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This page was generated on 2023-12-08 11:37:42 -0500 (Fri, 08 Dec 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4688
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4439
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4458
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 595/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
doubletrouble 1.2.1  (landing page)
Fabrício Almeida-Silva
Snapshot Date: 2023-12-07 14:05:05 -0500 (Thu, 07 Dec 2023)
git_url: https://git.bioconductor.org/packages/doubletrouble
git_branch: RELEASE_3_18
git_last_commit: ef82a21
git_last_commit_date: 2023-11-08 05:11:31 -0500 (Wed, 08 Nov 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows 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
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for doubletrouble on lconway


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: 1.2.1
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_1.2.1.tar.gz
StartedAt: 2023-12-07 20:01:38 -0500 (Thu, 07 Dec 2023)
EndedAt: 2023-12-07 20:07:24 -0500 (Thu, 07 Dec 2023)
EllapsedTime: 345.9 seconds
RetCode: 0
Status:   OK  
CheckDir: doubletrouble.Rcheck
Warnings: 0

Command output

##############################################################################
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### 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_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/doubletrouble.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘doubletrouble/DESCRIPTION’ ... OK
* this is package ‘doubletrouble’ version ‘1.2.1’
* 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 ‘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 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 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
pairs2kaks          5.282  2.105   8.456
classify_gene_pairs 6.689  0.248   7.011
* 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

doubletrouble.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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")
CDS length is not a multiple of 3 for pair YGR032W, YLR342W
Bayesian Information Criterion (BIC): 
          E         V
1 -5588.359 -5588.359
2 -4806.157 -4294.228

Top 3 models based on the BIC criterion: 
      V,2       E,2       E,1 
-4294.228 -4806.157 -5588.359 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 50 ]
> 
> proc.time()
   user  system elapsed 
 25.321   2.781  28.272 

Example timings

doubletrouble.Rcheck/doubletrouble-Ex.timings

nameusersystemelapsed
cds_scerevisiae0.0530.0050.057
classify_gene_pairs6.6890.2487.011
classify_genes0.0220.0020.024
diamond_inter0.0420.0020.044
diamond_intra0.0380.0020.040
find_ks_peaks0.1090.0050.117
get_anchors_list1.1120.0361.163
get_intron_counts1.5740.0351.625
get_segmental1.0900.0391.143
get_tandem_proximal1.7810.0551.856
get_transposed1.2080.0471.268
get_transposed_classes2.6380.0812.750
gmax_ks0.2500.0050.258
pairs2kaks5.2822.1058.456
plot_ks_peaks1.3320.5440.510
scerevisiae_kaks0.0140.0020.017
split_pairs_by_peak0.3270.0330.361
yeast_annot0.2160.0100.229
yeast_seq0.2910.0130.306