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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SparseArray.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings SparseArray_1.7.6.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/SparseArray.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 option '--no-vignettes'
* checking for file 'SparseArray/DESCRIPTION' ... OK
* this is package 'SparseArray' version '1.7.6'
* 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 'SparseArray' can be installed ... WARNING
Found the following significant warnings:
  OPBufTree.c:271:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  SVT_SparseArray_class.c:645:23: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
See 'E:/biocbuild/bbs-3.21-bioc/meat/SparseArray.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rowsum-methods.Rd: dgCMatrix-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 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
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'SparseArray-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NaArray-Math-methods
> ### Title: 'Math' and 'Math2' methods for NaArray objects
> ### Aliases: NaArray-Math-methods NaArray_Math_methods NaArray-Math
> ###   NaArray_Math NaArray-math-methods NaArray_math_methods NaArray-math
> ###   NaArray_math NaArray-Math2-methods NaArray_Math2_methods
> ###   NaArray-Math2 NaArray_Math2 NaArray-math2-methods
> ###   NaArray_math2_methods NaArray-math2 NaArray_math2 Math,NaArray-method
> ###   Math2,NaArray-method round,NaArray-method signif,NaArray-method
> ### Keywords: array methods arith
> 
> ### ** Examples
> 
> nam <- NaArray(dim=c(15, 6))
> nam[c(2, 6, 12:17, 22:33, 55, 59:62, 90)] <-
+                c(runif(22)*1e4, Inf, -Inf, NA, NaN)
> 
> log(nam)
Warning in .Call2(.NAME, ..., PACKAGE = "SparseArray") : NaNs produced
<15 x 6 NaMatrix> of type "double" [nnacount=25 (28%)]:
          [,1]     [,2]     [,3]     [,4]     [,5]     [,6]
 [1,]       NA 9.153426 9.202214       NA      NaN       NA
 [2,] 7.884233 8.796033 8.242849       NA       NA       NA
 [3,]       NA       NA 8.958598       NA       NA       NA
 [4,]       NA       NA       NA       NA       NA       NA
 [5,]       NA       NA       NA       NA       NA       NA
  ...        .        .        .        .        .        .
[11,]       NA 8.834953       NA       NA       NA       NA
[12,] 8.653215 8.253498       NA       NA       NA       NA
[13,] 9.114058 8.948770       NA       NA       NA       NA
[14,] 7.609277 8.512581       NA 7.659843       NA       NA
[15,] 9.103189 8.878523       NA      Inf       NA      NaN
> exp(nam)
<15 x 6 NaMatrix> of type "double" [nnacount=25 (28%)]:
      [,1] [,2] [,3] [,4] [,5] [,6]
 [1,]   NA  Inf  Inf   NA    0   NA
 [2,]  Inf  Inf  Inf   NA   NA   NA
 [3,]   NA   NA  Inf   NA   NA   NA
 [4,]   NA   NA   NA   NA   NA   NA
 [5,]   NA   NA   NA   NA   NA   NA
  ...    .    .    .    .    .    .
[11,]   NA  Inf   NA   NA   NA   NA
[12,]  Inf  Inf   NA   NA   NA   NA
[13,]  Inf  Inf   NA   NA   NA   NA
[14,]  Inf  Inf   NA  Inf   NA   NA
[15,]  Inf  Inf   NA  Inf   NA  NaN
> cos(nam)
Warning in .Call2(.NAME, ..., PACKAGE = "SparseArray") : NaNs produced
<15 x 6 NaMatrix> of type "double" [nnacount=25 (28%)]:
             [,1]        [,2]        [,3]        [,4]        [,5]        [,6]
 [1,]          NA  -0.9998651  -0.4950179          NA         NaN          NA
 [2,]  -0.9043939  -0.3543529   0.5609061          NA          NA          NA
 [3,]          NA          NA  -0.5490205          NA          NA          NA
 [4,]          NA          NA          NA          NA          NA          NA
 [5,]          NA          NA          NA          NA          NA          NA
  ...           .           .           .           .           .           .
[11,]          NA -0.90701040          NA          NA          NA          NA
[12,] -0.15988120 -0.42608705          NA          NA          NA          NA
[13,] -0.96470867  0.05856411          NA          NA          NA          NA
[14,]  0.99654310  0.75858504          NA -0.65985418          NA          NA
[15,]  0.49049417  0.70564603          NA         NaN          NA         NaN
> lgamma(nam)
<15 x 6 NaMatrix> of type "double" [nnacount=25 (28%)]:
          [,1]     [,2]     [,3]     [,4]     [,5]     [,6]
 [1,]       NA 77019.74 81354.57       NA      Inf       NA
 [2,] 18275.21 51512.53 27522.17       NA       NA       NA
 [3,]       NA       NA 61870.18       NA       NA       NA
 [4,]       NA       NA       NA       NA       NA       NA
 [5,]       NA       NA       NA       NA       NA       NA
  ...        .        .        .        .        .        .
[11,]       NA 53824.42       NA       NA       NA       NA
[12,] 43838.29 27857.75       NA       NA       NA       NA
[13,] 73688.87 61189.37       NA       NA       NA       NA
[14,] 13326.83 37386.72       NA 14125.45       NA       NA
[15,] 72794.58 56534.22       NA      Inf       NA      NaN
> 
> ## Sanity checks:
> m <- as.matrix(nam)
> stopifnot(
+   suppressWarnings(identical(as.matrix(log(nam)), log(m))),
+   identical(as.matrix(exp(nam)), exp(m)),
+   suppressWarnings(identical(as.matrix(cos(nam)), cos(m))),
+   suppressWarnings(identical(as.matrix(lgamma(nam)), lgamma(m)))
+ )
Error: identical(as.matrix(exp(nam)), exp(m)) is not TRUE
Execution halted
* 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:
  Backtrace:
      ▆
   1. └─SparseArray (local) .test_Math_op(m, svt2, op) at test-SparseArray-Math-methods.R:48:9
   2.   └─testthat::expect_identical(as.array(current), expected) at test-SparseArray-Math-methods.R:30:9
  ── Failure ('test-SparseArray-Math-methods.R:49:9'): 'Math' ops on SVT_SparseArray objects ──
  as.array(current) not identical to `expected`.
  Objects equal but not identical
  Backtrace:
      ▆
   1. └─SparseArray (local) .test_Math_op(a, svt3, op) at test-SparseArray-Math-methods.R:49:9
   2.   └─testthat::expect_identical(as.array(current), expected) at test-SparseArray-Math-methods.R:30:9
  
  [ FAIL 9 | WARN 0 | SKIP 0 | PASS 28567 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 1 WARNING, 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/SparseArray.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL SparseArray
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'SparseArray' ...
** this is package 'SparseArray' version '1.7.6'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o
ExtendableJaggedArray.c: In function '_move_ExtendableJaggedArrays_to_SVT':
ExtendableJaggedArray.c:129:25: warning: 'nzvals_p' may be used uninitialized [-Wmaybe-uninitialized]
  129 |                         free(nzvals_p);
      |                         ^~~~~~~~~~~~~~
ExtendableJaggedArray.c:111:22: note: 'nzvals_p' was declared here
  111 |                 int *nzvals_p, *nzoffs_p;
      |                      ^~~~~~~~
ExtendableJaggedArray.c:125:25: warning: 'nzoffs_p' may be used uninitialized [-Wmaybe-uninitialized]
  125 |                         free(nzoffs_p);
      |                         ^~~~~~~~~~~~~~
ExtendableJaggedArray.c:111:33: note: 'nzoffs_p' was declared here
  111 |                 int *nzvals_p, *nzoffs_p;
      |                                 ^~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c OPBufTree.c -o OPBufTree.o
OPBufTree.c: In function 'print_OPBuf':
OPBufTree.c:271:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  271 |                         Rprintf("%4lu", opbuf->xLoffs[k]);
      |                                  ~~~^   ~~~~~~~~~~~~~~~~
      |                                     |                |
      |                                     |                R_xlen_t {aka long long int}
      |                                     long unsigned int
      |                                  %4llu
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c R_init_SparseArray.c -o R_init_SparseArray.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c Rvector_summarization.c -o Rvector_summarization.o
Rvector_summarization.c:1370:12: warning: 'count_NA_list_elts' defined but not used [-Wunused-function]
 1370 | static int count_NA_list_elts(SEXP x)
      |            ^~~~~~~~~~~~~~~~~~
Rvector_summarization.c:1360:12: warning: 'any_NA_list_elt' defined but not used [-Wunused-function]
 1360 | static int any_NA_list_elt(SEXP x)
      |            ^~~~~~~~~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c Rvector_utils.c -o Rvector_utils.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SBT_utils.c -o SBT_utils.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o
SVT_SparseArray_class.c: In function 'C_from_SVT_SparseMatrix_to_CsparseMatrix':
SVT_SparseArray_class.c:645:23: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'R_xlen_t' {aka 'long long int'} [-Wformat=]
  645 |                 error("SVT_SparseMatrix object contains too many nonzero "
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  646 |                       "values (%ld) to \"fit\" in a CsparseMatrix derivative",
  647 |                       x_nzcount);
      |                       ~~~~~~~~~
      |                       |
      |                       R_xlen_t {aka long long int}
SVT_SparseArray_class.c:646:34: note: format string is defined here
  646 |                       "values (%ld) to \"fit\" in a CsparseMatrix derivative",
      |                                ~~^
      |                                  |
      |                                  long int
      |                                %lld
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseArray_abind.c -o SparseArray_abind.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseArray_aperm.c -o SparseArray_aperm.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseArray_subassignment.c -o SparseArray_subassignment.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseArray_subassignment_OLD.c -o SparseArray_subassignment_OLD.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseArray_subsetting.c -o SparseArray_subsetting.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseArray_summarization.c -o SparseArray_summarization.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseMatrix_mult.c -o SparseMatrix_mult.o
SparseMatrix_mult.c:346:13: warning: 'crossprod2_doublemat_doubleSV' defined but not used [-Wunused-function]
  346 | static void crossprod2_doublemat_doubleSV(
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SparseMatrix_mult.c:306:13: warning: 'crossprod2_doubleSV_doublemat' defined but not used [-Wunused-function]
  306 | static void crossprod2_doubleSV_doublemat(
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseVec.c -o SparseVec.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseVec_Arith.c -o SparseVec_Arith.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseVec_Compare.c -o SparseVec_Compare.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseVec_Logic.c -o SparseVec_Logic.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseVec_Math.c -o SparseVec_Math.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c SparseVec_dotprod.c -o SparseVec_dotprod.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c XVector_stubs.c -o XVector_stubs.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c argcheck_utils.c -o argcheck_utils.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c coerceVector2.c -o coerceVector2.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c leaf_utils.c -o leaf_utils.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c randomSparseArray.c -o randomSparseArray.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c readSparseCSV.c -o readSparseCSV.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c rowsum_methods.c -o rowsum_methods.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c sparseMatrix_utils.c -o sparseMatrix_utils.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c test.c -o test.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/XVector/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -fopenmp   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c thread_control.c -o thread_control.o
gcc -shared -s -static-libgcc -o SparseArray.dll tmp.def ExtendableJaggedArray.o IRanges_stubs.o OPBufTree.o R_init_SparseArray.o Rvector_summarization.o Rvector_utils.o S4Vectors_stubs.o SBT_utils.o SVT_SparseArray_class.o SparseArray_Arith_methods.o SparseArray_Compare_methods.o SparseArray_Complex_methods.o SparseArray_Logic_methods.o SparseArray_Math_methods.o SparseArray_abind.o SparseArray_aperm.o SparseArray_dim_tuning.o SparseArray_matrixStats.o SparseArray_misc_methods.o SparseArray_subassignment.o SparseArray_subassignment_OLD.o SparseArray_subsetting.o SparseArray_summarization.o SparseMatrix_mult.o SparseVec.o SparseVec_Arith.o SparseVec_Compare.o SparseVec_Logic.o SparseVec_Math.o SparseVec_dotprod.o XVector_stubs.o argcheck_utils.o coerceVector2.o leaf_utils.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o thread_control.o -fopenmp -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/R/library/00LOCK-SparseArray/00new/SparseArray/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 (SparseArray)

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> library(testthat)
> library(SparseArray)
Loading required package: Matrix
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: 'IRanges'

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

    windows


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 9 | WARN 0 | SKIP 0 | PASS 28567 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-NaArray-Math-methods.R:43:5'): 'Math' ops on NaArray objects ──
as.array(current) not identical to `expected`.
Objects equal but not identical
Backtrace:
    ▆
 1. └─SparseArray (local) .test_NaMath_op(a, naa, op) at test-NaArray-Math-methods.R:43:5
 2.   └─testthat::expect_identical(as.array(current), expected) at test-NaArray-Math-methods.R:30:9
── Failure ('test-NaArray-Math-methods.R:43:5'): 'Math' ops on NaArray objects ──
as.array(current) not identical to `expected`.
1/120 mismatches
[53] -0.818 - 0.979 == -1.8
Backtrace:
    ▆
 1. └─SparseArray (local) .test_NaMath_op(a, naa, op) at test-NaArray-Math-methods.R:43:5
 2.   └─testthat::expect_identical(as.array(current), expected) at test-NaArray-Math-methods.R:30:9
── Failure ('test-NaArray-Math-methods.R:43:5'): 'Math' ops on NaArray objects ──
as.array(current) not identical to `expected`.
Objects equal but not identical
Backtrace:
    ▆
 1. └─SparseArray (local) .test_NaMath_op(a, naa, op) at test-NaArray-Math-methods.R:43:5
 2.   └─testthat::expect_identical(as.array(current), expected) at test-NaArray-Math-methods.R:30:9
── Failure ('test-NaArray-Math-methods.R:43:5'): 'Math' ops on NaArray objects ──
as.array(current) not identical to `expected`.
1/120 mismatches
[53] -0.575 - 0.204 == -0.779
Backtrace:
    ▆
 1. └─SparseArray (local) .test_NaMath_op(a, naa, op) at test-NaArray-Math-methods.R:43:5
 2.   └─testthat::expect_identical(as.array(current), expected) at test-NaArray-Math-methods.R:30:9
── Failure ('test-NaArray-Math-methods.R:43:5'): 'Math' ops on NaArray objects ──
as.array(current) not identical to `expected`.
Objects equal but not identical
Backtrace:
    ▆
 1. └─SparseArray (local) .test_NaMath_op(a, naa, op) at test-NaArray-Math-methods.R:43:5
 2.   └─testthat::expect_identical(as.array(current), expected) at test-NaArray-Math-methods.R:30:9
── Failure ('test-SparseArray-Math-methods.R:49:9'): 'Math' ops on SVT_SparseArray objects ──
as.array(current) not identical to `expected`.
Objects equal but not identical
Backtrace:
    ▆
 1. └─SparseArray (local) .test_Math_op(a, svt3, op) at test-SparseArray-Math-methods.R:49:9
 2.   └─testthat::expect_identical(as.array(current), expected) at test-SparseArray-Math-methods.R:30:9
── Failure ('test-SparseArray-Math-methods.R:49:9'): 'Math' ops on SVT_SparseArray objects ──
as.array(current) not identical to `expected`.
1/120 mismatches
[53] -0.818 - 0.979 == -1.8
Backtrace:
    ▆
 1. └─SparseArray (local) .test_Math_op(a, svt3, op) at test-SparseArray-Math-methods.R:49:9
 2.   └─testthat::expect_identical(as.array(current), expected) at test-SparseArray-Math-methods.R:30:9
── Failure ('test-SparseArray-Math-methods.R:48:9'): 'Math' ops on SVT_SparseArray objects ──
as.array(current) not identical to `expected`.
Objects equal but not identical
Backtrace:
    ▆
 1. └─SparseArray (local) .test_Math_op(m, svt2, op) at test-SparseArray-Math-methods.R:48:9
 2.   └─testthat::expect_identical(as.array(current), expected) at test-SparseArray-Math-methods.R:30:9
── Failure ('test-SparseArray-Math-methods.R:49:9'): 'Math' ops on SVT_SparseArray objects ──
as.array(current) not identical to `expected`.
Objects equal but not identical
Backtrace:
    ▆
 1. └─SparseArray (local) .test_Math_op(a, svt3, op) at test-SparseArray-Math-methods.R:49:9
 2.   └─testthat::expect_identical(as.array(current), expected) at test-SparseArray-Math-methods.R:30:9

[ FAIL 9 | WARN 0 | SKIP 0 | PASS 28567 ]
Error: Test failures
Execution halted