| Back to Build/check report for BioC 3.17 | 
  | 
This page was generated on 2023-02-08 01:15:21 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs | 
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 | 
| 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 proDA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/proDA.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 1515/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| proDA 1.13.0  (landing page) Constantin Ahlmann-Eltze 
  | kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: proDA | 
| Version: 1.13.0 | 
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:proDA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings proDA_1.13.0.tar.gz | 
| StartedAt: 2023-02-07 11:57:19 -0000 (Tue, 07 Feb 2023) | 
| EndedAt: 2023-02-07 12:05:09 -0000 (Tue, 07 Feb 2023) | 
| EllapsedTime: 470.8 seconds | 
| RetCode: 0 | 
| Status: OK | 
| CheckDir: proDA.Rcheck | 
| Warnings: 0 | 
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:proDA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings proDA_1.13.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/proDA.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* 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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘proDA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proDA’ version ‘1.13.0’
* 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 ‘proDA’ 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 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 ... 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 ...
  ‘Introduction.Rmd’ using ‘UTF-8’... OK
  ‘data-import.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
proDA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL proDA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘proDA’ ... ** using staged installation ** R ** 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 (proDA)
proDA.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "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(proDA)
> 
> test_check("proDA")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 126 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• Very slow (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 126 ]
> 
> proc.time()
   user  system elapsed 
156.444   0.375 168.134 
proDA.Rcheck/proDA-Ex.timings
| name | user | system | elapsed | |
| abundances | 1.219 | 0.064 | 1.450 | |
| as_replicate | 0 | 0 | 0 | |
| cash-proDAFit-method | 0.957 | 0.004 | 0.988 | |
| coefficient_variance_matrices | 0.957 | 0.004 | 1.014 | |
| coefficients | 0.944 | 0.000 | 0.947 | |
| convergence | 0.933 | 0.000 | 0.936 | |
| dist_approx | 1.631 | 0.000 | 1.698 | |
| dist_approx_impl | 1.499 | 0.000 | 1.776 | |
| feature_parameters | 0.934 | 0.000 | 0.980 | |
| generate_synthetic_data | 0.033 | 0.000 | 0.034 | |
| hyper_parameters | 0.925 | 0.000 | 1.184 | |
| invprobit | 0.005 | 0.000 | 0.005 | |
| median_normalization | 0.004 | 0.000 | 0.005 | |
| mply_dbl | 0.006 | 0.000 | 0.007 | |
| pd_lm | 0.015 | 0.000 | 0.015 | |
| pd_row_t_test | 2.358 | 0.004 | 2.528 | |
| proDA | 2.288 | 0.000 | 2.523 | |
| reference_level | 0.794 | 0.000 | 0.815 | |
| result_names | 0.937 | 0.004 | 0.956 | |
| test_diff | 3.871 | 0.000 | 4.100 | |