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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cTRAP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cTRAP_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/cTRAP.Rcheck’
* using R version 4.3.3 (2024-02-29)
* 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 Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cTRAP/DESCRIPTION’ ... OK
* this is package ‘cTRAP’ version ‘1.20.0’
* 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:
  .devcontainer
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 ‘cTRAP’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
* checking package 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
Found the following possibly unsafe calls:
File ‘cTRAP/R/shinyInterface_session.R’:
  assignInNamespace("dataTablesFilter", dt_mod, "DT")
* 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 ... NOTE
  Note: found 1 marked UTF-8 string
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘cTRAP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: filterCMapMetadata
> ### Title: Filter CMap metadata
> ### Aliases: filterCMapMetadata
> 
> ### ** Examples
> 
> cmapMetadata <- loadCMapData("cmapMetadata.txt", "metadata")
cmapMetadata.txt not found: downloading data...
trying URL 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE92742&format=file&file=GSE92742_Broad_LINCS_sig_info.txt.gz'
Content type 'application/octet-stream' length 11124404 bytes (10.6 MB)

downloaded 123 KB

Warning in download.file(link, file, mode = mode) :
  downloaded length 0 != reported length 0
Warning in download.file(link, file, mode = mode) :
  URL 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE92742&format=file&file=GSE92742_Broad_LINCS_sig_info.txt.gz': status was 'Transferred a partial file'
Error in download.file(link, file, mode = mode) : 
  download from 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE92742&format=file&file=GSE92742_Broad_LINCS_sig_info.txt.gz' failed
Calls: loadCMapData ... loadCMapMetadata -> downloadIfNotFound -> download.file
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  [ FAIL 1 | WARN 2 | SKIP 2 | PASS 243 ]
  
  ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
  • On Bioconductor (1): 'test_ENCODE.R:16:5'
  • empty test (1): 'test_drugSetEnrichment.R:88:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_plots.R:62:5'): Plot only ranked perturbations ───────────────
  plot$guides$colour not equal to "none".
  target is NULL, current is character
  
  [ FAIL 1 | WARN 2 | SKIP 2 | PASS 243 ]
  Error: Test failures
  Execution halted
* 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 ERRORs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/cTRAP.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cTRAP
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘cTRAP’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (cTRAP)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.230   0.052   0.269 

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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(cTRAP)
> 
> test_check("cTRAP")
trying URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/expressionDrugSensitivityCorGDSC7.qs'
downloaded 31.6 MB

trying URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/compound_descriptors_NCI60_2D.qs'
downloaded 2.1 MB

[ FAIL 1 | WARN 2 | SKIP 2 | PASS 243 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test_ENCODE.R:16:5'
• empty test (1): 'test_drugSetEnrichment.R:88:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plots.R:62:5'): Plot only ranked perturbations ───────────────
plot$guides$colour not equal to "none".
target is NULL, current is character

[ FAIL 1 | WARN 2 | SKIP 2 | PASS 243 ]
Error: Test failures
Execution halted