##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:beachmat.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings beachmat_2.21.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/beachmat.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beachmat/DESCRIPTION’ ... OK
* this is package ‘beachmat’ version ‘2.21.3’
* 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 ‘beachmat’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... NOTE
  installed size is 127.4Mb
  sub-directories of 1Mb or more:
    include    1.6Mb
    libs     125.1Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘DelayedArray:::bplapply2’
  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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
colBlockApply 18.534  0.487  32.886
* 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:
    8.             └─DelayedArray (local) FUN(X[[i]], ...)
    9.               └─DelayedArray (local) FUN(viewport, ...)
   10.                 └─S4Arrays::read_block(x, viewport, as.sparse = as.sparse)
   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.                       └─SparseArray::extract_sparse_array(x, Nindex)
   16.                         └─S4Arrays:::subset_by_Nindex(x, index)
   17.                           ├─BiocGenerics::do.call(`[`, c(list(x), subscripts, list(drop = drop)))
   18.                           └─base::do.call(`[`, c(list(x), subscripts, list(drop = drop)))
  
  [ FAIL 4 | WARN 15 | SKIP 0 | PASS 17373 ]
  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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/beachmat.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL beachmat
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘beachmat’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c delayed_isometric_binary.cpp -o delayed_isometric_binary.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c delayed_isometric_math.cpp -o delayed_isometric_math.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c delayed_isometric_unary.cpp -o delayed_isometric_unary.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c delayed_other.cpp -o delayed_other.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c dense_matrix.cpp -o dense_matrix.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c fragment_sparse_rows.cpp -o fragment_sparse_rows.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c sparse_matrix.cpp -o sparse_matrix.o
In file included from ../inst/include/tatami/tatami.hpp:8,
                 from ../inst/include/tatami_r/UnknownMatrix.hpp:5,
                 from ../inst/include/tatami_r/tatami_r.hpp:4,
                 from ../inst/include/Rtatami.h:8,
                 from sparse_matrix.cpp:1:
../inst/include/tatami/sparse/CompressedSparseMatrix.hpp: In instantiation of ‘tatami::CompressedSparseMatrix<Value_, Index_, ValueStorage_, IndexStorage_, PointerStorage_>::CompressedSparseMatrix(Index_, Index_, ValueStorage_, IndexStorage_, PointerStorage_, bool, bool) [with Value_ = double; Index_ = int; ValueStorage_ = tatami::ArrayView<int>; IndexStorage_ = tatami::ArrayView<int>; PointerStorage_ = tatami::ArrayView<int>]’:
sparse_matrix.cpp:13:12:   required from ‘tatami::NumericMatrix* store_sparse_matrix(XVector_, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int, bool) [with T_ = int; XVector_ = Rcpp::Vector<10, Rcpp::PreserveStorage>; tatami::NumericMatrix = tatami::Matrix<double, int>; Rcpp::IntegerVector = Rcpp::Vector<13>]’
sparse_matrix.cpp:36:111:   required from here
../inst/include/tatami/sparse/CompressedSparseMatrix.hpp:534:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  534 |                 for (size_t j = start + 1; j < end; ++j) {
      |                                            ~~^~~~~
../inst/include/tatami/sparse/CompressedSparseMatrix.hpp: In instantiation of ‘tatami::CompressedSparseMatrix<Value_, Index_, ValueStorage_, IndexStorage_, PointerStorage_>::CompressedSparseMatrix(Index_, Index_, ValueStorage_, IndexStorage_, PointerStorage_, bool, bool) [with Value_ = double; Index_ = int; ValueStorage_ = tatami::ArrayView<double>; IndexStorage_ = tatami::ArrayView<int>; PointerStorage_ = tatami::ArrayView<int>]’:
sparse_matrix.cpp:13:12:   required from ‘tatami::NumericMatrix* store_sparse_matrix(XVector_, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int, bool) [with T_ = double; XVector_ = Rcpp::Vector<14, Rcpp::PreserveStorage>; tatami::NumericMatrix = tatami::Matrix<double, int>; Rcpp::IntegerVector = Rcpp::Vector<13>]’
sparse_matrix.cpp:40:114:   required from here
../inst/include/tatami/sparse/CompressedSparseMatrix.hpp:534:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c tatami_utils.cpp -o tatami_utils.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c unknown_matrix.cpp -o unknown_matrix.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o beachmat.so RcppExports.o delayed_isometric_binary.o delayed_isometric_math.o delayed_isometric_unary.o delayed_other.o dense_matrix.o fragment_sparse_rows.o sparse_matrix.o tatami_utils.o unknown_matrix.o -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-beachmat/00new/beachmat/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 (beachmat)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(beachmat)
> test_check("beachmat")
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘.../DESCRIPTION’ ... OK
* preparing ‘morebeachtests’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘morebeachtests_1.0.0.tar.gz’

── R CMD check ─────────────────────────────────────────────────────────────────
* using log directory ‘/home/biocbuild/tmp/RtmpZHXXcP/file3c034b1e2afb39/morebeachtests.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘morebeachtests/DESCRIPTION’ ... OK
* this is package ‘morebeachtests’ version ‘1.0.0’
* 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 ‘morebeachtests’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
* 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 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 ... OK
* checking for missing documentation entries ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
  ‘/home/biocbuild/tmp/RtmpZHXXcP/file3c034b1e2afb39/morebeachtests.Rcheck/00check.log’
for details.
[ FAIL 4 | WARN 15 | SKIP 0 | PASS 17373 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-apply.R:303:5'): apply preserves sparsity in sparse DelayedMatrices ──
is(out[[1]], "SparseArraySeed") is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test-apply.R:307:5'): apply preserves sparsity in sparse DelayedMatrices ──
is(out[[1]], "SparseArraySeed") is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test-apply.R:311:5'): apply preserves sparsity in sparse DelayedMatrices ──
`out2` not identical to lapply(out, as, Class = "dgCMatrix").
Component 1: Attributes: < Names: 5 string mismatches >
Component 1: Attributes: < Length mismatch: comparison on first 6 components >
Component 1: Attributes: < Component 1: Numeric: lengths (1, 2) differ >
Component 1: Attributes: < Component 2: Length mismatch: comparison on first 2 components >
Component 1: Attributes: < Component 2: Component 1: Modes: list, NULL >
Component 1: Attributes: < Component 2: Component 1: Lengths: 2, 0 >
Component 1: Attributes: < Component 2: Component 1: current is not list-like >
Component 1: Attributes: < Component 2: Component 2: Modes: list, NULL >
Component 1: Attributes: < Component 2: Component 2: Lengths: 2, 0 >
...
── Error ('test-apply.R:314:5'): apply preserves sparsity in sparse DelayedMatrices ──
<notSubsettableError/error/condition>
Error in `.Primitive("[")(new("SparseArraySeed", dim = c(10L, 10L), nzindex = structure(c(1L, 
2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 1L, 2L, 3L, 4L, 5L, 6L, 
7L, 8L, 9L, 10L), dim = c(10L, 2L)), nzdata = 1:10, dimnames = list(
    NULL, NULL)), , , drop = FALSE)`: object of type 'S4' is not subsettable
Backtrace:
     ▆
  1. └─beachmat::colBlockApply(sas, identity) at test-apply.R:314:5
  2.   └─beachmat:::.blockApply2(...)
  3.     └─DelayedArray::blockApply(...)
  4.       └─DelayedArray::gridApply(...)
  5.         └─S4Arrays:::bplapply2(...)
  6.           ├─BiocGenerics::lapply(X, FUN, ...)
  7.           └─base::lapply(X, FUN, ...)
  8.             └─DelayedArray (local) FUN(X[[i]], ...)
  9.               └─DelayedArray (local) FUN(viewport, ...)
 10.                 └─S4Arrays::read_block(x, viewport, as.sparse = as.sparse)
 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.                       └─SparseArray::extract_sparse_array(x, Nindex)
 16.                         └─S4Arrays:::subset_by_Nindex(x, index)
 17.                           ├─BiocGenerics::do.call(`[`, c(list(x), subscripts, list(drop = drop)))
 18.                           └─base::do.call(`[`, c(list(x), subscripts, list(drop = drop)))

[ FAIL 4 | WARN 15 | SKIP 0 | PASS 17373 ]
Error: Test failures
Execution halted