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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:BiocSingular.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BiocSingular_1.26.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BiocSingular.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocSingular/DESCRIPTION’ ... OK
* this is package ‘BiocSingular’ version ‘1.26.1’
* 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 ‘BiocSingular’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... OK
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... WARNING
Missing link(s) in Rd file 'options.Rd':
  ‘blockGrid’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BiocSingularParam.Rd: DelayedMatrix-class, bpparam
  DeferredMatrix.Rd: ScaledMatrix-class
  LowRankMatrix.Rd: DelayedMatrix-class, DelayedArray
  options.Rd: irlba, rsvd, ScaledMatrix-class, blockGrid
  runExactSVD.Rd: BiocParallelParam-class
  runIrlbaSVD.Rd: irlba, BiocParallelParam-class
  runRandomSVD.Rd: rsvd, BiocParallelParam-class
  runSVD.Rd: BiocParallelParam-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 ... 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’

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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL BiocSingular
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘BiocSingular’ ...
** this is package ‘BiocSingular’ version ‘1.26.1’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++17
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c compute_scale.cpp -o compute_scale.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/assorthead/include/tatami_stats/grouped_variances.hpp:5,
                 from /home/biocbuild/R/R-4.5.0/site-library/assorthead/include/tatami_stats/tatami_stats.hpp:7,
                 from compute_scale.cpp:2:
/home/biocbuild/R/R-4.5.0/site-library/assorthead/include/tatami_stats/variances.hpp: In instantiation of ‘std::pair<_FIter, _FIter> tatami_stats::variances::direct(const Value_*, Index_, Index_, bool) [with Output_ = double; Value_ = double; Index_ = int]’:
compute_scale.cpp:114:66:   required from here
  114 |                     auto paired = tatami_stats::variances::direct(range.value, range.number, NR, false);
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0/site-library/assorthead/include/tatami_stats/variances.hpp:98:29: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
   98 | std::pair<Output_, Output_> direct(const Value_* value, Index_ num_nonzero, Index_ num_all, bool skip_nan) {
      |                             ^~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o BiocSingular.so RcppExports.o compute_scale.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-BiocSingular/00new/BiocSingular/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 (BiocSingular)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 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(BiocSingular)
> library(testthat)
> test_check("BiocSingular")
Error in setwd(dirname(path)) : cannot change working directory
Calls: test_check ... source_dir -> lapply -> FUN -> source_file -> setwd
Execution halted