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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SurfR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SurfR_1.3.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SurfR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SurfR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SurfR’ version ‘1.3.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘SurfR’ 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 ... NOTE
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
enrichr_download 0.114   0.01  10.297
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      ▆
   1. └─SurfR::Gene2SProtein(c("EPCAM"), output_tsv = FALSE) at test_SurfR.R:8:3
   2.   ├─BiocFileCache::bfcrpath(bfc, surfaceome_table_url)
   3.   └─BiocFileCache::bfcrpath(bfc, surfaceome_table_url)
  ── Error ('test_SurfR.R:111:3'): Splot ─────────────────────────────────────────
  Error in `bfcrpath(bfc, surfaceome_table_url)`: not all 'rnames' found or unique.
  Backtrace:
      ▆
   1. └─SurfR::Gene2SProtein(ind_deg$DEG2_df$GeneID, input_type = "gene_name") at test_SurfR.R:111:3
   2.   ├─BiocFileCache::bfcrpath(bfc, surfaceome_table_url)
   3.   └─BiocFileCache::bfcrpath(bfc, surfaceome_table_url)
  
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 7 ]
  Error: Test failures
  Execution halted
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/SurfR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SurfR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SurfR’ ...
** 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 (SurfR)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(SurfR)

> 
> test_check("SurfR")
adding rname 'https://wlab.ethz.ch/surfaceome/table_S3_surfaceome.xlsx'
adding rname 'https://wlab.ethz.ch/surfaceome/table_S3_surfaceome.xlsx'
[ FAIL 2 | WARN 2 | SKIP 0 | PASS 7 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_SurfR.R:8:3'): Gene2SProtein -package core function- tests ─────
Error in `bfcrpath(bfc, surfaceome_table_url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─SurfR::Gene2SProtein(c("EPCAM"), output_tsv = FALSE) at test_SurfR.R:8:3
 2.   ├─BiocFileCache::bfcrpath(bfc, surfaceome_table_url)
 3.   └─BiocFileCache::bfcrpath(bfc, surfaceome_table_url)
── Error ('test_SurfR.R:111:3'): Splot ─────────────────────────────────────────
Error in `bfcrpath(bfc, surfaceome_table_url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─SurfR::Gene2SProtein(ind_deg$DEG2_df$GeneID, input_type = "gene_name") at test_SurfR.R:111:3
 2.   ├─BiocFileCache::bfcrpath(bfc, surfaceome_table_url)
 3.   └─BiocFileCache::bfcrpath(bfc, surfaceome_table_url)

[ FAIL 2 | WARN 2 | SKIP 0 | PASS 7 ]
Error: Test failures
Execution halted