Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-12-23 12:06 -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 603/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
doubletrouble 1.6.0  (landing page)
Fabrício Almeida-Silva
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/doubletrouble
git_branch: RELEASE_3_20
git_last_commit: 3e5e5a2
git_last_commit_date: 2024-10-29 11:16:27 -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 doubletrouble on merida1

To the developers/maintainers of the doubletrouble package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/doubletrouble.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: doubletrouble
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:doubletrouble.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings doubletrouble_1.6.0.tar.gz
StartedAt: 2024-12-20 02:45:53 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 02:57:03 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 670.5 seconds
RetCode: 0
Status:   OK  
CheckDir: doubletrouble.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:doubletrouble.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings doubletrouble_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/doubletrouble.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘doubletrouble/DESCRIPTION’ ... OK
* this is package ‘doubletrouble’ version ‘1.6.0’
* 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 ‘doubletrouble’ 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
classify_gene_pairs    13.194  0.535  14.948
get_transposed_classes  5.373  0.122   6.119
pairs2kaks              3.467  0.164   7.564
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

doubletrouble.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL doubletrouble
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘doubletrouble’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 (doubletrouble)

Tests output

doubletrouble.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-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(doubletrouble)
> 
> test_check("doubletrouble")
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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: GenomeInfoDb
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
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")'.


Attaching package: 'txdbmaker'

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

    UCSCFeatureDbTableSchema, browseUCSCtrack, getChromInfoFromBiomart,
    makeFDbPackageFromUCSC, makeFeatureDbFromUCSC, makePackageName,
    makeTxDb, makeTxDbFromBiomart, makeTxDbFromEnsembl,
    makeTxDbFromGFF, makeTxDbFromGRanges, makeTxDbFromUCSC,
    makeTxDbPackage, makeTxDbPackageFromBiomart,
    makeTxDbPackageFromUCSC, supportedMiRBaseBuildValues,
    supportedUCSCFeatureDbTables, supportedUCSCFeatureDbTracks,
    supportedUCSCtables

Calculating rates for species 'Scerevisiae'
For species Scerevisiae, the lengths of 1 CDS are not multiples of 3. Removing them...
Bayesian Information Criterion (BIC): 
          E         V
1 -5627.215 -5627.215
2 -4833.369 -4312.906

Top 3 models based on the BIC criterion: 
      V,2       E,2       E,1 
-4312.906 -4833.369 -5627.215 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 69 ]
> 
> proc.time()
   user  system elapsed 
 49.419   3.841  57.876 

Example timings

doubletrouble.Rcheck/doubletrouble-Ex.timings

nameusersystemelapsed
cds_scerevisiae0.0060.0030.009
classify_gene_pairs13.194 0.53514.948
classify_genes0.0490.0030.058
diamond_inter0.0640.0040.076
diamond_intra0.0680.0030.076
duplicates2counts0.0790.0040.095
find_ks_peaks0.1910.0080.223
fungi_kaks0.0350.0020.044
get_anchors_list1.9860.0572.225
get_intron_counts4.5340.0694.866
get_segmental1.8790.0662.067
get_tandem_proximal1.4720.0291.589
get_transposed2.2270.0692.556
get_transposed_classes5.3730.1226.119
gmax_ks0.3690.0060.419
pairs2kaks3.4670.1647.564
plot_duplicate_freqs3.5380.8201.011
plot_ks_distro1.4160.1831.731
plot_ks_peaks0.6210.0690.734
plot_rates_by_species0.5370.0620.639
split_pairs_by_peak0.7030.0510.799
yeast_annot0.3870.0200.433
yeast_seq0.3990.0170.440