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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:SparseArray.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings SparseArray_1.4.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SparseArray.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    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 ‘SparseArray/DESCRIPTION’ ... OK
* this is package ‘SparseArray’ version ‘1.4.3’
* 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 ‘SparseArray’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* 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 ... 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
File ‘SparseArray/libs/SparseArray.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’

Compiled code should not call non-API entry points in R.

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
thread-control        63.096  0.500  52.269
SVT_SparseArray-class 14.283  1.213  15.530
rowsum-methods         7.385  0.575   7.975
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/SparseArray.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL SparseArray
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘SparseArray’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o
ExtendableJaggedArray.c: In function ‘_move_ExtendableJaggedArrays_to_SVT’:
ExtendableJaggedArray.c:124:4: warning: ‘nzoffs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  124 |    free(nzoffs);
      |    ^~~~~~~~~~~~
ExtendableJaggedArray.c:128:4: warning: ‘nzvals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  128 |    free(nzvals);
      |    ^~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c R_init_SparseArray.c -o R_init_SparseArray.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Rvector_summarization.c -o Rvector_summarization.o
Rvector_summarization.c:1274:12: warning: ‘count_NA_list_elts’ defined but not used [-Wunused-function]
 1274 | static int count_NA_list_elts(SEXP x)
      |            ^~~~~~~~~~~~~~~~~~
Rvector_summarization.c:1262:12: warning: ‘any_NA_list_elt’ defined but not used [-Wunused-function]
 1262 | static int any_NA_list_elt(SEXP x)
      |            ^~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c Rvector_utils.c -o Rvector_utils.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c SBT_utils.c -o SBT_utils.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c SparseArray_Ops_methods.c -o SparseArray_Ops_methods.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c SparseArray_abind.c -o SparseArray_abind.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c SparseArray_aperm.c -o SparseArray_aperm.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c SparseArray_class.c -o SparseArray_class.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c SparseArray_subassignment.c -o SparseArray_subassignment.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c SparseArray_subsetting.c -o SparseArray_subsetting.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c SparseArray_summarization.c -o SparseArray_summarization.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c SparseMatrix_mult.c -o SparseMatrix_mult.o
SparseMatrix_mult.c:356:13: warning: ‘crossprod2_doublemat_doubleSV’ defined but not used [-Wunused-function]
  356 | static void crossprod2_doublemat_doubleSV(
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SparseMatrix_mult.c:316:13: warning: ‘crossprod2_doubleSV_doublemat’ defined but not used [-Wunused-function]
  316 | static void crossprod2_doubleSV_doublemat(
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c SparseVec_Arith.c -o SparseVec_Arith.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c SparseVec_Compare.c -o SparseVec_Compare.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c SparseVec_Logic.c -o SparseVec_Logic.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c SparseVec_Math.c -o SparseVec_Math.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c SparseVec_dotprod.c -o SparseVec_dotprod.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c coerceVector2.c -o coerceVector2.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c leaf_utils.c -o leaf_utils.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c matrixStats_methods.c -o matrixStats_methods.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c randomSparseArray.c -o randomSparseArray.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c readSparseCSV.c -o readSparseCSV.o
readSparseCSV.c: In function ‘C_readSparseCSV_as_SVT_SparseMatrix’:
readSparseCSV.c:148:3: warning: ‘nzoffs_buf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  148 |   IntAE_extend(ae, increase_buflength(ae->_buflength));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSparseCSV.c:296:22: note: ‘nzoffs_buf’ was declared here
  296 |  IntAE *nzvals_buf, *nzoffs_buf;
      |                      ^~~~~~~~~~
readSparseCSV.c:147:21: warning: ‘nzvals_buf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  147 |  if (ae->_nelt == ae->_buflength)
      |                   ~~^~~~~~~~~~~~
readSparseCSV.c:296:9: note: ‘nzvals_buf’ was declared here
  296 |  IntAE *nzvals_buf, *nzoffs_buf;
      |         ^~~~~~~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c rowsum_methods.c -o rowsum_methods.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c sparseMatrix_utils.c -o sparseMatrix_utils.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c test.c -o test.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/IRanges/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/XVector/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -c thread_control.c -o thread_control.o
gcc -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o SparseArray.so ExtendableJaggedArray.o IRanges_stubs.o R_init_SparseArray.o Rvector_summarization.o Rvector_utils.o S4Vectors_stubs.o SBT_utils.o SVT_SparseArray_class.o SparseArray_Complex_methods.o SparseArray_Math_methods.o SparseArray_Ops_methods.o SparseArray_abind.o SparseArray_aperm.o SparseArray_class.o SparseArray_dim_tuning.o SparseArray_subassignment.o SparseArray_subsetting.o SparseArray_summarization.o SparseMatrix_mult.o SparseVec_Arith.o SparseVec_Compare.o SparseVec_Logic.o SparseVec_Math.o SparseVec_dotprod.o XVector_stubs.o coerceVector2.o leaf_utils.o matrixStats_methods.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o thread_control.o -fopenmp -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-SparseArray/00new/SparseArray/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 (SparseArray)

R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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.

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(testthat)
> library(SparseArray)
Loading required package: Matrix
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    expand, unname

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: S4Arrays
Loading required package: abind
Loading required package: IRanges

Attaching package: 'S4Arrays'

The following object is masked from 'package:abind':

    abind

The following object is masked from 'package:base':

    rowsum

> 
> test_check("SparseArray")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5978 ]
> 
> proc.time()
   user  system elapsed 
 38.835   1.407  40.228