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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_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/cTRAP.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 ‘cTRAP/DESCRIPTION’ ... OK
* this is package ‘cTRAP’ version ‘1.24.0’
* 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 ... 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 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                            user system elapsed
plotDrugSetEnrichment                    170.857  2.221 173.215
convertGeneIdentifiers                    22.565  2.022  29.045
plot.referenceComparison                  20.565  1.477  22.640
analyseDrugSetEnrichment                  16.533  1.792  18.187
plot.perturbationChanges                  15.404  0.855  16.827
filterCMapMetadata                        10.841  0.897   8.776
prepareDrugSets                            6.585  4.344  10.643
plotTargetingDrugsVSsimilarPerturbations   7.015  0.806   7.888
prepareCMapPerturbations                   6.056  0.360   4.439
loadCMapData                               5.127  0.395   4.015
predictTargetingDrugs                      4.681  0.645   5.351
downloadENCODEknockdownMetadata            3.245  0.444  12.402
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/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/4.4-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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.198   0.053   0.239 

R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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.

> 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 0 | WARN 0 | SKIP 2 | PASS 243 ]

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

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 243 ]
> 
> proc.time()
   user  system elapsed 
 59.514   5.580  63.639