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This page was generated on 2023-12-02 11:39:05 -0500 (Sat, 02 Dec 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_64R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" 4601
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-11-14 r85524 ucrt) -- "Unsuffered Consequences" 4344
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" 4369
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2023-11-01 r85459) -- "Unsuffered Consequences" 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

Package 1561/2225HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
proDA 1.17.1  (landing page)
Constantin Ahlmann-Eltze
Snapshot Date: 2023-12-01 14:00:13 -0500 (Fri, 01 Dec 2023)
git_url: https://git.bioconductor.org/packages/proDA
git_branch: devel
git_last_commit: 7cf02e2
git_last_commit_date: 2023-10-30 04:46:10 -0500 (Mon, 30 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    NA  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for proDA on kunpeng2


To the developers/maintainers of the proDA package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: proDA
Version: 1.17.1
Command: /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:proDA.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings proDA_1.17.1.tar.gz
StartedAt: 2023-12-02 07:14:37 -0000 (Sat, 02 Dec 2023)
EndedAt: 2023-12-02 07:20:39 -0000 (Sat, 02 Dec 2023)
EllapsedTime: 362.7 seconds
RetCode: 0
Status:   OK  
CheckDir: proDA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:proDA.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings proDA_1.17.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/proDA.Rcheck’
* using R Under development (unstable) (2023-11-01 r85459)
* using platform: aarch64-unknown-linux-gnu
* 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
* using option ‘--no-vignettes’
* checking for file ‘proDA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proDA’ version ‘1.17.1’
* 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 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 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

proDA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD INSTALL proDA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4-devel-2023.11.02/site-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)

Tests output

proDA.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-11-01 r85459) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 (1) ═══════════════════════════════════════════════════════════
• Very slow (1): 'test-proDA.R:66:3'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 126 ]
> 
> proc.time()
   user  system elapsed 
159.092   1.976 162.164 

Example timings

proDA.Rcheck/proDA-Ex.timings

nameusersystemelapsed
abundances1.8490.0471.903
as_replicate000
cash-proDAFit-method0.8750.0960.973
coefficient_variance_matrices0.9290.0080.940
coefficients0.9090.0030.915
convergence0.8960.0080.906
dist_approx1.5610.0041.568
dist_approx_impl1.4100.0081.421
feature_parameters0.9080.0040.915
generate_synthetic_data0.0350.0000.035
hyper_parameters0.9080.0120.922
invprobit0.0040.0000.004
median_normalization0.0040.0000.004
mply_dbl0.0060.0000.007
pd_lm0.0110.0040.016
pd_row_t_test2.3120.0162.333
proDA2.2260.0122.244
reference_level0.7620.0040.768
result_names0.9020.0040.908
test_diff3.8060.0283.844