##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gDRcore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gDRcore_1.9.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/gDRcore.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-23 23:49:57 UTC
* using option ‘--no-vignettes’
* checking for file ‘gDRcore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRcore’ version ‘1.9.7’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gDRcore’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': ‘data.table:::patterns’
  See the note in ?`:::` about the use of this operator.
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fit_SE.combinations.Rd: SummarizedExperiment-class
  runDrugResponseProcessingPipelineFxns.Rd: SummarizedExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘gDRcore/libs/gDRcore.so’:
  Found non-API call to R: ‘STRING_PTR’
This entry point may be removed soon.

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘gDRcore-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert_mae_to_raw_data
> ### Title: Transform mae into raw data
> ### Aliases: convert_mae_to_raw_data
> ### Keywords: convert_to_raw_data
> 
> ### ** Examples
> 
> mae <- gDRutils::get_synthetic_data("finalMAE_small")
Error: For file : Failed to open for reading. Does the file exist? Do you have file permissions? Is the file name long? (>255 chars)
Execution halted
* 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. └─gDRutils::get_synthetic_data("finalMAE_combo_2dose_nonoise2") at test-fit_SE.R:35:3
   2.   └─qs2::qs_read(system.file("testdata", qs, package = "gDRtestData"))
  ── Error ('test-fit_SE.R:52:3'): fit_SE.combinations works as expected ─────────
  <<not available>/C++Error/error/condition>
  Error: For file : Failed to open for reading. Does the file exist? Do you have file permissions? Is the file name long? (>255 chars)
  Backtrace:
      ▆
   1. └─gDRutils::get_synthetic_data("finalMAE_combo_matrix_small") at test-fit_SE.R:52:3
   2.   └─qs2::qs_read(system.file("testdata", qs, package = "gDRtestData"))
  
  [ FAIL 9 | WARN 0 | SKIP 0 | PASS 196 ]
  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: 2 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/gDRcore.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gDRcore
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘gDRcore’ ...
** this is package ‘gDRcore’ version ‘1.9.7’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gDRcore.cpp -o gDRcore.o
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o gDRcore.so gDRcore.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-gDRcore/00new/gDRcore/libs
** R
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gDRcore)

R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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("gDRcore")
> library("testthat")
> 
> test_check("gDRcore")
Saving _problems/test-convert_se_to_raw_data-3.R
Saving _problems/test-convert_se_to_raw_data-18.R
Saving _problems/test-create_SE-71.R
Saving _problems/test-finalMAE_medium-3.R
Saving _problems/test-finalMAE_small_no_noise-3.R
Saving _problems/test-finalMAE_wLigand-3.R
Saving _problems/test-fit_SE-25.R
Saving _problems/test-fit_SE-35.R
Saving _problems/test-fit_SE-52.R
[ FAIL 9 | WARN 0 | SKIP 0 | PASS 196 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-convert_se_to_raw_data.R:3:3'): convert_mae_to_raw_data works as expected with sa data ──
<<not available>/C++Error/error/condition>
Error: For file : Failed to open for reading. Does the file exist? Do you have file permissions? Is the file name long? (>255 chars)
Backtrace:
    ▆
 1. └─gDRutils::get_synthetic_data(data) at test-convert_se_to_raw_data.R:3:3
 2.   └─qs2::qs_read(system.file("testdata", qs, package = "gDRtestData"))
── Error ('test-convert_se_to_raw_data.R:18:3'): convert_mae_to_raw_data works as expected with matrix data ──
<<not available>/C++Error/error/condition>
Error: For file : Failed to open for reading. Does the file exist? Do you have file permissions? Is the file name long? (>255 chars)
Backtrace:
    ▆
 1. └─gDRutils::get_synthetic_data(data) at test-convert_se_to_raw_data.R:18:3
 2.   └─qs2::qs_read(system.file("testdata", qs, package = "gDRtestData"))
── Error ('test-create_SE.R:71:3'): create_SE swaps drugs properly ─────────────
<<not available>/C++Error/error/condition>
Error: For file : Failed to open for reading. Does the file exist? Do you have file permissions? Is the file name long? (>255 chars)
Backtrace:
    ▆
 1. └─gDRutils::get_synthetic_data("finalMAE_combo_matrix_small") at test-create_SE.R:71:3
 2.   └─qs2::qs_read(system.file("testdata", qs, package = "gDRtestData"))
── Error ('test-finalMAE_medium.R:3:3'): medium: test_synthetic_data ───────────
<<not available>/C++Error/error/condition>
Error: For file : Failed to open for reading. Does the file exist? Do you have file permissions? Is the file name long? (>255 chars)
Backtrace:
    ▆
 1. └─gDRutils::get_synthetic_data(data) at test-finalMAE_medium.R:3:3
 2.   └─qs2::qs_read(system.file("testdata", qs, package = "gDRtestData"))
── Error ('test-finalMAE_small_no_noise.R:3:3'): small_no_noise: test_synthetic_data ──
<<not available>/C++Error/error/condition>
Error: For file : Failed to open for reading. Does the file exist? Do you have file permissions? Is the file name long? (>255 chars)
Backtrace:
    ▆
 1. └─gDRutils::get_synthetic_data(data) at test-finalMAE_small_no_noise.R:3:3
 2.   └─qs2::qs_read(system.file("testdata", qs, package = "gDRtestData"))
── Error ('test-finalMAE_wLigand.R:3:3'): wLigand: test_synthetic_data ─────────
<<not available>/C++Error/error/condition>
Error: For file : Failed to open for reading. Does the file exist? Do you have file permissions? Is the file name long? (>255 chars)
Backtrace:
    ▆
 1. └─gDRutils::get_synthetic_data(data) at test-finalMAE_wLigand.R:3:3
 2.   └─qs2::qs_read(system.file("testdata", qs, package = "gDRtestData"))
── Error ('test-fit_SE.R:25:3'): fit_SE errors as expected ─────────────────────
<<not available>/C++Error/error/condition>
Error: For file : Failed to open for reading. Does the file exist? Do you have file permissions? Is the file name long? (>255 chars)
Backtrace:
    ▆
 1. └─gDRutils::get_synthetic_data("finalMAE_combo_2dose_nonoise2") at test-fit_SE.R:25:3
 2.   └─qs2::qs_read(system.file("testdata", qs, package = "gDRtestData"))
── Error ('test-fit_SE.R:35:3'): fit_SE works as expected ──────────────────────
<<not available>/C++Error/error/condition>
Error: For file : Failed to open for reading. Does the file exist? Do you have file permissions? Is the file name long? (>255 chars)
Backtrace:
    ▆
 1. └─gDRutils::get_synthetic_data("finalMAE_combo_2dose_nonoise2") at test-fit_SE.R:35:3
 2.   └─qs2::qs_read(system.file("testdata", qs, package = "gDRtestData"))
── Error ('test-fit_SE.R:52:3'): fit_SE.combinations works as expected ─────────
<<not available>/C++Error/error/condition>
Error: For file : Failed to open for reading. Does the file exist? Do you have file permissions? Is the file name long? (>255 chars)
Backtrace:
    ▆
 1. └─gDRutils::get_synthetic_data("finalMAE_combo_matrix_small") at test-fit_SE.R:52:3
 2.   └─qs2::qs_read(system.file("testdata", qs, package = "gDRtestData"))

[ FAIL 9 | WARN 0 | SKIP 0 | PASS 196 ]
Error:
! Test failures.
Execution halted