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This page was generated on 2023-10-20 09:38:01 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 587/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
doubletrouble 1.0.0  (landing page)
Fabrício Almeida-Silva
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/doubletrouble
git_branch: RELEASE_3_17
git_last_commit: c7acec6
git_last_commit_date: 2023-04-25 11:41:36 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for doubletrouble on kjohnson2


To the developers/maintainers of the doubletrouble 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: doubletrouble
Version: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2023-10-17 16:39:11 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 16:46:35 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 444.2 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_1.0.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/doubletrouble.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘doubletrouble/DESCRIPTION’ ... OK
* this is package ‘doubletrouble’ version ‘1.0.0’
* 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 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 4.828  1.321  11.124
* 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-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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 16 | SKIP 0 | PASS 49 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 49 ]
> 
> proc.time()
   user  system elapsed 
 22.962   2.118  38.623 

Example timings

doubletrouble.Rcheck/doubletrouble-Ex.timings

nameusersystemelapsed
cds_scerevisiae0.0510.0050.083
classify_gene_pairs2.9440.2024.753
classify_genes1.1290.0431.805
classify_ssd_pairs2.0120.0723.214
diamond_inter0.0400.0040.065
diamond_intra0.0430.0040.062
find_ks_peaks0.1170.0050.184
get_anchors_list0.7610.0361.253
get_transposed1.5300.0642.434
get_wgd_pairs0.8230.0391.321
gmax_ks0.2170.0070.336
pairs2kaks 4.828 1.32111.124
plot_ks_peaks1.2950.3670.727
scerevisiae_kaks0.0140.0020.025
split_pairs_by_peak0.4060.0370.678
yeast_annot0.0170.0030.029
yeast_seq0.3010.0170.494