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This page was generated on 2022-01-17 11:11:32 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1179/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MMAPPR2 1.9.0  (landing page)
Jonathon Hill
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/MMAPPR2
git_branch: master
git_last_commit: dd99ccf
git_last_commit_date: 2021-10-26 12:52:40 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64... NOT SUPPORTED ...
palomino3Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MMAPPR2
Version: 1.9.0
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_1.9.0.tar.gz
StartedAt: 2022-01-17 03:01:25 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 03:08:56 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 450.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MMAPPR2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/MMAPPR2.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MMAPPR2/DESCRIPTION’ ... OK
* this is package ‘MMAPPR2’ version ‘1.9.0’
* 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
  .git_fetch_output.txt
  .git_merge_output.txt
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-3.15-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/4.2/Resources/library’
* installing *source* package ‘MMAPPR2’ ...
** 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 (MMAPPR2)

Tests output

MMAPPR2.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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)
> 
> BiocParallel::register(BiocParallel::SerialParam())
> 
> testthat::test_check("MMAPPR2")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• samtools not in path (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 122 ]
> 
> proc.time()
   user  system elapsed 
 28.775   1.186  29.989 

Example timings

MMAPPR2.Rcheck/MMAPPR2-Ex.timings

nameusersystemelapsed
MmapprData-getters0.0120.0120.026
MmapprParam-functions0.0080.0100.019
MmapprParam0.0070.0080.018
calculateDistance0.0080.0100.020
generateCandidates0.0080.0110.020
loessFit0.0080.0110.021
mmappr0.0080.0090.018
outputMmapprData0.0070.0110.020
peakRefinement0.0070.0090.018
prePeak0.0080.0100.020
tempOutputFolder0.0080.0100.019