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This page was generated on 2024-12-23 12:05 -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 1852/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scanMiRApp 1.12.0  (landing page)
Pierre-Luc Germain
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/scanMiRApp
git_branch: RELEASE_3_20
git_last_commit: 4732d5d
git_last_commit_date: 2024-10-29 11:02:47 -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 scanMiRApp on palomino8

To the developers/maintainers of the scanMiRApp package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scanMiRApp.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: scanMiRApp
Version: 1.12.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scanMiRApp.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings scanMiRApp_1.12.0.tar.gz
StartedAt: 2024-12-20 05:36:35 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 05:42:28 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 353.1 seconds
RetCode: 0
Status:   OK  
CheckDir: scanMiRApp.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scanMiRApp.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings scanMiRApp_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/scanMiRApp.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'scanMiRApp/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scanMiRApp' version '1.12.0'
* 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 whether package 'scanMiRApp' 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 dependencies in R code ... NOTE
':::' calls which should be '::':
  'BSgenome.Hsapiens.UCSC.hg38:::BSgenome.Hsapiens.UCSC.hg38'
  'BSgenome.Mmusculus.UCSC.mm10:::BSgenome.Mmusculus.UCSC.mm10'
  'BSgenome.Mmusculus.UCSC.mm39:::BSgenome.Mmusculus.UCSC.mm39'
  'BSgenome.Rnorvegicus.UCSC.rn6:::BSgenome.Rnorvegicus.UCSC.rn6'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.fakeAnno: no visible binding for global variable 'SampleTranscript'
.fakeAnno: no visible binding for global variable 'SampleKdModel'
plotSitesOnUTR: no visible binding for global variable 'logKd'
plotSitesOnUTR: no visible binding for global variable 'note'
plotSitesOnUTR: no visible binding for global variable 'type'
Undefined global functions or variables:
  SampleKdModel SampleTranscript logKd note type
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/scanMiRApp.Rcheck/00check.log'
for details.


Installation output

scanMiRApp.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL scanMiRApp
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'scanMiRApp' ...
** 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 (scanMiRApp)

Tests output

scanMiRApp.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(scanMiRApp)
Loading required package: scanMiR
> 
> test_check("scanMiRApp")
Loading annotation
Extracting transcripts
Scanning with 1 thread(s)
Loading annotation
Extracting transcripts
Scanning with 1 thread(s)
Prepare miRNA model
Get Transcript Sequence
Scan
Prepare miRNA model
Get Transcript Sequence
Scan
[ FAIL 0 | WARN 1 | SKIP 2 | PASS 13 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-shiny.R:10:3'
• empty test (1): 'test-utils.R:46:1'

[ FAIL 0 | WARN 1 | SKIP 2 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
  24.64    1.25   26.20 

Example timings

scanMiRApp.Rcheck/scanMiRApp-Ex.timings

nameusersystemelapsed
IndexedFst-class0.030.030.06
ScanMiRAnno1.220.051.27
enrichedMirTxPairs0.670.040.72
getTranscriptSequence1.970.142.11
plotSitesOnUTR2.610.022.63
runFullScan0.950.000.95
save-load-IndexedFst0.020.000.01
scanMiRApp000
scanMiRserver0.530.010.56
scanMiRui0.240.040.81