0.043 | 0.000 | 0.045 | |
| fitHURDLE | 0.921 | 0.000 | 0.925 | |
| fitModels | 3.699 | 0.055 | 3.765 | |
| fitNB | 0.061 | 0.000 | 0.062 | |
| fitZIG | 0.073 | 0.000 | 0.073 | |
| fitZINB | 0.594 | 0.016 | 0.611 | |
| getDA | 0.105 | 0.012 | 0.118 | |
| getPositives | 0.115 | 0.000 | 0.115 | |
| getStatistics | 0.094 | 0.008 | 0.102 | |
| get_counts_metadata | 0.252 | 0.000 | 0.252 | |
| iterative_ordering | 0.014 | 0.000 | 0.015 | |
| meanDifferences | 0.002 | 0.000 | 0.003 | |
| norm_CSS | 0.099 | 0.000 | 0.099 | |
| norm_DESeq2 | 0.654 | 0.016 | 0.671 | |
| norm_TSS | 0.048 | 0.000 | 0.047 | |
| norm_edgeR | 0.054 | 0.000 | 0.054 | |
| plotConcordance | 6.678 | 0.060 | 6.754 | |
| plotContingency | 1.622 | 0.000 | 1.625 | |
| plotEnrichment | 1.651 | 0.008 | 1.667 | |
| plotFDR | 3.105 | 0.008 | 3.119 | |
| plotFPR | 3.060 | 0.016 | 3.083 | |
| plotKS | 3.124 | 0.004 | 3.137 | |
| plotLogP | 3.266 | 0.036 | 3.309 | |
| plotMD | 5.354 | 0.051 | 5.425 | |
| plotMutualFindings | 1.678 | 0.016 | 1.698 | |
| plotPositives | 1.078 | 0.012 | 1.093 | |
| plotQQ | 3.112 | 0.004 | 3.121 | |
| plotRMSE | 4.541 | 0.032 | 4.581 | |
| prepareObserved | 0.002 | 0.000 | 0.002 | |
| runDA | 0.725 | 0.000 | 0.728 | |
| runMocks | 1.041 | 0.004 | 1.047 | |
| runNormalizations | 0.663 | 0.008 | 0.673 | |
| runSplits | 5.214 | 0.051 | 5.276 | |
| setNormalizations | 0.000 | 0.000 | 0.001 | |
| set_ALDEx2 | 0.009 | 0.000 | 0.010 | |
| set_ANCOM | 0.011 | 0.000 | 0.013 | |
| set_DESeq2 | 0.008 | 0.003 | 0.012 | |
| set_MAST | 0.005 | 0.000 | 0.005 | |
| set_NOISeq | 0.005 | 0.000 | 0.005 | |
| set_Seurat | 0.009 | 0.000 | 0.009 | |
| set_basic | 0.002 | 0.000 | 0.002 | |
| set_corncob | 0.006 | 0.000 | 0.006 | |
| set_dearseq | 0.003 | 0.000 | 0.003 | |
| set_edgeR | 0.018 | 0.000 | 0.018 | |
| set_limma | 0.012 | 0.000 | 0.012 | |
| set_metagenomeSeq | 0.008 | 0.000 | 0.008 | |
| weights_ZINB | 0.612 | 0.012 | 0.624 | |