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This page was generated on 2024-03-29 11:37:05 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
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 1481/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OutSplice 1.2.0  (landing page)
Theresa Guo
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/OutSplice
git_branch: RELEASE_3_18
git_last_commit: 2035f79
git_last_commit_date: 2023-10-24 11:48:51 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for OutSplice on palomino4


To the developers/maintainers of the OutSplice package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OutSplice.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: OutSplice
Version: 1.2.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OutSplice.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings OutSplice_1.2.0.tar.gz
StartedAt: 2024-03-28 03:33:48 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 03:41:25 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 456.8 seconds
RetCode: 0
Status:   OK  
CheckDir: OutSplice.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OutSplice.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings OutSplice_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/OutSplice.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'OutSplice/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OutSplice' version '1.2.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'OutSplice' 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 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
calcBurden: no visible binding for global variable 'FisherP2'
calcBurden: no visible binding for global variable 'Row.names'
calcBurden: no visible global function definition for 'na.omit'
calcBurden: no visible binding for global variable 'FisherP1'
dotheogsa: no visible binding for global variable 'median'
dotheogsa: no visible global function definition for 'fisher.test'
dotheogsa: no visible global function definition for 'p.adjust'
dotheogsa: no visible binding for global variable 'Row.names'
outspliceAnalysis: no visible global function definition for
  'read.table'
outspliceAnalysis: no visible global function definition for
  'capture.output'
outspliceTCGA: no visible global function definition for 'read.table'
outspliceTCGA: no visible global function definition for
  'capture.output'
plotJunctionData: no visible binding for global variable
  'FisherAnalyses'
plotJunctionData: no visible global function definition for 'pdf'
plotJunctionData: no visible binding for global variable 'junc.RPM'
plotJunctionData: no visible binding for global variable
  'geneAnnotations'
plotJunctionData: no visible global function definition for 'par'
plotJunctionData: no visible binding for global variable 'pheno'
plotJunctionData: no visible binding for global variable
  'junc.RPM.norm'
plotJunctionData: no visible global function definition for 'barplot'
plotJunctionData: no visible global function definition for 'title'
plotJunctionData: no visible binding for global variable
  'NORM.gene_expr.norm'
plotJunctionData: no visible binding for global variable 'gene_expr'
plotJunctionData: no visible global function definition for 'plot.new'
plotJunctionData: no visible global function definition for 'dev.off'
processMatrices2: no visible binding for global variable 'median'
saveResults: no visible global function definition for 'write.table'
subset_overEx: no visible binding for global variable 'FisherP2'
subset_underEx: no visible binding for global variable 'FisherP1'
Undefined global functions or variables:
  FisherAnalyses FisherP1 FisherP2 NORM.gene_expr.norm Row.names
  barplot capture.output dev.off fisher.test geneAnnotations gene_expr
  junc.RPM junc.RPM.norm median na.omit p.adjust par pdf pheno plot.new
  read.table title write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "barplot", "par", "plot.new", "title")
  importFrom("stats", "fisher.test", "median", "na.omit", "p.adjust")
  importFrom("utils", "capture.output", "read.table", "write.table")
to your NAMESPACE file.
* 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
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
outspliceAnalysis 16.87   0.40   17.34
outspliceTCGA     12.19   0.19   12.58
* 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.18-bioc/meat/OutSplice.Rcheck/00check.log'
for details.



Installation output

OutSplice.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL OutSplice
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'OutSplice' ...
** 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 (OutSplice)

Tests output

OutSplice.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(OutSplice)

> library(testthat)
> 
> test_check("OutSplice")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  45.78    1.95   48.51 

Example timings

OutSplice.Rcheck/OutSplice-Ex.timings

nameusersystemelapsed
outspliceAnalysis16.87 0.4017.34
outspliceTCGA12.19 0.1912.58
plotJunctionData0.140.000.24