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This page was generated on 2024-12-19 15:01 -0500 (Thu, 19 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
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 126/430HostnameOS / ArchINSTALLBUILDCHECK
FieldEffectCrc 1.17.0  (landing page)
Christopher Dampier
Snapshot Date: 2024-12-19 07:30 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/FieldEffectCrc
git_branch: devel
git_last_commit: c0c5b3d
git_last_commit_date: 2024-10-29 09:51:18 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published


CHECK results for FieldEffectCrc on nebbiolo1

To the developers/maintainers of the FieldEffectCrc package:
- 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: FieldEffectCrc
Version: 1.17.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:FieldEffectCrc.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings FieldEffectCrc_1.17.0.tar.gz
StartedAt: 2024-12-19 12:30:26 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 12:40:42 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 616.2 seconds
RetCode: 0
Status:   OK  
CheckDir: FieldEffectCrc.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:FieldEffectCrc.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings FieldEffectCrc_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/FieldEffectCrc.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘FieldEffectCrc/DESCRIPTION’ ... OK
* this is package ‘FieldEffectCrc’ version ‘1.17.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘FieldEffectCrc’ 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 whether startup messages can be suppressed ... 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
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
FieldEffectCrc 17.608  1.933  20.691
cohort_A        6.976  0.942   8.492
reorder_assays  4.294  0.533   5.062
cohort_C        4.175  0.430   5.166
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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

FieldEffectCrc.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL FieldEffectCrc
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘FieldEffectCrc’ ...
** 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 (FieldEffectCrc)

Tests output

FieldEffectCrc.Rcheck/tests/runTests.Rout


R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
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.

> BiocGenerics:::testPackage("FieldEffectCrc")
see ?FieldEffectCrc and browseVignettes('FieldEffectCrc') for documentation
loading from cache
require("SummarizedExperiment")
see ?FieldEffectCrc and browseVignettes('FieldEffectCrc') for documentation
loading from cache
see ?FieldEffectCrc and browseVignettes('FieldEffectCrc') for documentation
loading from cache


RUNIT TEST PROTOCOL -- Thu Dec 19 12:37:55 2024 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
FieldEffectCrc RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 13.329   1.106  15.208 

Example timings

FieldEffectCrc.Rcheck/FieldEffectCrc-Ex.timings

nameusersystemelapsed
FieldEffectCrc17.608 1.93320.691
cohort_A6.9760.9428.492
cohort_B2.5990.2683.427
cohort_C4.1750.4305.166
make_txi4.0840.5174.837
reorder_assays4.2940.5335.062