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This page was generated on 2023-10-20 09:38:04 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1013/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IntramiRExploreR 1.22.0  (landing page)
Surajit Bhattacharya
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/IntramiRExploreR
git_branch: RELEASE_3_17
git_last_commit: 5d711e5
git_last_commit_date: 2023-04-25 11:32:52 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for IntramiRExploreR on kjohnson2


To the developers/maintainers of the IntramiRExploreR 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: IntramiRExploreR
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IntramiRExploreR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IntramiRExploreR_1.22.0.tar.gz
StartedAt: 2023-10-18 02:29:05 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 02:30:45 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 100.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: IntramiRExploreR.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IntramiRExploreR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IntramiRExploreR_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/IntramiRExploreR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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 Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IntramiRExploreR/DESCRIPTION’ ... OK
* this is package ‘IntramiRExploreR’ version ‘1.22.0’
* 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:
  .travis.yml
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 ‘IntramiRExploreR’ can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'FGNet_report(feaResults_topGO, ': unused argument (plotKeggPw = FALSE) 
  Warning: Package 'IntramiRExploreR' is deprecated and will be removed from
See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/IntramiRExploreR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... NOTE
  installed size is 13.2Mb
  sub-directories of 1Mb or more:
    data  12.9Mb
* 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 ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* 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 startup messages can be suppressed ... 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
GetGOS_ALL: possible error in FGNet_report(feaResults_topGO, plotKeggPw
  = FALSE): unused argument (plotKeggPw = FALSE)
* 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 LazyData ... WARNING
  LazyData DB of 12.9 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... 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 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/IntramiRExploreR.Rcheck/00check.log’
for details.



Installation output

IntramiRExploreR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘IntramiRExploreR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'FGNet_report(feaResults_topGO, ': unused argument (plotKeggPw = FALSE) 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'IntramiRExploreR' is deprecated and will be removed from
  Bioconductor version 3.14
** testing if installed package can be loaded from final location
Warning: Package 'IntramiRExploreR' is deprecated and will be removed from
  Bioconductor version 3.14
** testing if installed package keeps a record of temporary installation path
* DONE (IntramiRExploreR)

Tests output

IntramiRExploreR.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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(IntramiRExploreR)
Warning message:
Package 'IntramiRExploreR' is deprecated and will be removed from
  Bioconductor version 3.14 
> 
> test_check("IntramiRExploreR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  1.239   0.147   2.131 

Example timings

IntramiRExploreR.Rcheck/IntramiRExploreR-Ex.timings

nameusersystemelapsed
Gene_Visualisation1.5350.1282.694
GetGOS_ALL000
IntramiRExploreR000
Visualisation1.0730.0871.759
extract_HostGene0.0020.0010.002
extract_intragenic_miR0.0020.0010.003
genes_Stat1.0320.0671.672
miRTargets_Stat1.1680.1071.958