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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:SparseArray.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings SparseArray_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SparseArray.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* 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 ‘1.2.0’
* 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 R 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 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 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
SVT_SparseArray-class 14.704  1.521  16.255
rowsum-methods         6.941  0.663   7.619
* 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:
      ▆
   1. └─SparseArray (local) .test_sym_crossprod_SparseMatrix(m0, svt0) at test-SparseMatrix-mult.R:56:4
   2.   └─testthat (local) EXPECT_FUN(cp, crossprod(svt, m)) at test-SparseMatrix-mult.R:36:4
  ── Failure ('test-SparseMatrix-mult.R:56:5'): crossprod()/tcrossprod() on input objects of type "double" ──
  `cp` not equal to crossprod(m, svt).
  1/9 mismatches
  [7] NaN - Inf == NaN
  Backtrace:
      ▆
   1. └─SparseArray (local) .test_sym_crossprod_SparseMatrix(m0, svt0) at test-SparseMatrix-mult.R:56:4
   2.   └─testthat (local) EXPECT_FUN(cp, crossprod(m, svt)) at test-SparseMatrix-mult.R:37:4
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 5796 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/SparseArray.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL SparseArray
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘SparseArray’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o
ExtendableJaggedArray.c: In function ‘_move_ExtendableJaggedArrays_to_SVT’:
ExtendableJaggedArray.c:142:4: warning: ‘vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  142 |    free(vals);
      |    ^~~~~~~~~~
ExtendableJaggedArray.c:138:4: warning: ‘offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  138 |    free(offs);
      |    ^~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c R_init_SparseArray.c -o R_init_SparseArray.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -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-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c Rvector_utils.c -o Rvector_utils.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c SBT_utils.c -o SBT_utils.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c SparseArray_Ops_methods.c -o SparseArray_Ops_methods.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c SparseArray_abind.c -o SparseArray_abind.o
SparseArray_abind.c: In function ‘REC_abind_SVTs’:
SparseArray_abind.c:157:4: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  157 |    copy_Rvector_elts_FUN(lv_vals, 0, ans_vals, k1, lv_len);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SparseArray_abind.c:136:46: note: ‘lv_vals’ was declared here
  136 |  SEXP SVT, ans, ans_offs, ans_vals, lv_offs, lv_vals;
      |                                              ^~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c SparseArray_aperm.c -o SparseArray_aperm.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c SparseArray_class.c -o SparseArray_class.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o
SparseArray_dim_tuning.c: In function ‘REC_tune_SVT’:
SparseArray_dim_tuning.c:260:40: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  260 |  if (SVT == R_NilValue || nops == ndim && cumallKEEP[ndim - 1])
      |                           ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c SparseArray_subassignment.c -o SparseArray_subassignment.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c SparseArray_subsetting.c -o SparseArray_subsetting.o
SparseArray_subsetting.c: In function ‘REC_subset_SVT’:
SparseArray_subsetting.c:139:35: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  139 |  build_lookup_table(lookup_table, INTEGER(lv_offs), lv_len);
      |                                   ^~~~~~~~~~~~~~~~
SparseArray_subsetting.c:129:7: note: ‘lv_offs’ was declared here
  129 |  SEXP lv_offs, lv_vals, ans_offs, ans_vals, ans;
      |       ^~~~~~~
SparseArray_subsetting.c:157:33: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  157 |  ans_vals = PROTECT(allocVector(TYPEOF(lv_vals), ans_len));
      |                                 ^~~~~~
SparseArray_subsetting.c:129:16: note: ‘lv_vals’ was declared here
  129 |  SEXP lv_offs, lv_vals, ans_offs, ans_vals, ans;
      |                ^~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c SparseArray_summarization.c -o SparseArray_summarization.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c SparseMatrix_mult.c -o SparseMatrix_mult.o
SparseMatrix_mult.c:392:13: warning: ‘crossprod2_mat_lv_double’ defined but not used [-Wunused-function]
  392 | static void crossprod2_mat_lv_double(const double *mat1, SEXP lv2,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~
SparseMatrix_mult.c:354:13: warning: ‘crossprod2_lv_mat_double’ defined but not used [-Wunused-function]
  354 | static void crossprod2_lv_mat_double(SEXP lv1, const double *mat2,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~
SparseMatrix_mult.c: In function ‘expand_int_lv’:
SparseMatrix_mult.c:96:24: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   96 |  _copy_ints_to_offsets(INTEGER(lv_vals), INTEGER(lv_offs), lv_len, x);
      |                        ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c:96:42: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   96 |  _copy_ints_to_offsets(INTEGER(lv_vals), INTEGER(lv_offs), lv_len, x);
      |                                          ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c: In function ‘lv_has_no_NA’:
SparseMatrix_mult.c:44:19: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   44 |  return has_no_NA(INTEGER(lv_vals), lv_len);
      |                   ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c: In function ‘lv_has_no_NaN_or_Inf’:
SparseMatrix_mult.c:35:27: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   35 |  return has_no_NaN_or_Inf(REAL(lv_vals), lv_len);
      |                           ^~~~~~~~~~~~~
SparseMatrix_mult.c: In function ‘expand_double_lv’:
SparseMatrix_mult.c:85:27: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   85 |  _copy_doubles_to_offsets(REAL(lv_vals), INTEGER(lv_offs), lv_len, x);
      |                           ^~~~~~~~~~~~~
SparseMatrix_mult.c:85:42: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   85 |  _copy_doubles_to_offsets(REAL(lv_vals), INTEGER(lv_offs), lv_len, x);
      |                                          ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c: In function ‘C_crossprod2_SVT_SVT’:
SparseMatrix_mult.c:44:19: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   44 |  return has_no_NA(INTEGER(lv_vals), lv_len);
      |                   ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c:41:16: note: ‘lv_vals’ was declared here
   41 |  SEXP lv_offs, lv_vals;
      |                ^~~~~~~
SparseMatrix_mult.c:44:19: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   44 |  return has_no_NA(INTEGER(lv_vals), lv_len);
      |                   ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c:41:16: note: ‘lv_vals’ was declared here
   41 |  SEXP lv_offs, lv_vals;
      |                ^~~~~~~
SparseMatrix_mult.c: In function ‘C_crossprod1_SVT’:
SparseMatrix_mult.c:44:19: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   44 |  return has_no_NA(INTEGER(lv_vals), lv_len);
      |                   ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c:41:16: note: ‘lv_vals’ was declared here
   41 |  SEXP lv_offs, lv_vals;
      |                ^~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c coerceVector2.c -o coerceVector2.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c leaf_vector_Arith.c -o leaf_vector_Arith.o
leaf_vector_Arith.c: In function ‘Rpow_double’:
leaf_vector_Arith.c:164:12: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  164 |  if (x < 0 && y == R_PosInf || x == R_NegInf && y != trunc(y))
      |      ~~~~~~^~~~~~~~~~~~~~~~
leaf_vector_Arith.c: In function ‘mult0_leaf_vector’:
leaf_vector_Arith.c:436:6: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  436 |  if (TYPEOF(lv_vals) == INTSXP) {
      |      ^~~~~~~~~~~~~~~
leaf_vector_Arith.c:434:14: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  434 |  lv_offs_p = INTEGER(lv_offs);
      |              ^~~~~~~~~~~~~~~~
leaf_vector_Arith.c: In function ‘_unary_minus_leaf_vector’:
leaf_vector_Arith.c:94:25: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   94 |    double *ans_vals_p = REAL(ans_vals);
      |                         ^~~~~~~~~~~~~~
leaf_vector_Arith.c:109:8: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  109 |  ans = _new_leaf_vector(lv_offs, ans_vals);
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
leaf_vector_Arith.c: In function ‘_Arith_lv1_v2’:
leaf_vector_Arith.c:384:6: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  384 |  if (TYPEOF(lv1_vals) == INTSXP) {
      |      ^~~~~~~~~~~~~~~~
leaf_vector_Arith.c:381:12: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  381 |  offs1_p = INTEGER(lv1_offs);
      |            ^~~~~~~~~~~~~~~~~
leaf_vector_Arith.c: In function ‘_Arith_lv1_lv2’:
leaf_vector_Arith.c:520:7: warning: ‘lv2_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  520 |   if (TYPEOF(lv2_vals) == INTSXP) {
      |       ^~~~~~~~~~~~~~~~
leaf_vector_Arith.c:516:12: warning: ‘lv2_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  516 |  offs2_p = INTEGER(lv2_offs);
      |            ^~~~~~~~~~~~~~~~~
leaf_vector_Arith.c:519:6: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  519 |  if (TYPEOF(lv1_vals) == INTSXP) {
      |      ^~~~~~~~~~~~~~~~
leaf_vector_Arith.c:515:12: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  515 |  offs1_p = INTEGER(lv1_offs);
      |            ^~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c leaf_vector_Compare.c -o leaf_vector_Compare.o
leaf_vector_Compare.c: In function ‘Compare_lv1_zero’:
leaf_vector_Compare.c:645:12: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  645 |     offs1, COMPLEX(lv1_vals), lv1_len, Rcomplex0,
      |            ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c:626:10: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  626 |  offs1 = INTEGER(lv1_offs);
      |          ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c: In function ‘_Compare_lv1_v2’:
leaf_vector_Compare.c:669:10: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  669 |  switch (TYPEOF(lv1_vals)) {
      |          ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c:668:10: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  668 |  offs1 = INTEGER(lv1_offs);
      |          ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c: In function ‘_Compare_lv1_lv2’:
leaf_vector_Compare.c:582:11: warning: ‘lv2_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  582 |  Rtype2 = TYPEOF(lv2_vals);
      |           ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c:576:17: note: ‘lv2_vals’ was declared here
  576 |  SEXP lv2_offs, lv2_vals;
      |                 ^~~~~~~~
leaf_vector_Compare.c:581:10: warning: ‘lv2_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  581 |  offs2 = INTEGER(lv2_offs);
      |          ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c:576:7: note: ‘lv2_offs’ was declared here
  576 |  SEXP lv2_offs, lv2_vals;
      |       ^~~~~~~~
leaf_vector_Compare.c:542:11: warning: ‘lv2_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  542 |  Rtype2 = TYPEOF(lv2_vals);
      |           ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c:536:17: note: ‘lv2_vals’ was declared here
  536 |  SEXP lv2_offs, lv2_vals;
      |                 ^~~~~~~~
leaf_vector_Compare.c:541:10: warning: ‘lv2_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  541 |  offs2 = INTEGER(lv2_offs);
      |          ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c:536:7: note: ‘lv2_offs’ was declared here
  536 |  SEXP lv2_offs, lv2_vals;
      |       ^~~~~~~~
leaf_vector_Compare.c:502:11: warning: ‘lv2_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  502 |  Rtype2 = TYPEOF(lv2_vals);
      |           ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c:496:17: note: ‘lv2_vals’ was declared here
  496 |  SEXP lv2_offs, lv2_vals;
      |                 ^~~~~~~~
leaf_vector_Compare.c:501:10: warning: ‘lv2_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  501 |  offs2 = INTEGER(lv2_offs);
      |          ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c:496:7: note: ‘lv2_offs’ was declared here
  496 |  SEXP lv2_offs, lv2_vals;
      |       ^~~~~~~~
leaf_vector_Compare.c:462:11: warning: ‘lv2_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  462 |  Rtype2 = TYPEOF(lv2_vals);
      |           ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c:456:17: note: ‘lv2_vals’ was declared here
  456 |  SEXP lv2_offs, lv2_vals;
      |                 ^~~~~~~~
leaf_vector_Compare.c:461:10: warning: ‘lv2_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  461 |  offs2 = INTEGER(lv2_offs);
      |          ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c:456:7: note: ‘lv2_offs’ was declared here
  456 |  SEXP lv2_offs, lv2_vals;
      |       ^~~~~~~~
leaf_vector_Compare.c:720:11: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  720 |  Rtype1 = TYPEOF(lv1_vals);
      |           ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c:719:10: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  719 |  offs1 = INTEGER(lv1_offs);
      |          ^~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c leaf_vector_Logic.c -o leaf_vector_Logic.o
leaf_vector_Logic.c: In function ‘_Logic_lv1_lv2’:
leaf_vector_Logic.c:88:23: warning: ‘lv2_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   88 |    INTEGER(lv2_offs), INTEGER(lv2_vals), lv2_len,
      |                       ^~~~~~~~~~~~~~~~~
leaf_vector_Logic.c:88:4: warning: ‘lv2_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   88 |    INTEGER(lv2_offs), INTEGER(lv2_vals), lv2_len,
      |    ^~~~~~~~~~~~~~~~~
leaf_vector_Logic.c:87:23: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   87 |    INTEGER(lv1_offs), INTEGER(lv1_vals), lv1_len,
      |                       ^~~~~~~~~~~~~~~~~
leaf_vector_Logic.c:87:4: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   87 |    INTEGER(lv1_offs), INTEGER(lv1_vals), lv1_len,
      |    ^~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c leaf_vector_dotprod.c -o leaf_vector_dotprod.o
leaf_vector_dotprod.c: In function ‘_dotprod_leaf_vectors’:
leaf_vector_dotprod.c:55:23: warning: ‘lv2_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   55 |    INTEGER(lv2_offs), REAL(lv2_vals), lv2_len,
      |                       ^~~~~~~~~~~~~~
leaf_vector_dotprod.c:55:4: warning: ‘lv2_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   55 |    INTEGER(lv2_offs), REAL(lv2_vals), lv2_len,
      |    ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c:54:23: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   54 |    INTEGER(lv1_offs), REAL(lv1_vals), lv1_len,
      |                       ^~~~~~~~~~~~~~
leaf_vector_dotprod.c:54:4: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   54 |    INTEGER(lv1_offs), REAL(lv1_vals), lv1_len,
      |    ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c: In function ‘_dotprod_leaf_vector_and_finite_col’:
leaf_vector_dotprod.c:81:12: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   81 |  vals1_p = REAL(lv1_vals);
      |            ^~~~~~~~~~~~~~
leaf_vector_dotprod.c:80:12: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   80 |  offs1_p = INTEGER(lv1_offs);
      |            ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c: In function ‘_dotprod_leaf_vector_and_double_col’:
leaf_vector_dotprod.c:104:12: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  104 |  vals1_p = REAL(lv1_vals);
      |            ^~~~~~~~~~~~~~
leaf_vector_dotprod.c:103:12: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  103 |  offs1_p = INTEGER(lv1_offs);
      |            ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c: In function ‘_dotprod_leaf_vector_and_noNA_int_col’:
leaf_vector_dotprod.c:141:12: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  141 |  vals1_p = INTEGER(lv1_vals);
      |            ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c:140:12: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  140 |  offs1_p = INTEGER(lv1_offs);
      |            ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c: In function ‘_dotprod_leaf_vector_and_int_col’:
leaf_vector_dotprod.c:166:12: warning: ‘lv1_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  166 |  vals1_p = INTEGER(lv1_vals);
      |            ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c:165:12: warning: ‘lv1_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  165 |  offs1_p = INTEGER(lv1_offs);
      |            ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c: In function ‘_dotprod0_leaf_vector’:
leaf_vector_dotprod.c:222:30: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  222 |  return _dotprod0_double_col(REAL(lv_vals), lv_len);
      |                              ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c leaf_vector_summarization.c -o leaf_vector_summarization.o
leaf_vector_summarization.c: In function ‘_summarize_leaf_vector’:
leaf_vector_summarization.c:21:2: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   21 |  _summarize_Rvector(lv_vals, summarize_op, res);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c leaf_vector_utils.c -o leaf_vector_utils.o
leaf_vector_utils.c: In function ‘_remove_zeros_from_leaf_vector’:
leaf_vector_utils.c:169:12: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  169 |  ans_len = _collect_offsets_of_nonzero_Rsubvec_elts(
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  170 |     lv_vals, 0, lv_len,
      |     ~~~~~~~~~~~~~~~~~~~
  171 |     offs_buf);
      |     ~~~~~~~~~
leaf_vector_utils.c:178:22: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  178 |  _copy_selected_ints(INTEGER(lv_offs), offs_buf, ans_len,
      |                      ^~~~~~~~~~~~~~~~
leaf_vector_utils.c: In function ‘_coerce_leaf_vector’:
leaf_vector_utils.c:207:36: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  207 |  if (_coercion_can_introduce_zeros(TYPEOF(lv_vals), new_Rtype))
      |                                    ^~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/include/Rdefines.h:41,
                 from leaf_vector_utils.h:4,
                 from leaf_vector_utils.c:4:
/home/biocbuild/R/R-4.3.1/include/Rinternals.h:368:20: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  368 | #define PROTECT(s) Rf_protect(s)
      |                    ^~~~~~~~~~
leaf_vector_utils.c:200:7: note: ‘lv_offs’ was declared here
  200 |  SEXP lv_offs, lv_vals, ans_vals, ans;
      |       ^~~~~~~
leaf_vector_utils.c: In function ‘_subassign_leaf_vector_with_Rvector’:
leaf_vector_utils.c:239:10: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  239 |  Rtype = TYPEOF(lv_vals);
      |          ^~~~~~~~~~~~~~~
leaf_vector_utils.c:287:12: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  287 |  offs1_p = INTEGER(lv_offs);
      |            ^~~~~~~~~~~~~~~~
leaf_vector_utils.c: In function ‘_lv_apply_to_REALSXP’:
leaf_vector_utils.c:374:13: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  374 |  in_Rtype = TYPEOF(lv_vals);
      |             ^~~~~~~~~~~~~~~
leaf_vector_utils.c:373:9: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  373 |  offs = INTEGER(lv_offs);
      |         ^~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c matrixStats_methods.c -o matrixStats_methods.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c randomSparseArray.c -o randomSparseArray.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c readSparseCSV.c -o readSparseCSV.o
readSparseCSV.c: In function ‘C_readSparseCSV_as_SVT_SparseMatrix’:
readSparseCSV.c:148:3: warning: ‘vals_buf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  148 |   IntAE_extend(ae, increase_buflength(ae->_buflength));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSparseCSV.c:307:20: note: ‘vals_buf’ was declared here
  307 |  IntAE *offs_buf, *vals_buf;
      |                    ^~~~~~~~
readSparseCSV.c:147:21: warning: ‘offs_buf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  147 |  if (ae->_nelt == ae->_buflength)
      |                   ~~^~~~~~~~~~~~
readSparseCSV.c:307:9: note: ‘offs_buf’ was declared here
  307 |  IntAE *offs_buf, *vals_buf;
      |         ^~~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c rowsum_methods.c -o rowsum_methods.o
rowsum_methods.c: In function ‘C_rowsum_SVT’:
rowsum_methods.c:109:4: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  109 |    INTEGER(lv_vals), INTEGER(lv_offs), lv_len,
      |    ^~~~~~~~~~~~~~~~
rowsum_methods.c:98:24: note: ‘lv_vals’ was declared here
   98 |  SEXP subSVT, lv_offs, lv_vals;
      |                        ^~~~~~~
rowsum_methods.c:109:22: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  109 |    INTEGER(lv_vals), INTEGER(lv_offs), lv_len,
      |                      ^~~~~~~~~~~~~~~~
rowsum_methods.c:98:15: note: ‘lv_offs’ was declared here
   98 |  SEXP subSVT, lv_offs, lv_vals;
      |               ^~~~~~~
rowsum_methods.c:88:4: warning: ‘lv_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   88 |    REAL(lv_vals), INTEGER(lv_offs), lv_len,
      |    ^~~~~~~~~~~~~
rowsum_methods.c:78:24: note: ‘lv_vals’ was declared here
   78 |  SEXP subSVT, lv_offs, lv_vals;
      |                        ^~~~~~~
rowsum_methods.c:88:19: warning: ‘lv_offs’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   88 |    REAL(lv_vals), INTEGER(lv_offs), lv_len,
      |                   ^~~~~~~~~~~~~~~~
rowsum_methods.c:78:15: note: ‘lv_offs’ was declared here
   78 |  SEXP subSVT, lv_offs, lv_vals;
      |               ^~~~~~~
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c sparseMatrix_utils.c -o sparseMatrix_utils.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.3.1/site-library/XVector/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c test.c -o test.o
gcc -shared -L/home/biocbuild/R/R-4.3.1/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 XVector_stubs.o coerceVector2.o leaf_vector_Arith.o leaf_vector_Compare.o leaf_vector_Logic.o leaf_vector_dotprod.o leaf_vector_summarization.o leaf_vector_utils.o matrixStats_methods.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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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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'help.start()' for an HTML browser interface to help.
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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, sort, 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 2 | WARN 1 | SKIP 0 | PASS 5796 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-SparseMatrix-mult.R:56:5'): crossprod()/tcrossprod() on input objects of type "double" ──
`cp` not equal to crossprod(svt, m).
1/9 mismatches
[3] NaN - Inf == NaN
Backtrace:
    ▆
 1. └─SparseArray (local) .test_sym_crossprod_SparseMatrix(m0, svt0) at test-SparseMatrix-mult.R:56:4
 2.   └─testthat (local) EXPECT_FUN(cp, crossprod(svt, m)) at test-SparseMatrix-mult.R:36:4
── Failure ('test-SparseMatrix-mult.R:56:5'): crossprod()/tcrossprod() on input objects of type "double" ──
`cp` not equal to crossprod(m, svt).
1/9 mismatches
[7] NaN - Inf == NaN
Backtrace:
    ▆
 1. └─SparseArray (local) .test_sym_crossprod_SparseMatrix(m0, svt0) at test-SparseMatrix-mult.R:56:4
 2.   └─testthat (local) EXPECT_FUN(cp, crossprod(m, svt)) at test-SparseMatrix-mult.R:37:4

[ FAIL 2 | WARN 1 | SKIP 0 | PASS 5796 ]
Error: Test failures
Execution halted