Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1596/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
proDA 1.20.0  (landing page)
Constantin Ahlmann-Eltze
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/proDA
git_branch: RELEASE_3_20
git_last_commit: 5a26168
git_last_commit_date: 2024-10-29 10:38:54 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for proDA on teran2

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.

raw results


Summary

Package: proDA
Version: 1.20.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:proDA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings proDA_1.20.0.tar.gz
StartedAt: 2024-11-20 07:42:35 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 07:47:05 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 269.3 seconds
RetCode: 0
Status:   OK  
CheckDir: proDA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:proDA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings proDA_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/proDA.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘proDA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proDA’ version ‘1.20.0’
* 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 code 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

proDA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL proDA
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
 76.712   0.590  85.115 

Example timings

proDA.Rcheck/proDA-Ex.timings

nameusersystemelapsed
abundances1.2150.0801.483
as_replicate0.0000.0000.001
cash-proDAFit-method0.4580.1010.588
coefficient_variance_matrices0.4420.0010.492
coefficients0.4320.0050.459
convergence0.4310.0030.454
dist_approx0.7390.0071.011
dist_approx_impl0.6740.0000.676
feature_parameters0.4380.0000.467
generate_synthetic_data0.0170.0000.017
hyper_parameters0.4410.0000.485
invprobit0.0020.0010.006
median_normalization0.0020.0000.002
mply_dbl0.0040.0000.007
pd_lm0.0090.0000.016
pd_row_t_test1.1130.0121.259
proDA1.0560.0031.074
reference_level0.3600.0000.363
result_names0.4320.0000.437
test_diff1.8550.0071.911