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This page was generated on 2022-04-13 12:08:12 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 IntramiRExploreR on machv2


To the developers/maintainers of the IntramiRExploreR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IntramiRExploreR.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 947/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IntramiRExploreR 1.16.0  (landing page)
Surajit Bhattacharya
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/IntramiRExploreR
git_branch: RELEASE_3_14
git_last_commit: c1d31e7
git_last_commit_date: 2021-10-26 13:12:36 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: IntramiRExploreR
Version: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2022-04-12 14:32:52 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 14:34:14 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 81.8 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/IntramiRExploreR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IntramiRExploreR/DESCRIPTION’ ... OK
* this is package ‘IntramiRExploreR’ version ‘1.16.0’
* 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-3.14-bioc/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 13.4Mb
  sub-directories of 1Mb or more:
    data  13.1Mb
* 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 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/IntramiRExploreR.Rcheck/00check.log’
for details.



Installation output

IntramiRExploreR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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
   ‘IntramiRExploreR_vignettes.Rmd’ using ‘UTF-8’ 
** 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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  1.775   0.180   1.933 

Example timings

IntramiRExploreR.Rcheck/IntramiRExploreR-Ex.timings

nameusersystemelapsed
Gene_Visualisation1.7460.2321.980
GetGOS_ALL000
IntramiRExploreR000
Visualisation1.1490.1231.282
extract_HostGene0.0010.0010.002
extract_intragenic_miR0.0020.0020.004
genes_Stat1.2460.1321.379
miRTargets_Stat1.4120.1981.610