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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:beachmat.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings beachmat_2.23.6.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/beachmat.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'beachmat/DESCRIPTION' ... OK
* this is package 'beachmat' version '2.23.6'
* 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) 13.3.0'
* checking C++ specification ... OK
* checking installed package size ... INFO
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
* 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 ... 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 ... 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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/libs/x64/beachmat.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
colBlockApply 12.08   1.32   25.71
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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: 1 WARNING, 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/beachmat.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL beachmat
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'beachmat' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
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:/rtools44/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:/rtools44/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:/rtools44/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:/rtools44/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:/rtools44/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:/rtools44/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:/rtools44/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:/rtools44/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:/rtools44/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:/rtools44/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:/rtools44/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:/rtools44/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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/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/R/library/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)

R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

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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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 20606 ]
> 
> proc.time()
   user  system elapsed 
  97.29    3.54  258.48