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This page was generated on 2024-04-18 11:32:18 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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 1850/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scanMiR 1.8.2  (landing page)
Pierre-Luc Germain
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/scanMiR
git_branch: RELEASE_3_18
git_last_commit: 6400e75
git_last_commit_date: 2024-02-11 10:21:38 -0400 (Sun, 11 Feb 2024)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for scanMiR on kjohnson1


To the developers/maintainers of the scanMiR package:
- 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: scanMiR
Version: 1.8.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scanMiR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scanMiR_1.8.2.tar.gz
StartedAt: 2024-04-18 02:34:19 -0400 (Thu, 18 Apr 2024)
EndedAt: 2024-04-18 02:36:41 -0400 (Thu, 18 Apr 2024)
EllapsedTime: 142.1 seconds
RetCode: 0
Status:   OK  
CheckDir: scanMiR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scanMiR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scanMiR_1.8.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/scanMiR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scanMiR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scanMiR’ version ‘1.8.2’
* 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 ‘scanMiR’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
.aggregateSiteInfo: no visible binding for global variable ‘ORF’
.aggregateSiteInfo: no visible global function definition for ‘.’
.aggregateSiteInfo: no visible binding for global variable
  ‘ORF.canonical’
.aggregateSiteInfo: no visible binding for global variable
  ‘ORF.nonCanonical’
.aggregateSiteInfo: no visible binding for global variable ‘..cols’
.aggregate_miRNA: no visible binding for global variable ‘ORF’
.aggregate_miRNA: no visible binding for global variable ‘log_kd’
.aggregate_miRNA: no visible binding for global variable ‘orf.length’
.aggregate_miRNA: no visible binding for global variable ‘utr.length’
.aggregate_miRNA: no visible binding for global variable ‘utr_score’
.aggregate_miRNA: no visible binding for global variable ‘orf_score’
dummyKdData: no visible binding for global variable ‘SampleKdModel’
plotKdModel: no visible binding for global variable ‘seed’
plotKdModel: no visible binding for global variable ‘log_kd’
viewTargetAlignment: no visible binding for global variable ‘x’
viewTargetAlignment: no visible binding for global variable ‘y’
viewTargetAlignment: no visible binding for global variable ‘label’
Undefined global functions or variables:
  . ..cols ORF ORF.canonical ORF.nonCanonical SampleKdModel label
  log_kd orf.length orf_score seed utr.length utr_score x y
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/scanMiR.Rcheck/00check.log’
for details.



Installation output

scanMiR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘scanMiR’ ...
** using staged installation
** R
** data
** 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 (scanMiR)

Tests output

scanMiR.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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(scanMiR)
> 
> test_check("scanMiR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 76 ]
> 
> proc.time()
   user  system elapsed 
 11.840   0.459  12.582 

Example timings

scanMiR.Rcheck/scanMiR-Ex.timings

nameusersystemelapsed
KdModel0.0040.0010.006
KdModelList-methods0.0100.0020.012
KdModelList0.0020.0010.004
SampleKdModel0.0010.0020.002
aggregateMatches0.6000.0090.617
assignKdType0.1780.0030.181
conservation0.0010.0020.004
dummyKdData0.0050.0020.007
findSeedMatches0.3910.0030.397
get3pAlignment0.0180.0000.022
get8merRange0.0030.0010.005
getKdModel0.0690.0020.072
getKmers0.0010.0010.001
getMatchTypes0.0010.0000.002
getRandomSeq0.0010.0000.001
getSeed8mers0.0020.0000.003
plotKdModel0.3160.0100.343
removeOverlappingRanges0.2250.0090.235
viewTargetAlignment0.5260.0040.532