| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:26 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 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 150/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| benchdamic 1.7.0 (landing page) Matteo Calgaro
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | TIMEOUT | |||||||||
| Package: benchdamic |
| Version: 1.7.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings benchdamic_1.7.0.tar.gz |
| StartedAt: 2023-05-09 09:28:16 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 10:08:17 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 2400.8 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: benchdamic.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings benchdamic_1.7.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/benchdamic.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* 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 6.279 0.148 6.428
createConcordance 6.057 0.044 6.101
areaCAT 5.375 0.056 5.433
DA_ALDEx2 4.899 0.256 5.160
plotMD 5.025 0.044 5.069
runSplits 4.953 0.052 5.006
* 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/bbs-3.17-bioc/R/bin/R CMD INSTALL benchdamic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/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 Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
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
93.614 2.600 115.918
benchdamic.Rcheck/benchdamic-Ex.timings
| name | user | system | elapsed | |
| CAT | 0.006 | 0.000 | 0.006 | |
| DA_ALDEx2 | 4.899 | 0.256 | 5.160 | |
| DA_ANCOM | 3.359 | 0.104 | 3.463 | |
| DA_DESeq2 | 3.683 | 0.099 | 3.783 | |
| DA_MAST | 1.882 | 0.044 | 1.924 | |
| DA_NOISeq | 1.775 | 0.032 | 1.808 | |
| DA_Seurat | 0.796 | 0.008 | 0.803 | |
| DA_basic | 0.039 | 0.004 | 0.043 | |
| DA_corncob | 1.685 | 0.039 | 1.751 | |
| DA_dearseq | 0.066 | 0.004 | 0.070 | |
| DA_edgeR | 0.215 | 0.004 | 0.219 | |
| DA_limma | 0.089 | 0.000 | 0.089 | |
| DA_metagenomeSeq | 0.419 | 0.008 | 0.427 | |
| RMSE | 0.001 | 0.000 | 0.001 | |
| addKnowledge | 0.201 | 0.004 | 0.205 | |
| areaCAT | 5.375 | 0.056 | 5.433 | |
| checkNormalization | 0 | 0 | 0 | |
| createColors | 0.006 | 0.000 | 0.006 | |
| createConcordance | 6.057 | 0.044 | 6.101 | |
| createEnrichment | 0.322 | 0.004 | 0.326 | |
| createMocks | 0.003 | 0.000 | 0.003 | |
| createPositives | 1.190 | 0.008 | 1.198 | |
| createSplits | 0.036 | 0.000 | 0.037 | |
| createTIEC | 3.294 | 0.036 | 3.330 | |
| enrichmentTest | 0.141 | 0.016 | 0.156 | |
| extractDA | 0.315 | 0.020 | 0.335 | |
| extractStatistics | 0.234 | 0.000 | 0.234 | |
| fitDM | 0.041 | 0.000 | 0.041 | |
| fitHURDLE | 0.863 | 0.000 | 0.863 | |
| fitModels | 3.397 | 0.060 | 3.457 | |
| fitNB | 0.058 | 0.000 | 0.058 | |
| fitZIG | 0.068 | 0.000 | 0.068 | |
| fitZINB | 0.655 | 0.000 | 0.654 | |
| getDA | 0.100 | 0.000 | 0.101 | |
| getPositives | 0.097 | 0.004 | 0.101 | |
| getStatistics | 0.086 | 0.009 | 0.096 | |
| get_counts_metadata | 0.224 | 0.006 | 0.229 | |
| iterative_ordering | 0.010 | 0.003 | 0.013 | |
| meanDifferences | 0.002 | 0.000 | 0.003 | |
| norm_CSS | 0.092 | 0.000 | 0.092 | |
| norm_DESeq2 | 0.543 | 0.012 | 0.556 | |
| norm_TSS | 0.042 | 0.004 | 0.046 | |
| norm_edgeR | 0.052 | 0.000 | 0.052 | |
| plotConcordance | 6.279 | 0.148 | 6.428 | |
| plotContingency | 1.595 | 0.016 | 1.611 | |
| plotEnrichment | 1.516 | 0.004 | 1.520 | |
| plotFDR | 3.010 | 0.032 | 3.044 | |
| plotFPR | 3.09 | 0.04 | 3.13 | |
| plotKS | 2.931 | 0.016 | 2.948 | |
| plotLogP | 3.014 | 0.040 | 3.055 | |
| plotMD | 5.025 | 0.044 | 5.069 | |
| plotMutualFindings | 1.518 | 0.008 | 1.526 | |
| plotPositives | 1.075 | 0.004 | 1.079 | |
| plotQQ | 2.956 | 0.028 | 2.986 | |
| plotRMSE | 4.150 | 0.052 | 4.202 | |
| prepareObserved | 0.001 | 0.000 | 0.002 | |
| runDA | 0.653 | 0.036 | 0.688 | |
| runMocks | 0.962 | 0.012 | 0.975 | |
| runNormalizations | 0.615 | 0.011 | 0.625 | |
| runSplits | 4.953 | 0.052 | 5.006 | |
| setNormalizations | 0.000 | 0.000 | 0.001 | |
| set_ALDEx2 | 0.008 | 0.000 | 0.009 | |
| set_ANCOM | 0.009 | 0.000 | 0.009 | |
| set_DESeq2 | 0.01 | 0.00 | 0.01 | |
| set_MAST | 0.001 | 0.003 | 0.005 | |
| set_NOISeq | 0.005 | 0.000 | 0.004 | |
| set_Seurat | 0.008 | 0.000 | 0.008 | |
| set_basic | 0.003 | 0.000 | 0.002 | |
| set_corncob | 0.006 | 0.000 | 0.006 | |
| set_dearseq | 0.003 | 0.000 | 0.003 | |
| set_edgeR | 0.017 | 0.000 | 0.017 | |
| set_limma | 0.012 | 0.000 | 0.012 | |
| set_metagenomeSeq | 0.007 | 0.000 | 0.006 | |
| weights_ZINB | 0.580 | 0.016 | 0.596 | |