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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Herper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Herper_1.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Herper.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Herper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Herper’ version ‘1.17.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘Herper’ 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 code 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 ... OK
* 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 ... ERROR
Running examples in ‘Herper-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: list_CondaPkgs
> ### Title: List Conda packages.
> ### Aliases: list_CondaPkgs
> 
> ### ** Examples
> 
> condaPaths <- install_CondaTools("salmon", "herper_env")
* Using Miniconda at: /Users/biocbuild/Library/r-miniconda-arm64
The environment 'herper_env' already exists but the tools were not installed because the 'updateEnv' argument was set to FALSE. 

Conda and Environment Information
pathToConda : /Users/biocbuild/Library/r-miniconda-arm64/bin/conda
environment : herper_env
pathToEnvBin : /Users/biocbuild/Library/r-miniconda-arm64/envs/herper_env/bin
> list_CondaPkgs("herper_env")
Error in `[.data.frame`(result, , c("name", "version", "channel", "platform")) : 
  undefined columns selected
Calls: list_CondaPkgs -> [ -> [.data.frame
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/Herper.Rcheck/00check.log’
for details.