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This page was generated on 2024-03-28 11:37:02 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1849/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scanMiRApp 1.9.3  (landing page)
Pierre-Luc Germain
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/scanMiRApp
git_branch: devel
git_last_commit: d5739a3
git_last_commit_date: 2024-03-13 15:53:45 -0400 (Wed, 13 Mar 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for scanMiRApp on nebbiolo1


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: 1.9.3
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:scanMiRApp.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings scanMiRApp_1.9.3.tar.gz
StartedAt: 2024-03-28 02:22:50 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 02:29:51 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 420.9 seconds
RetCode: 0
Status:   OK  
CheckDir: scanMiRApp.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:scanMiRApp.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings scanMiRApp_1.9.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/scanMiRApp.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘scanMiRApp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scanMiRApp’ version ‘1.9.3’
* 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 ‘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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'txdbmaker'
  All declared Imports should be used.
':::' 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'
Undefined global functions or variables:
  SampleKdModel SampleTranscript logKd note
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/scanMiRApp.Rcheck/00check.log’
for details.


Installation output

scanMiRApp.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL scanMiRApp
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 3 | 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 3 | SKIP 2 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 23.107   1.044  24.164 

Example timings

scanMiRApp.Rcheck/scanMiRApp-Ex.timings

nameusersystemelapsed
IndexedFst-class0.0420.0040.047
ScanMiRAnno1.0590.0611.119
enrichedMirTxPairs0.7880.0640.852
getTranscriptSequence2.6760.3403.016
plotSitesOnUTR1.7980.1031.902
runFullScan0.9530.0360.989
save-load-IndexedFst0.0120.0000.011
scanMiRApp000
scanMiRserver0.4790.0150.494
scanMiRui0.1670.0080.176