Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 189/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioCor 1.30.0  (landing page)
Lluís Revilla Sancho
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/BioCor
git_branch: RELEASE_3_20
git_last_commit: c0e4197
git_last_commit_date: 2024-10-29 10:18:04 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for BioCor on nebbiolo2

To the developers/maintainers of the BioCor package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioCor.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: BioCor
Version: 1.30.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BioCor.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BioCor_1.30.0.tar.gz
StartedAt: 2024-12-19 20:32:50 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 20:42:24 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 574.0 seconds
RetCode: 0
Status:   OK  
CheckDir: BioCor.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BioCor.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BioCor_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BioCor.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 ‘BioCor/DESCRIPTION’ ... OK
* this is package ‘BioCor’ version ‘1.30.0’
* 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 ‘BioCor’ 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 ... NOTE
checkRd: (-1) mclusterSim.Rd:28: Lost braces
    28 | cluster are found they are combined using code{\link{combineScores}}.
       |                                               ^
* 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 ‘spelling.R’
  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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/BioCor.Rcheck/00check.log’
for details.


Installation output

BioCor.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘BioCor’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function from function ‘clusterGeneSim’ in package ‘BioCor’
Creating a generic function from function ‘clusterSim’ in package ‘BioCor’
Creating a generic function from function ‘geneSim’ in package ‘BioCor’
Creating a generic function from function ‘mclusterGeneSim’ in package ‘BioCor’
Creating a generic function from function ‘mclusterSim’ in package ‘BioCor’
Creating a generic function from function ‘mgeneSim’ in package ‘BioCor’
Creating a generic function from function ‘mpathSim’ in package ‘BioCor’
Creating a generic function from function ‘pathSim’ in package ‘BioCor’
** help
*** installing help indices
*** copying figures
** 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 (BioCor)

Tests output

BioCor.Rcheck/tests/spelling.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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.129   0.033   0.150 

BioCor.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("BioCor")
> 
> if (requireNamespace("testthat", quietly = TRUE)) {
+   library("testthat")
+   test_check("BioCor")
+ }
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 314 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 314 ]
> 
> proc.time()
   user  system elapsed 
 12.876   0.706  13.647 

Example timings

BioCor.Rcheck/BioCor-Ex.timings

nameusersystemelapsed
AintoB0.0000.0000.001
addSimilarities0.0040.0030.006
clusterGeneSim2.2410.1012.341
clusterSim1.4830.0561.538
combinadic0.0000.0000.001
combineScores0.0050.0000.005
combineSources0.0020.0000.001
conversions0.0010.0000.000
diceSim0.0000.0000.001
duplicateIndices000
geneSim3.7250.5924.318
mclusterGeneSim1.8630.2292.092
mclusterSim1.4280.0681.496
mgeneSim2.7580.3553.113
mpathSim2.7500.0482.797
pathSim2.1310.0442.175
plot_similarity2.3790.0512.430
removeDup0.0030.0000.003
seq2mat0.0010.0000.001
similarities0.0030.0000.003
weighted0.0010.0000.000