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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:cTRAP.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings cTRAP_1.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/cTRAP.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘cTRAP/DESCRIPTION’ ... OK
* this is package ‘cTRAP’ version ‘1.29.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 27 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 ... 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 ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 loading without being on the library search path ... 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")

plotComparison: no visible binding for global variable ‘.data’
plotMetricDistribution: no visible binding for global variable ‘.data’
plotSingleCorr: no visible binding for global variable ‘.data’
plotTargetingDrug: no visible binding for global variable ‘.data’
plotTargetingDrugsVSsimilarPerturbations: no visible binding for global
  variable ‘.data’
Undefined global functions or variables:
  .data
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'compareWithAllMethods.Rd':
  ‘rankByAscending’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                            user system elapsed
plotDrugSetEnrichment                    242.540  1.972 244.555
plot.referenceComparison                  20.456  0.431  20.892
convertGeneIdentifiers                    14.832  2.023  17.825
analyseDrugSetEnrichment                  14.178  1.976  48.735
plot.perturbationChanges                  14.140  0.284  14.426
prepareDrugSets                            4.924  5.081   9.993
filterCMapMetadata                         6.816  0.773   7.944
plotTargetingDrugsVSsimilarPerturbations   5.731  0.217   5.948
downloadENCODEknockdownMetadata            3.103  0.711  59.532
* 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:
   1. └─cTRAP::loadExpressionDrugSensitivityAssociation("GDSC 7") at test_drugSensitivity.R:4:1
   2.   └─cTRAP:::downloadIfNotFound(link, file)
   3.     └─utils::download.file(link, file, mode = mode)
  ── Error ('test_drugSetEnrichment.R:6:1'): (code run outside of `test_that()`) ──
  Error in `download.file(link, file, mode = mode)`: cannot open URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/compound_descriptors_NCI60_2D.qs'
  Backtrace:
      ▆
   1. └─cTRAP::loadDrugDescriptors("NCI60", "2D") at test_drugSetEnrichment.R:6:1
   2.   └─cTRAP:::loadRemotePreProcessedData(default, file, path)
   3.     └─cTRAP:::downloadIfNotFound(link, file)
   4.       └─utils::download.file(link, file, mode = mode)
  
  [ FAIL 2 | WARN 2 | SKIP 1 | PASS 192 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘cTRAP.Rmd’ using rmarkdown
trying URL 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE92742&format=file&file=GSE92742_Broad_LINCS_sig_info.txt.gz'

Quitting from cTRAP.Rmd:110-124 [CMap metadata conditions]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download.file()`:
! cannot open URL 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE92742&format=file&file=GSE92742_Broad_LINCS_sig_info.txt.gz'
---
Backtrace:
    ▆
 1. └─cTRAP::loadCMapData("cmapMetadata.txt", type = "metadata")
 2.   └─cTRAP:::loadCMapMetadata(file, nas)
 3.     └─cTRAP:::downloadIfNotFound(link, file)
 4.       └─utils::download.file(link, file, mode = mode)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'cTRAP.Rmd' failed with diagnostics:
cannot open URL 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE92742&format=file&file=GSE92742_Broad_LINCS_sig_info.txt.gz'
--- failed re-building ‘cTRAP.Rmd’

SUMMARY: processing the following file failed:
  ‘cTRAP.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/cTRAP.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL cTRAP
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘cTRAP’ ...
** this is package ‘cTRAP’ version ‘1.29.0’
** 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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.138   0.031   0.155 

R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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'
trying URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/compound_descriptors_NCI60_2D.qs'
[ FAIL 2 | WARN 2 | SKIP 1 | PASS 192 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test_ENCODE.R:16:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_drugSensitivity.R:4:1'): (code run outside of `test_that()`) ───
Error in `download.file(link, file, mode = mode)`: cannot open URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/expressionDrugSensitivityCorGDSC7.qs'
Backtrace:
    ▆
 1. └─cTRAP::loadExpressionDrugSensitivityAssociation("GDSC 7") at test_drugSensitivity.R:4:1
 2.   └─cTRAP:::downloadIfNotFound(link, file)
 3.     └─utils::download.file(link, file, mode = mode)
── Error ('test_drugSetEnrichment.R:6:1'): (code run outside of `test_that()`) ──
Error in `download.file(link, file, mode = mode)`: cannot open URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/compound_descriptors_NCI60_2D.qs'
Backtrace:
    ▆
 1. └─cTRAP::loadDrugDescriptors("NCI60", "2D") at test_drugSetEnrichment.R:6:1
 2.   └─cTRAP:::loadRemotePreProcessedData(default, file, path)
 3.     └─cTRAP:::downloadIfNotFound(link, file)
 4.       └─utils::download.file(link, file, mode = mode)

[ FAIL 2 | WARN 2 | SKIP 1 | PASS 192 ]
Error: Test failures
Execution halted