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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SparseArray.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SparseArray_1.0.12.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SparseArray.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SparseArray/DESCRIPTION’ ... OK
* this is package ‘SparseArray’ version ‘1.0.12’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 ... ERROR
Running examples in ‘SparseArray-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SparseArray-summarization
> ### Title: SparseArray summarization methods
> ### Aliases: SparseArray-summarization SparseArray_summarization
> ###   anyNA,SparseArray-method range.COO_SparseArray
> ###   range,COO_SparseArray-method range.SVT_SparseArray
> ###   range,SVT_SparseArray-method mean,SparseArray-method
> ###   var,SparseArray,ANY-method sd,SparseArray-method
> ### Keywords: array methods algebra arith
> 
> ### ** Examples
> 
> m0 <- matrix(0L, nrow=6, ncol=4)
> m0[c(1:2, 8, 10, 15:17, 24)] <- (1:8)*10L
> m0[5, 2] <- NA
> svt0 <- as(m0, "SVT_SparseMatrix")
> svt0
<6 x 4 SVT_SparseMatrix> of type "integer" (nzcount=9):
     [,1] [,2] [,3] [,4]
[1,]   10    0    0    0
[2,]   20   30    0    0
[3,]    0    0   50    0
[4,]    0   40   60    0
[5,]    0   NA   70    0
[6,]    0    0    0   80
> 
> anyNA(svt0)
[1] TRUE
> 
> range(svt0)
[1] NA NA
> 
> range(svt0, na.rm=TRUE)
[1]  0 80
> 
> sum(svt0, na.rm=TRUE)
[1] 360
> 
> sd(svt0, na.rm=TRUE)
[1] 25.90649
> 
> ## Sanity checks:
> stopifnot(
+   identical(anyNA(svt0), anyNA(m0)),
+   identical(range(svt0), range(m0)),
+   identical(range(svt0, na.rm=TRUE), range(m0, na.rm=TRUE)),
+   identical(sum(svt0), sum(m0)),
+   identical(sum(svt0, na.rm=TRUE), sum(m0, na.rm=TRUE)),
+   identical(sd(svt0, na.rm=TRUE), sd(m0, na.rm=TRUE))
+ )
Error: identical(sd(svt0, na.rm = TRUE), sd(m0, na.rm = TRUE)) 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:
      ▆
   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: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SparseArray.Rcheck/00check.log’
for details.