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This page was generated on 2023-04-12 11:05:18 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 scanMiRApp on nebbiolo2


To the developers/maintainers of the scanMiRApp package:
- Please 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 How and When does the builder pull? When will my changes propagate? 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 1778/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scanMiRApp 1.4.0  (landing page)
Pierre-Luc Germain
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/scanMiRApp
git_branch: RELEASE_3_16
git_last_commit: e15546d
git_last_commit_date: 2022-11-01 11:25:25 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: scanMiRApp
Version: 1.4.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:scanMiRApp.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings scanMiRApp_1.4.0.tar.gz
StartedAt: 2023-04-10 23:42:03 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 23:47:57 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 353.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: scanMiRApp.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:scanMiRApp.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings scanMiRApp_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/scanMiRApp.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘scanMiRApp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scanMiRApp’ version ‘1.4.0’
* 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 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 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: 'BSgenome.Mmusculus.UCSC.mm39'
':::' calls which should be '::':
  'BSgenome.Hsapiens.UCSC.hg38:::BSgenome.Hsapiens.UCSC.hg38'
  'BSgenome.Mmusculus.UCSC.mm10:::BSgenome.Mmusculus.UCSC.mm10'
  'BSgenome.Rnorvegicus.UCSC.rn6:::BSgenome.Rnorvegicus.UCSC.rn6'
  See the note in ?`:::` about the use of this operator.
Unavailable namespace imported from by a ':::' call: 'BSgenome.Mmusculus.UCSC.mm39'
  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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘IndexedFST.Rmd’ using ‘UTF-8’... OK
  ‘scanMiRApp.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/scanMiRApp.Rcheck/00check.log’
for details.



Installation output

scanMiRApp.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL scanMiRApp
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-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 version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(scanMiRApp)
> 
> 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 ═══════════════════════════════════════════════════════════════
• On CRAN (1)
• empty test (1)

[ FAIL 0 | WARN 1 | SKIP 2 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 21.616   1.066  23.852 

Example timings

scanMiRApp.Rcheck/scanMiRApp-Ex.timings

nameusersystemelapsed
IndexedFst-class0.0390.0010.038
ScanMiRAnno0.7530.0950.850
enrichedMirTxPairs0.6350.0170.650
getTranscriptSequence2.8950.0834.313
plotSitesOnUTR3.9130.1204.907
runFullScan2.3910.0404.221
save-load-IndexedFst0.0170.0040.021
scanMiRApp000
scanMiRserver1.0680.0041.076
scanMiRui0.3460.0120.501