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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:glmGamPoi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings glmGamPoi_1.17.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/glmGamPoi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘glmGamPoi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘glmGamPoi’ version ‘1.17.3’
* 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 ‘glmGamPoi’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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:
   20.                               ├─methods::as(extract_sparse_array(x@seed, index), "COO_SparseArray")
   21.                               │ └─methods:::.class1(object)
   22.                               ├─SparseArray::extract_sparse_array(x@seed, index)
   23.                               └─DelayedArray::extract_sparse_array(x@seed, index)
   24.                                 ├─SparseArray::extract_sparse_array(x@seed, index)
   25.                                 └─DelayedArray::extract_sparse_array(x@seed, index)
   26.                                   ├─SparseArray::extract_sparse_array(x@seed, seed_index)
   27.                                   └─SparseArray::extract_sparse_array(x@seed, seed_index)
   28.                                     └─S4Arrays:::subset_by_Nindex(x, index)
   29.                                       ├─BiocGenerics::do.call(`[`, c(list(x), subscripts, list(drop = drop)))
   30.                                       └─base::do.call(`[`, c(list(x), subscripts, list(drop = drop)))
  
  [ FAIL 1 | WARN 420 | SKIP 4 | PASS 451 ]
  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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/glmGamPoi.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL glmGamPoi
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘glmGamPoi’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c beta_estimation.cpp -o beta_estimation.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c deviance.cpp -o deviance.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c overdispersion.cpp -o overdispersion.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c utils.cpp -o utils.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o glmGamPoi.so RcppExports.o beta_estimation.o deviance.o overdispersion.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-glmGamPoi/00new/glmGamPoi/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (glmGamPoi)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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(glmGamPoi)
> 
> test_check("glmGamPoi")
[ FAIL 1 | WARN 420 | SKIP 4 | PASS 451 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• Printing tests should be run interactively (1): 'test-printing.R:1:1'
• empty test (2): 'test-test_de.R:60:1', 'test-test_de.R:93:1'
• isNamespaceLoaded("devtools") is not TRUE (1): 'test-glm_gp.R:413:3'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-residuals.R:48:3'): residual calculation works with Delayed Matrix ──
<notSubsettableError/error/condition>
Error in `.Primitive("[")(new("SparseArraySeed", dim = c(2L, 4L), nzindex = structure(integer(0), dim = c(0L, 
2L)), nzdata = logical(0), dimnames = list(NULL, NULL)), , , 
    drop = FALSE)`: object of type 'S4' is not subsettable
Backtrace:
     ▆
  1. └─glmGamPoi::glm_gp(Y_hdf5, X, size_factors = FALSE, overdispersion = 1/0.7) at test-residuals.R:48:3
  2.   └─glmGamPoi:::glm_gp_impl(...)
  3.     └─glmGamPoi:::combine_size_factors_and_offset(...)
  4.       └─HDF5Array::writeHDF5Array(offset_matrix)
  5.         └─DelayedArray::BLOCK_write_to_sink(sink, x, verbose = verbose)
  6.           └─DelayedArray::sinkApply(...)
  7.             └─DelayedArray::gridReduce(FUN_WRAPPER, grid, sink, FUN, ..., verbose = verbose)
  8.               └─DelayedArray (local) FUN(viewport, init, ...)
  9.                 └─DelayedArray (local) FUN(init, viewport, ...)
 10.                   └─S4Arrays::read_block(x, viewport, as.sparse = NA)
 11.                     └─S4Arrays:::.NEW_read_block(x, viewport, as.sparse = as.sparse)
 12.                       ├─SparseArray::read_block_as_sparse(x, viewport)
 13.                       └─SparseArray::read_block_as_sparse(x, viewport)
 14.                         ├─SparseArray::extract_sparse_array(x, Nindex)
 15.                         └─DelayedArray::extract_sparse_array(x, Nindex)
 16.                           ├─SparseArray::extract_sparse_array(x@seed, index)
 17.                           └─DelayedArray::extract_sparse_array(x@seed, index)
 18.                             ├─SparseArray::extract_sparse_array(x@seed, seed_index)
 19.                             └─DelayedArray::extract_sparse_array(x@seed, seed_index)
 20.                               ├─methods::as(extract_sparse_array(x@seed, index), "COO_SparseArray")
 21.                               │ └─methods:::.class1(object)
 22.                               ├─SparseArray::extract_sparse_array(x@seed, index)
 23.                               └─DelayedArray::extract_sparse_array(x@seed, index)
 24.                                 ├─SparseArray::extract_sparse_array(x@seed, index)
 25.                                 └─DelayedArray::extract_sparse_array(x@seed, index)
 26.                                   ├─SparseArray::extract_sparse_array(x@seed, seed_index)
 27.                                   └─SparseArray::extract_sparse_array(x@seed, seed_index)
 28.                                     └─S4Arrays:::subset_by_Nindex(x, index)
 29.                                       ├─BiocGenerics::do.call(`[`, c(list(x), subscripts, list(drop = drop)))
 30.                                       └─base::do.call(`[`, c(list(x), subscripts, list(drop = drop)))

[ FAIL 1 | WARN 420 | SKIP 4 | PASS 451 ]
Error: Test failures
Execution halted