| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:34 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 153/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| benchdamic 1.5.2 (landing page) Matteo Calgaro
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: benchdamic |
| Version: 1.5.2 |
| 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_1.5.2.tar.gz |
| StartedAt: 2023-04-12 04:52:02 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 05:24:36 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 1953.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: benchdamic.Rcheck |
| Warnings: 0 |
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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_1.5.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/benchdamic.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘benchdamic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘benchdamic’ version ‘1.5.2’
* 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
* 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 ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
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/site-library’ * installing *source* package ‘benchdamic’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 1 | SKIP 0 | PASS 292 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 292 ]
>
> proc.time()
user system elapsed
69.659 3.515 87.846
benchdamic.Rcheck/benchdamic-Ex.timings
| name | user | system | elapsed | |
| CAT | 0.005 | 0.000 | 0.005 | |
| DA_ALDEx2 | 3.619 | 0.116 | 3.736 | |
| DA_ANCOM | 1.414 | 0.080 | 1.495 | |
| DA_DESeq2 | 4.001 | 0.096 | 4.097 | |
| DA_MAST | 0.582 | 0.012 | 0.594 | |
| DA_NOISeq | 1.512 | 0.048 | 1.561 | |
| DA_Seurat | 0.777 | 0.004 | 0.781 | |
| DA_basic | 0.028 | 0.000 | 0.027 | |
| DA_corncob | 1.116 | 0.012 | 1.137 | |
| DA_dearseq | 0.140 | 0.004 | 0.144 | |
| DA_edgeR | 0.160 | 0.000 | 0.161 | |
| DA_limma | 0.065 | 0.000 | 0.066 | |
| DA_metagenomeSeq | 0.257 | 0.000 | 0.256 | |
| RMSE | 0.001 | 0.000 | 0.000 | |
| addKnowledge | 0.159 | 0.000 | 0.158 | |
| areaCAT | 3.729 | 0.048 | 3.776 | |
| checkNormalization | 0.001 | 0.000 | 0.000 | |
| createColors | 0.005 | 0.000 | 0.004 | |
| createConcordance | 4.276 | 0.072 | 4.348 | |
| createEnrichment | 0.242 | 0.000 | 0.241 | |
| createMocks | 0.002 | 0.001 | 0.002 | |
| createPositives | 0.783 | 0.006 | 0.790 | |
| createSplits | 0.028 | 0.000 | 0.028 | |
| createTIEC | 2.520 | 0.044 | 2.564 | |
| enrichmentTest | 0.152 | 0.000 | 0.152 | |
| extractDA | 0.168 | 0.000 | 0.168 | |
| extractStatistics | 0.166 | 0.000 | 0.167 | |
| fitDM | 0.029 | 0.000 | 0.029 | |
| fitHURDLE | 0.353 | 0.004 | 0.357 | |
| fitModels | 1.231 | 0.036 | 1.266 | |
| fitNB | 0.043 | 0.000 | 0.043 | |
| fitZIG | 0.052 | 0.000 | 0.052 | |
| fitZINB | 0.433 | 0.008 | 0.441 | |
| getDA | 0.069 | 0.008 | 0.078 | |
| getPositives | 0.081 | 0.000 | 0.081 | |
| getStatistics | 0.058 | 0.008 | 0.066 | |
| get_counts_metadata | 0.221 | 0.000 | 0.221 | |
| iterative_ordering | 0.01 | 0.00 | 0.01 | |
| meanDifferences | 0.002 | 0.000 | 0.001 | |
| norm_CSS | 0.072 | 0.000 | 0.072 | |
| norm_DESeq2 | 0.446 | 0.000 | 0.446 | |
| norm_TSS | 0.046 | 0.000 | 0.046 | |
| norm_edgeR | 0.036 | 0.000 | 0.036 | |
| plotConcordance | 4.738 | 0.112 | 4.850 | |
| plotContingency | 1.067 | 0.000 | 1.068 | |
| plotEnrichment | 1.071 | 0.000 | 1.071 | |
| plotFDR | 2.073 | 0.004 | 2.076 | |
| plotFPR | 2.079 | 0.008 | 2.088 | |
| plotKS | 2.067 | 0.028 | 2.095 | |
| plotLogP | 2.196 | 0.016 | 2.213 | |
| plotMD | 2.673 | 0.028 | 2.701 | |
| plotMutualFindings | 1.213 | 0.032 | 1.244 | |
| plotPositives | 0.795 | 0.012 | 0.807 | |
| plotQQ | 2.185 | 0.016 | 2.200 | |
| plotRMSE | 1.947 | 0.064 | 2.011 | |
| prepareObserved | 0.001 | 0.000 | 0.001 | |
| runDA | 0.519 | 0.000 | 0.520 | |
| runMocks | 0.752 | 0.000 | 0.753 | |
| runNormalizations | 0.518 | 0.000 | 0.518 | |
| runSplits | 3.819 | 0.100 | 3.919 | |
| setNormalizations | 0 | 0 | 0 | |
| set_ALDEx2 | 0.008 | 0.000 | 0.008 | |
| set_ANCOM | 0.008 | 0.000 | 0.008 | |
| set_DESeq2 | 0.008 | 0.000 | 0.008 | |
| set_MAST | 0.003 | 0.000 | 0.003 | |
| set_NOISeq | 0.003 | 0.000 | 0.003 | |
| set_Seurat | 0.006 | 0.000 | 0.006 | |
| set_basic | 0.002 | 0.000 | 0.002 | |
| set_corncob | 0.004 | 0.000 | 0.004 | |
| set_dearseq | 0.002 | 0.000 | 0.002 | |
| set_edgeR | 0.012 | 0.000 | 0.012 | |
| set_limma | 0.008 | 0.000 | 0.008 | |
| set_metagenomeSeq | 0.005 | 0.000 | 0.005 | |
| weights_ZINB | 0.428 | 0.000 | 0.428 | |