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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no beachmat_2.23.7.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc-longtests/meat/beachmat.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'beachmat/DESCRIPTION' ... OK
* this is package 'beachmat' version '2.23.7'
* 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 whether package 'beachmat' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* checking C++ specification ... OK
* checking installed package size ... INFO
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
* 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 dependencies in R code ... WARNING
'loadNamespace' or 'requireNamespace' call not declared from: 'beachmat.tiledb'
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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  colBlockApply.Rd: CsparseMatrix-class, SparseMatrix-class,
    ArrayGrid-class, DelayedMatrix-class, blockApply, currentViewport,
    getAutoBlockSize, dgCMatrix-class
  realizeFileBackedMatrix.Rd: DelayedMatrix-class, path,
    dgCMatrix-class, is_sparse
  tatami-utils.Rd: dgCMatrix-class
  toCsparse.Rd: SparseMatrix-class, CsparseMatrix-class
  whichNonZero.Rd: nzwhich, nzvals
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 ... SKIPPED
* 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 ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
 WARNING
directory 'longtests' not found
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  'E:/biocbuild/bbs-3.21-bioc-longtests/meat/beachmat.Rcheck/00check.log'
for details.

* installing *source* package 'beachmat' ...
** this is package 'beachmat' version '2.23.7'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
using C++17
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c constant_matrix.cpp -o constant_matrix.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c delayed_isometric_binary.cpp -o delayed_isometric_binary.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c delayed_isometric_math.cpp -o delayed_isometric_math.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c delayed_isometric_unary.cpp -o delayed_isometric_unary.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c delayed_other.cpp -o delayed_other.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c dense_matrix.cpp -o dense_matrix.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c fragment_sparse_rows.cpp -o fragment_sparse_rows.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c na_cast.cpp -o na_cast.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c sparse_matrix.cpp -o sparse_matrix.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c tatami_utils.cpp -o tatami_utils.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c unknown_matrix.cpp -o unknown_matrix.o
g++ -shared -s -static-libgcc -o beachmat.dll tmp.def RcppExports.o constant_matrix.o delayed_isometric_binary.o delayed_isometric_math.o delayed_isometric_unary.o delayed_other.o dense_matrix.o fragment_sparse_rows.o na_cast.o sparse_matrix.o tatami_utils.o unknown_matrix.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc-longtests/meat/beachmat.Rcheck/00LOCK-beachmat/00new/beachmat/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (beachmat)