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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 1321/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MouseFM 1.16.0  (landing page)
Matthias Munz
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/MouseFM
git_branch: RELEASE_3_20
git_last_commit: 6f0f81d
git_last_commit_date: 2024-10-29 11:06:51 -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 MouseFM on merida1

To the developers/maintainers of the MouseFM package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MouseFM.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: MouseFM
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MouseFM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MouseFM_1.16.0.tar.gz
StartedAt: 2024-12-20 06:23:18 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 06:32:23 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 545.7 seconds
RetCode: 0
Status:   OK  
CheckDir: MouseFM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MouseFM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MouseFM_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MouseFM.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 ‘MouseFM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MouseFM’ version ‘1.16.0’
* 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 ‘MouseFM’ 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 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 ... NOTE
File ‘MouseFM/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("\n  ---------\n  For example usage please run: vignette('MouseFM')\n  \n  Support me: http://matthiasmunz.de/support_me\n\n  Citation appreciated:\n  Munz M, Khodaygani M, Aherrahrou Z, Busch H, Wohlers I (2021) In silico candidate variant and gene identification using inbred mouse strains. PeerJ. doi:10.7717/peerj.11017\n  \n  Github Repo: https://github.com/matmu/MouseFM\n  MouseFM Backend: https://github.com/matmu/MouseFM-Backend\n  ---------",     domain = NULL, appendLF = TRUE)

See section ‘Good practice’ in '?.onAttach'.
* 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
vis_reduction_factors 68.929  0.467  72.816
get_top               23.039  0.271  24.149
prio                  22.374  0.092  23.486
fetch                  3.691  0.140   5.629
annotate_mouse_genes   3.238  0.111   5.947
annotate_consequences  0.663  0.014  11.572
GRanges2df             0.371  0.012   7.217
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/MouseFM.Rcheck/00check.log’
for details.


Installation output

MouseFM.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘MouseFM’ ...
** 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 (MouseFM)

Tests output

MouseFM.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.

> library(testthat)
> library(MouseFM)

  ---------
  For example usage please run: vignette('MouseFM')
  
  Support me: http://matthiasmunz.de/support_me

  Citation appreciated:
  Munz M, Khodaygani M, Aherrahrou Z, Busch H, Wohlers I (2021) In silico candidate variant and gene identification using inbred mouse strains. PeerJ. doi:10.7717/peerj.11017
  
  Github Repo: https://github.com/matmu/MouseFM
  MouseFM Backend: https://github.com/matmu/MouseFM-Backend
  ---------
> 
> test_check("MouseFM")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
132.725   1.561 141.884 

Example timings

MouseFM.Rcheck/MouseFM-Ex.timings

nameusersystemelapsed
GRanges2df0.3710.0127.217
annotate_consequences 0.663 0.01411.572
annotate_mouse_genes3.2380.1115.947
avail_chromosomes0.0050.0010.007
avail_consequences0.0030.0010.006
avail_strains0.0030.0020.005
df2GRanges0.1530.0070.673
fetch3.6910.1405.629
finemap0.1080.0020.623
getURL0.0010.0010.000
get_top23.039 0.27124.149
prio22.374 0.09223.486
ref_genome0.0000.0010.001
setURL0.0000.0010.000
vis_reduction_factors68.929 0.46772.816