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This page was generated on 2023-04-14 11:51:46 -0400 (Fri, 14 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4562
palomino3Windows Server 2022 Datacenterx644.3.0 alpha (2023-04-03 r84154 ucrt) 4330
merida1macOS 12.6.4 Montereyx86_644.3.0 beta (2023-04-08 r84203) -- "Already Tomorrow" 4287
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

CHECK results for MMAPPR2 on merida1


To the developers/maintainers of the MMAPPR2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MMAPPR2.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1254/2212HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MMAPPR2 1.13.0  (landing page)
Jonathon Hill
Snapshot Date: 2023-04-13 14:00:13 -0400 (Thu, 13 Apr 2023)
git_url: https://git.bioconductor.org/packages/MMAPPR2
git_branch: devel
git_last_commit: 3719f84
git_last_commit_date: 2022-11-01 11:20:05 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  

Summary

Package: MMAPPR2
Version: 1.13.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MMAPPR2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MMAPPR2_1.13.0.tar.gz
StartedAt: 2023-04-14 03:47:07 -0400 (Fri, 14 Apr 2023)
EndedAt: 2023-04-14 03:59:04 -0400 (Fri, 14 Apr 2023)
EllapsedTime: 716.9 seconds
RetCode: 0
Status:   OK  
CheckDir: MMAPPR2.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MMAPPR2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MMAPPR2_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/MMAPPR2.Rcheck’
* using R version 4.3.0 beta (2023-04-08 r84203)
* 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 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MMAPPR2/DESCRIPTION’ ... OK
* this is package ‘MMAPPR2’ version ‘1.13.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MMAPPR2’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/MMAPPR2.Rcheck/00check.log’
for details.



Installation output

MMAPPR2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MMAPPR2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘MMAPPR2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationDbi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationDbi’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘AnnotationDbi’
** testing if installed package keeps a record of temporary installation path
* DONE (MMAPPR2)

Tests output

MMAPPR2.Rcheck/tests/testthat.Rout


R version 4.3.0 beta (2023-04-08 r84203) -- "Already Tomorrow"
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.

> library(testthat)
> library(MMAPPR2)
Warning message:
replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'AnnotationDbi' 
> 
> BiocParallel::register(BiocParallel::SerialParam())
> 
> testthat::test_check("MMAPPR2")
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 122 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• samtools not in path (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 122 ]
> 
> proc.time()
   user  system elapsed 
 36.886   2.075  49.335 

Example timings

MMAPPR2.Rcheck/MMAPPR2-Ex.timings

nameusersystemelapsed
MmapprData-getters0.0160.0270.062
MmapprParam-functions0.0120.0200.042
MmapprParam0.0110.0200.045
calculateDistance0.0110.0250.052
generateCandidates0.0110.0190.041
loessFit0.0100.0180.041
mmappr0.0110.0200.043
outputMmapprData0.0110.0180.040
peakRefinement0.0090.0190.043
prePeak0.0110.0190.041
tempOutputFolder0.0110.0190.041