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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SparseArray.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings SparseArray_1.2.4.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/SparseArray.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* 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 '1.2.4'
* 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 ... OK
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.18-bioc/R/library/SparseArray/libs/x64/SparseArray.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'SparseArray/libs/x64/SparseArray.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
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 12.84   0.81   13.65
rowsum-methods         7.69   0.35    8.04
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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 NOTE
See
  'F:/biocbuild/bbs-3.18-bioc/meat/SparseArray.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL SparseArray
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* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'SparseArray' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o
ExtendableJaggedArray.c: In function '_move_ExtendableJaggedArrays_to_SVT':
ExtendableJaggedArray.c:142:25: warning: 'vals' may be used uninitialized [-Wmaybe-uninitialized]
  142 |                         free(vals);
      |                         ^~~~~~~~~~
ExtendableJaggedArray.c:120:21: note: 'vals' was declared here
  120 |         int *offs, *vals;
      |                     ^~~~
ExtendableJaggedArray.c:138:25: warning: 'offs' may be used uninitialized [-Wmaybe-uninitialized]
  138 |                         free(offs);
      |                         ^~~~~~~~~~
ExtendableJaggedArray.c:120:14: note: 'offs' was declared here
  120 |         int *offs, *vals;
      |              ^~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_SparseArray.c -o R_init_SparseArray.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rvector_utils.c -o Rvector_utils.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SBT_utils.c -o SBT_utils.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SparseArray_Ops_methods.c -o SparseArray_Ops_methods.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SparseArray_abind.c -o SparseArray_abind.o
In function 'concatenate_leaf_vectors',
    inlined from 'REC_abind_SVTs' at SparseArray_abind.c:195:10:
SparseArray_abind.c:157:25: warning: 'lv_vals' may be used uninitialized [-Wmaybe-uninitialized]
  157 |                         copy_Rvector_elts_FUN(lv_vals, 0, ans_vals, k1, lv_len);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SparseArray_abind.c: In function 'REC_abind_SVTs':
SparseArray_abind.c:136:53: note: 'lv_vals' was declared here
  136 |         SEXP SVT, ans, ans_offs, ans_vals, lv_offs, lv_vals;
      |                                                     ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SparseArray_aperm.c -o SparseArray_aperm.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SparseArray_class.c -o SparseArray_class.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o
SparseArray_dim_tuning.c: In function 'REC_tune_SVT':
SparseArray_dim_tuning.c:260:47: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
  260 |         if (SVT == R_NilValue || nops == ndim && cumallKEEP[ndim - 1])
      |                                  ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SparseArray_subassignment.c -o SparseArray_subassignment.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SparseArray_subsetting.c -o SparseArray_subsetting.o
In function 'subset_leaf_vector',
    inlined from 'REC_subset_SVT' at SparseArray_subsetting.c:181:10:
SparseArray_subsetting.c:139:42: warning: 'lv_offs' may be used uninitialized [-Wmaybe-uninitialized]
  139 |         build_lookup_table(lookup_table, INTEGER(lv_offs), lv_len);
      |                                          ^~~~~~~~~~~~~~~~
SparseArray_subsetting.c: In function 'REC_subset_SVT':
SparseArray_subsetting.c:129:14: note: 'lv_offs' was declared here
  129 |         SEXP lv_offs, lv_vals, ans_offs, ans_vals, ans;
      |              ^~~~~~~
SparseArray_subsetting.c:157:40: warning: 'lv_vals' may be used uninitialized [-Wmaybe-uninitialized]
  157 |         ans_vals = PROTECT(allocVector(TYPEOF(lv_vals), ans_len));
      |                                        ^~~~~~
SparseArray_subsetting.c:129:23: note: 'lv_vals' was declared here
  129 |         SEXP lv_offs, lv_vals, ans_offs, ans_vals, ans;
      |                       ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SparseArray_summarization.c -o SparseArray_summarization.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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_double_lv':
SparseMatrix_mult.c:85:34: warning: 'lv_vals' may be used uninitialized [-Wmaybe-uninitialized]
   85 |         _copy_doubles_to_offsets(REAL(lv_vals), INTEGER(lv_offs), lv_len, x);
      |                                  ^~~~~~~~~~~~~
SparseMatrix_mult.c:81:23: note: 'lv_vals' was declared here
   81 |         SEXP lv_offs, lv_vals;
      |                       ^~~~~~~
SparseMatrix_mult.c:85:49: warning: 'lv_offs' may be used uninitialized [-Wmaybe-uninitialized]
   85 |         _copy_doubles_to_offsets(REAL(lv_vals), INTEGER(lv_offs), lv_len, x);
      |                                                 ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c:81:14: note: 'lv_offs' was declared here
   81 |         SEXP lv_offs, lv_vals;
      |              ^~~~~~~
SparseMatrix_mult.c: In function 'lv_has_no_NA':
SparseMatrix_mult.c:44:26: warning: 'lv_vals' may be used uninitialized [-Wmaybe-uninitialized]
   44 |         return has_no_NA(INTEGER(lv_vals), lv_len);
      |                          ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c:41:23: note: 'lv_vals' was declared here
   41 |         SEXP lv_offs, lv_vals;
      |                       ^~~~~~~
SparseMatrix_mult.c: In function 'lv_has_no_NaN_or_Inf':
SparseMatrix_mult.c:35:34: warning: 'lv_vals' may be used uninitialized [-Wmaybe-uninitialized]
   35 |         return has_no_NaN_or_Inf(REAL(lv_vals), lv_len);
      |                                  ^~~~~~~~~~~~~
SparseMatrix_mult.c:32:23: note: 'lv_vals' was declared here
   32 |         SEXP lv_offs, lv_vals;
      |                       ^~~~~~~
SparseMatrix_mult.c: In function 'expand_int_lv':
SparseMatrix_mult.c:96:31: warning: 'lv_vals' may be used uninitialized [-Wmaybe-uninitialized]
   96 |         _copy_ints_to_offsets(INTEGER(lv_vals), INTEGER(lv_offs), lv_len, x);
      |                               ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c:92:23: note: 'lv_vals' was declared here
   92 |         SEXP lv_offs, lv_vals;
      |                       ^~~~~~~
SparseMatrix_mult.c:96:49: warning: 'lv_offs' may be used uninitialized [-Wmaybe-uninitialized]
   96 |         _copy_ints_to_offsets(INTEGER(lv_vals), INTEGER(lv_offs), lv_len, x);
      |                                                 ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c:92:14: note: 'lv_offs' was declared here
   92 |         SEXP lv_offs, lv_vals;
      |              ^~~~~~~
In function 'lv_has_no_NA',
    inlined from 'crossprod2_Rpp_int' at SparseMatrix_mult.c:801:14,
    inlined from 'C_crossprod2_SVT_SVT' at SparseMatrix_mult.c:1105:4:
SparseMatrix_mult.c:44:26: warning: 'lv_vals' may be used uninitialized [-Wmaybe-uninitialized]
   44 |         return has_no_NA(INTEGER(lv_vals), lv_len);
      |                          ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c: In function 'C_crossprod2_SVT_SVT':
SparseMatrix_mult.c:41:23: note: 'lv_vals' was declared here
   41 |         SEXP lv_offs, lv_vals;
      |                       ^~~~~~~
In function 'lv_has_no_NA',
    inlined from 'crossprod2_Lpp_int' at SparseMatrix_mult.c:833:14,
    inlined from 'C_crossprod2_SVT_SVT' at SparseMatrix_mult.c:1114:4:
SparseMatrix_mult.c:44:26: warning: 'lv_vals' may be used uninitialized [-Wmaybe-uninitialized]
   44 |         return has_no_NA(INTEGER(lv_vals), lv_len);
      |                          ^~~~~~~~~~~~~~~~
SparseMatrix_mult.c: In function 'C_crossprod2_SVT_SVT':
SparseMatrix_mult.c:41:23: note: 'lv_vals' was declared here
   41 |         SEXP lv_offs, lv_vals;
      |                       ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XVector_stubs.c -o XVector_stubs.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c coerceVector2.c -o coerceVector2.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c leaf_vector_Arith.c -o leaf_vector_Arith.o
leaf_vector_Arith.c: In function 'Rpow_double':
leaf_vector_Arith.c:164:19: 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:436:13: warning: 'lv_vals' may be used uninitialized [-Wmaybe-uninitialized]
  436 |         if (TYPEOF(lv_vals) == INTSXP) {
      |             ^~~~~~~~~~~~~~~
leaf_vector_Arith.c:430:23: note: 'lv_vals' was declared here
  430 |         SEXP lv_offs, lv_vals;
      |                       ^~~~~~~
leaf_vector_Arith.c:434:21: warning: 'lv_offs' may be used uninitialized [-Wmaybe-uninitialized]
  434 |         lv_offs_p = INTEGER(lv_offs);
      |                     ^~~~~~~~~~~~~~~~
leaf_vector_Arith.c:430:14: note: 'lv_offs' was declared here
  430 |         SEXP lv_offs, lv_vals;
      |              ^~~~~~~
leaf_vector_Arith.c: In function '_unary_minus_leaf_vector':
leaf_vector_Arith.c:67:43: warning: 'lv_vals' may be used uninitialized [-Wmaybe-uninitialized]
   67 |                         int *ans_vals_p = INTEGER(ans_vals);
      |                                           ^~~~~~~~~~~~~~~~~
leaf_vector_Arith.c:54:23: note: 'lv_vals' was declared here
   54 |         SEXP lv_offs, lv_vals, ans_vals, ans;
      |                       ^~~~~~~
leaf_vector_Arith.c:109:15: warning: 'lv_offs' may be used uninitialized [-Wmaybe-uninitialized]
  109 |         ans = _new_leaf_vector(lv_offs, ans_vals);
      |               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
leaf_vector_Arith.c:54:14: note: 'lv_offs' was declared here
   54 |         SEXP lv_offs, lv_vals, ans_vals, ans;
      |              ^~~~~~~
leaf_vector_Arith.c: In function '_Arith_lv1_v2':
leaf_vector_Arith.c:384:13: warning: 'lv1_vals' may be used uninitialized [-Wmaybe-uninitialized]
  384 |         if (TYPEOF(lv1_vals) == INTSXP) {
      |             ^~~~~~~~~~~~~~~~
leaf_vector_Arith.c:376:24: note: 'lv1_vals' was declared here
  376 |         SEXP lv1_offs, lv1_vals;
      |                        ^~~~~~~~
leaf_vector_Arith.c:381:19: warning: 'lv1_offs' may be used uninitialized [-Wmaybe-uninitialized]
  381 |         offs1_p = INTEGER(lv1_offs);
      |                   ^~~~~~~~~~~~~~~~~
leaf_vector_Arith.c:376:14: note: 'lv1_offs' was declared here
  376 |         SEXP lv1_offs, lv1_vals;
      |              ^~~~~~~~
leaf_vector_Arith.c: In function '_Arith_lv1_lv2':
leaf_vector_Arith.c:520:21: warning: 'lv2_vals' may be used uninitialized [-Wmaybe-uninitialized]
  520 |                 if (TYPEOF(lv2_vals) == INTSXP) {
      |                     ^~~~~~~~~~~~~~~~
leaf_vector_Arith.c:487:44: note: 'lv2_vals' was declared here
  487 |         SEXP lv1_offs, lv1_vals, lv2_offs, lv2_vals;
      |                                            ^~~~~~~~
leaf_vector_Arith.c:516:19: warning: 'lv2_offs' may be used uninitialized [-Wmaybe-uninitialized]
  516 |         offs2_p = INTEGER(lv2_offs);
      |                   ^~~~~~~~~~~~~~~~~
leaf_vector_Arith.c:487:34: note: 'lv2_offs' was declared here
  487 |         SEXP lv1_offs, lv1_vals, lv2_offs, lv2_vals;
      |                                  ^~~~~~~~
leaf_vector_Arith.c:519:13: warning: 'lv1_vals' may be used uninitialized [-Wmaybe-uninitialized]
  519 |         if (TYPEOF(lv1_vals) == INTSXP) {
      |             ^~~~~~~~~~~~~~~~
leaf_vector_Arith.c:487:24: note: 'lv1_vals' was declared here
  487 |         SEXP lv1_offs, lv1_vals, lv2_offs, lv2_vals;
      |                        ^~~~~~~~
leaf_vector_Arith.c:515:19: warning: 'lv1_offs' may be used uninitialized [-Wmaybe-uninitialized]
  515 |         offs1_p = INTEGER(lv1_offs);
      |                   ^~~~~~~~~~~~~~~~~
leaf_vector_Arith.c:487:14: note: 'lv1_offs' was declared here
  487 |         SEXP lv1_offs, lv1_vals, lv2_offs, lv2_vals;
      |              ^~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c leaf_vector_Compare.c -o leaf_vector_Compare.o
leaf_vector_Compare.c: In function 'Compare_lv1_zero':
leaf_vector_Compare.c:627:17: warning: 'lv1_vals' may be used uninitialized [-Wmaybe-uninitialized]
  627 |         switch (TYPEOF(lv1_vals)) {
      |                 ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c:622:24: note: 'lv1_vals' was declared here
  622 |         SEXP lv1_offs, lv1_vals;
      |                        ^~~~~~~~
leaf_vector_Compare.c:626:17: warning: 'lv1_offs' may be used uninitialized [-Wmaybe-uninitialized]
  626 |         offs1 = INTEGER(lv1_offs);
      |                 ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c:622:14: note: 'lv1_offs' was declared here
  622 |         SEXP lv1_offs, lv1_vals;
      |              ^~~~~~~~
leaf_vector_Compare.c: In function '_Compare_lv1_v2':
leaf_vector_Compare.c:669:17: warning: 'lv1_vals' may be used uninitialized [-Wmaybe-uninitialized]
  669 |         switch (TYPEOF(lv1_vals)) {
      |                 ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c:664:24: note: 'lv1_vals' was declared here
  664 |         SEXP lv1_offs, lv1_vals;
      |                        ^~~~~~~~
leaf_vector_Compare.c:668:17: warning: 'lv1_offs' may be used uninitialized [-Wmaybe-uninitialized]
  668 |         offs1 = INTEGER(lv1_offs);
      |                 ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c:664:14: note: 'lv1_offs' was declared here
  664 |         SEXP lv1_offs, lv1_vals;
      |              ^~~~~~~~
In function 'sparse_Compare_Rcomplexes_lv2',
    inlined from '_Compare_lv1_lv2' at leaf_vector_Compare.c:738:13:
leaf_vector_Compare.c:582:18: warning: 'lv2_vals' may be used uninitialized [-Wmaybe-uninitialized]
  582 |         Rtype2 = TYPEOF(lv2_vals);
      |                  ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c: In function '_Compare_lv1_lv2':
leaf_vector_Compare.c:576:24: note: 'lv2_vals' was declared here
  576 |         SEXP lv2_offs, lv2_vals;
      |                        ^~~~~~~~
In function 'sparse_Compare_Rcomplexes_lv2',
    inlined from '_Compare_lv1_lv2' at leaf_vector_Compare.c:738:13:
leaf_vector_Compare.c:581:17: warning: 'lv2_offs' may be used uninitialized [-Wmaybe-uninitialized]
  581 |         offs2 = INTEGER(lv2_offs);
      |                 ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c: In function '_Compare_lv1_lv2':
leaf_vector_Compare.c:576:14: note: 'lv2_offs' was declared here
  576 |         SEXP lv2_offs, lv2_vals;
      |              ^~~~~~~~
In function 'sparse_Compare_doubles_lv2',
    inlined from '_Compare_lv1_lv2' at leaf_vector_Compare.c:733:13:
leaf_vector_Compare.c:542:18: warning: 'lv2_vals' may be used uninitialized [-Wmaybe-uninitialized]
  542 |         Rtype2 = TYPEOF(lv2_vals);
      |                  ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c: In function '_Compare_lv1_lv2':
leaf_vector_Compare.c:536:24: note: 'lv2_vals' was declared here
  536 |         SEXP lv2_offs, lv2_vals;
      |                        ^~~~~~~~
In function 'sparse_Compare_doubles_lv2',
    inlined from '_Compare_lv1_lv2' at leaf_vector_Compare.c:733:13:
leaf_vector_Compare.c:541:17: warning: 'lv2_offs' may be used uninitialized [-Wmaybe-uninitialized]
  541 |         offs2 = INTEGER(lv2_offs);
      |                 ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c: In function '_Compare_lv1_lv2':
leaf_vector_Compare.c:536:14: note: 'lv2_offs' was declared here
  536 |         SEXP lv2_offs, lv2_vals;
      |              ^~~~~~~~
In function 'sparse_Compare_ints_lv2',
    inlined from '_Compare_lv1_lv2' at leaf_vector_Compare.c:728:13:
leaf_vector_Compare.c:502:18: warning: 'lv2_vals' may be used uninitialized [-Wmaybe-uninitialized]
  502 |         Rtype2 = TYPEOF(lv2_vals);
      |                  ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c: In function '_Compare_lv1_lv2':
leaf_vector_Compare.c:496:24: note: 'lv2_vals' was declared here
  496 |         SEXP lv2_offs, lv2_vals;
      |                        ^~~~~~~~
In function 'sparse_Compare_ints_lv2',
    inlined from '_Compare_lv1_lv2' at leaf_vector_Compare.c:728:13:
leaf_vector_Compare.c:501:17: warning: 'lv2_offs' may be used uninitialized [-Wmaybe-uninitialized]
  501 |         offs2 = INTEGER(lv2_offs);
      |                 ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c: In function '_Compare_lv1_lv2':
leaf_vector_Compare.c:496:14: note: 'lv2_offs' was declared here
  496 |         SEXP lv2_offs, lv2_vals;
      |              ^~~~~~~~
In function 'sparse_Compare_Rbytes_lv2',
    inlined from '_Compare_lv1_lv2' at leaf_vector_Compare.c:723:13:
leaf_vector_Compare.c:462:18: warning: 'lv2_vals' may be used uninitialized [-Wmaybe-uninitialized]
  462 |         Rtype2 = TYPEOF(lv2_vals);
      |                  ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c: In function '_Compare_lv1_lv2':
leaf_vector_Compare.c:456:24: note: 'lv2_vals' was declared here
  456 |         SEXP lv2_offs, lv2_vals;
      |                        ^~~~~~~~
In function 'sparse_Compare_Rbytes_lv2',
    inlined from '_Compare_lv1_lv2' at leaf_vector_Compare.c:723:13:
leaf_vector_Compare.c:461:17: warning: 'lv2_offs' may be used uninitialized [-Wmaybe-uninitialized]
  461 |         offs2 = INTEGER(lv2_offs);
      |                 ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c: In function '_Compare_lv1_lv2':
leaf_vector_Compare.c:456:14: note: 'lv2_offs' was declared here
  456 |         SEXP lv2_offs, lv2_vals;
      |              ^~~~~~~~
leaf_vector_Compare.c:720:18: warning: 'lv1_vals' may be used uninitialized [-Wmaybe-uninitialized]
  720 |         Rtype1 = TYPEOF(lv1_vals);
      |                  ^~~~~~~~~~~~~~~~
leaf_vector_Compare.c:705:24: note: 'lv1_vals' was declared here
  705 |         SEXP lv1_offs, lv1_vals;
      |                        ^~~~~~~~
leaf_vector_Compare.c:719:17: warning: 'lv1_offs' may be used uninitialized [-Wmaybe-uninitialized]
  719 |         offs1 = INTEGER(lv1_offs);
      |                 ^~~~~~~~~~~~~~~~~
leaf_vector_Compare.c:705:14: note: 'lv1_offs' was declared here
  705 |         SEXP lv1_offs, lv1_vals;
      |              ^~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c leaf_vector_Logic.c -o leaf_vector_Logic.o
leaf_vector_Logic.c: In function '_Logic_lv1_lv2':
leaf_vector_Logic.c:88:44: warning: 'lv2_vals' may be used uninitialized [-Wmaybe-uninitialized]
   88 |                         INTEGER(lv2_offs), INTEGER(lv2_vals), lv2_len,
      |                                            ^~~~~~~~~~~~~~~~~
leaf_vector_Logic.c:77:44: note: 'lv2_vals' was declared here
   77 |         SEXP lv1_offs, lv1_vals, lv2_offs, lv2_vals;
      |                                            ^~~~~~~~
leaf_vector_Logic.c:88:25: warning: 'lv2_offs' may be used uninitialized [-Wmaybe-uninitialized]
   88 |                         INTEGER(lv2_offs), INTEGER(lv2_vals), lv2_len,
      |                         ^~~~~~~~~~~~~~~~~
leaf_vector_Logic.c:77:34: note: 'lv2_offs' was declared here
   77 |         SEXP lv1_offs, lv1_vals, lv2_offs, lv2_vals;
      |                                  ^~~~~~~~
leaf_vector_Logic.c:87:44: warning: 'lv1_vals' may be used uninitialized [-Wmaybe-uninitialized]
   87 |                         INTEGER(lv1_offs), INTEGER(lv1_vals), lv1_len,
      |                                            ^~~~~~~~~~~~~~~~~
leaf_vector_Logic.c:77:24: note: 'lv1_vals' was declared here
   77 |         SEXP lv1_offs, lv1_vals, lv2_offs, lv2_vals;
      |                        ^~~~~~~~
leaf_vector_Logic.c:87:25: warning: 'lv1_offs' may be used uninitialized [-Wmaybe-uninitialized]
   87 |                         INTEGER(lv1_offs), INTEGER(lv1_vals), lv1_len,
      |                         ^~~~~~~~~~~~~~~~~
leaf_vector_Logic.c:77:14: note: 'lv1_offs' was declared here
   77 |         SEXP lv1_offs, lv1_vals, lv2_offs, lv2_vals;
      |              ^~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c leaf_vector_dotprod.c -o leaf_vector_dotprod.o
leaf_vector_dotprod.c: In function '_dotprod_leaf_vectors':
leaf_vector_dotprod.c:21:44: warning: 'lv2_vals' may be used uninitialized [-Wmaybe-uninitialized]
   21 |                         INTEGER(lv2_offs), REAL(lv2_vals), lv2_len,
      |                                            ^~~~~~~~~~~~~~
leaf_vector_dotprod.c:12:44: note: 'lv2_vals' was declared here
   12 |         SEXP lv1_offs, lv1_vals, lv2_offs, lv2_vals;
      |                                            ^~~~~~~~
leaf_vector_dotprod.c:21:25: warning: 'lv2_offs' may be used uninitialized [-Wmaybe-uninitialized]
   21 |                         INTEGER(lv2_offs), REAL(lv2_vals), lv2_len,
      |                         ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c:12:34: note: 'lv2_offs' was declared here
   12 |         SEXP lv1_offs, lv1_vals, lv2_offs, lv2_vals;
      |                                  ^~~~~~~~
leaf_vector_dotprod.c:20:44: warning: 'lv1_vals' may be used uninitialized [-Wmaybe-uninitialized]
   20 |                         INTEGER(lv1_offs), REAL(lv1_vals), lv1_len,
      |                                            ^~~~~~~~~~~~~~
leaf_vector_dotprod.c:12:24: note: 'lv1_vals' was declared here
   12 |         SEXP lv1_offs, lv1_vals, lv2_offs, lv2_vals;
      |                        ^~~~~~~~
leaf_vector_dotprod.c:20:25: warning: 'lv1_offs' may be used uninitialized [-Wmaybe-uninitialized]
   20 |                         INTEGER(lv1_offs), REAL(lv1_vals), lv1_len,
      |                         ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c:12:14: note: 'lv1_offs' was declared here
   12 |         SEXP lv1_offs, lv1_vals, lv2_offs, lv2_vals;
      |              ^~~~~~~~
leaf_vector_dotprod.c: In function '_dotprod_leaf_vector_and_finite_col':
leaf_vector_dotprod.c:47:19: warning: 'lv1_vals' may be used uninitialized [-Wmaybe-uninitialized]
   47 |         vals1_p = REAL(lv1_vals);
      |                   ^~~~~~~~~~~~~~
leaf_vector_dotprod.c:40:24: note: 'lv1_vals' was declared here
   40 |         SEXP lv1_offs, lv1_vals;
      |                        ^~~~~~~~
leaf_vector_dotprod.c:46:19: warning: 'lv1_offs' may be used uninitialized [-Wmaybe-uninitialized]
   46 |         offs1_p = INTEGER(lv1_offs);
      |                   ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c:40:14: note: 'lv1_offs' was declared here
   40 |         SEXP lv1_offs, lv1_vals;
      |              ^~~~~~~~
leaf_vector_dotprod.c: In function '_dotprod_leaf_vector_and_double_col':
leaf_vector_dotprod.c:71:19: warning: 'lv1_vals' may be used uninitialized [-Wmaybe-uninitialized]
   71 |         vals1_p = REAL(lv1_vals);
      |                   ^~~~~~~~~~~~~~
leaf_vector_dotprod.c:63:24: note: 'lv1_vals' was declared here
   63 |         SEXP lv1_offs, lv1_vals;
      |                        ^~~~~~~~
leaf_vector_dotprod.c:70:19: warning: 'lv1_offs' may be used uninitialized [-Wmaybe-uninitialized]
   70 |         offs1_p = INTEGER(lv1_offs);
      |                   ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c:63:14: note: 'lv1_offs' was declared here
   63 |         SEXP lv1_offs, lv1_vals;
      |              ^~~~~~~~
leaf_vector_dotprod.c: In function '_dotprod_leaf_vector_and_noNA_int_col':
leaf_vector_dotprod.c:107:19: warning: 'lv1_vals' may be used uninitialized [-Wmaybe-uninitialized]
  107 |         vals1_p = INTEGER(lv1_vals);
      |                   ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c:99:24: note: 'lv1_vals' was declared here
   99 |         SEXP lv1_offs, lv1_vals;
      |                        ^~~~~~~~
leaf_vector_dotprod.c:106:19: warning: 'lv1_offs' may be used uninitialized [-Wmaybe-uninitialized]
  106 |         offs1_p = INTEGER(lv1_offs);
      |                   ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c:99:14: note: 'lv1_offs' was declared here
   99 |         SEXP lv1_offs, lv1_vals;
      |              ^~~~~~~~
leaf_vector_dotprod.c: In function '_dotprod_leaf_vector_and_int_col':
leaf_vector_dotprod.c:132:19: warning: 'lv1_vals' may be used uninitialized [-Wmaybe-uninitialized]
  132 |         vals1_p = INTEGER(lv1_vals);
      |                   ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c:125:24: note: 'lv1_vals' was declared here
  125 |         SEXP lv1_offs, lv1_vals;
      |                        ^~~~~~~~
leaf_vector_dotprod.c:131:19: warning: 'lv1_offs' may be used uninitialized [-Wmaybe-uninitialized]
  131 |         offs1_p = INTEGER(lv1_offs);
      |                   ^~~~~~~~~~~~~~~~~
leaf_vector_dotprod.c:125:14: note: 'lv1_offs' was declared here
  125 |         SEXP lv1_offs, lv1_vals;
      |              ^~~~~~~~
leaf_vector_dotprod.c: In function '_dotprod0_leaf_vector':
leaf_vector_dotprod.c:188:37: warning: 'lv_vals' may be used uninitialized [-Wmaybe-uninitialized]
  188 |         return _dotprod0_double_col(REAL(lv_vals), lv_len);
      |                                     ^~~~~~~~~~~~~
leaf_vector_dotprod.c:185:23: note: 'lv_vals' was declared here
  185 |         SEXP lv_offs, lv_vals;
      |                       ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c leaf_vector_summarization.c -o leaf_vector_summarization.o
leaf_vector_summarization.c: In function '_summarize_leaf_vector':
leaf_vector_summarization.c:21:9: warning: 'lv_vals' may be used uninitialized [-Wmaybe-uninitialized]
   21 |         _summarize_Rvector(lv_vals, summarize_op, res);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
leaf_vector_summarization.c:14:23: note: 'lv_vals' was declared here
   14 |         SEXP lv_offs, lv_vals;
      |                       ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c leaf_vector_utils.c -o leaf_vector_utils.o
leaf_vector_utils.c: In function '_make_leaf_vector_from_bufs.part.0':
leaf_vector_utils.c:88:9: warning: 'ans_vals' may be used uninitialized [-Wmaybe-uninitialized]
   88 |         memcpy(DATAPTR(ans_vals), vals_buf, Rtype_size * buf_len);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
leaf_vector_utils.c:76:29: note: 'ans_vals' was declared here
   76 |         SEXP ans, ans_offs, ans_vals;
      |                             ^~~~~~~~
leaf_vector_utils.c:87:16: warning: 'ans_offs' may be used uninitialized [-Wmaybe-uninitialized]
   87 |         memcpy(INTEGER(ans_offs), offs_buf, sizeof(int) * buf_len);
      |                ^~~~~~~~~~~~~~~~~
leaf_vector_utils.c:76:19: note: 'ans_offs' was declared here
   76 |         SEXP ans, ans_offs, ans_vals;
      |                   ^~~~~~~~
leaf_vector_utils.c: In function '_remove_zeros_from_leaf_vector':
leaf_vector_utils.c:169:19: warning: 'lv_vals' may be used uninitialized [-Wmaybe-uninitialized]
  169 |         ans_len = _collect_offsets_of_nonzero_Rsubvec_elts(
      |                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  170 |                                 lv_vals, 0, lv_len,
      |                                 ~~~~~~~~~~~~~~~~~~~
  171 |                                 offs_buf);
      |                                 ~~~~~~~~~
leaf_vector_utils.c:165:23: note: 'lv_vals' was declared here
  165 |         SEXP lv_offs, lv_vals, ans_offs, ans_vals, ans;
      |                       ^~~~~~~
leaf_vector_utils.c:178:29: warning: 'lv_offs' may be used uninitialized [-Wmaybe-uninitialized]
  178 |         _copy_selected_ints(INTEGER(lv_offs), offs_buf, ans_len,
      |                             ^~~~~~~~~~~~~~~~
leaf_vector_utils.c:165:14: note: 'lv_offs' was declared here
  165 |         SEXP lv_offs, lv_vals, ans_offs, ans_vals, ans;
      |              ^~~~~~~
leaf_vector_utils.c: In function '_coerce_leaf_vector':
leaf_vector_utils.c:207:43: warning: 'lv_vals' may be used uninitialized [-Wmaybe-uninitialized]
  207 |         if (_coercion_can_introduce_zeros(TYPEOF(lv_vals), new_Rtype))
      |                                           ^~~~~~~~~~~~~~~
leaf_vector_utils.c:200:23: note: 'lv_vals' was declared here
  200 |         SEXP lv_offs, lv_vals, ans_vals, ans;
      |                       ^~~~~~~
In file included from F:/biocbuild/bbs-3.18-bioc/R/include/Rdefines.h:41,
                 from leaf_vector_utils.h:4,
                 from leaf_vector_utils.c:4:
F:/biocbuild/bbs-3.18-bioc/R/include/Rinternals.h:368:25: warning: 'lv_offs' may be used uninitialized [-Wmaybe-uninitialized]
  368 | #define PROTECT(s)      Rf_protect(s)
      |                         ^~~~~~~~~~
leaf_vector_utils.c:200:14: 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:294:25: warning: 'ans_vals' may be used uninitialized [-Wmaybe-uninitialized]
  294 |                         copy_Rvector_elt_FUN(lv_vals, (R_xlen_t) k1,
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  295 |                                              ans_vals, (R_xlen_t) k);
      |                                              ~~~~~~~~~~~~~~~~~~~~~~~
leaf_vector_utils.c:231:47: note: 'ans_vals' was declared here
  231 |         SEXP lv_offs, lv_vals, ans, ans_offs, ans_vals;
      |                                               ^~~~~~~~
leaf_vector_utils.c:289:22: warning: 'ans_offs' may be used uninitialized [-Wmaybe-uninitialized]
  289 |         ans_offs_p = INTEGER(ans_offs);
      |                      ^~~~~~~~~~~~~~~~~
leaf_vector_utils.c:231:37: note: 'ans_offs' was declared here
  231 |         SEXP lv_offs, lv_vals, ans, ans_offs, ans_vals;
      |                                     ^~~~~~~~
leaf_vector_utils.c:239:17: warning: 'lv_vals' may be used uninitialized [-Wmaybe-uninitialized]
  239 |         Rtype = TYPEOF(lv_vals);
      |                 ^~~~~~~~~~~~~~~
leaf_vector_utils.c:231:23: note: 'lv_vals' was declared here
  231 |         SEXP lv_offs, lv_vals, ans, ans_offs, ans_vals;
      |                       ^~~~~~~
leaf_vector_utils.c:287:19: warning: 'lv_offs' may be used uninitialized [-Wmaybe-uninitialized]
  287 |         offs1_p = INTEGER(lv_offs);
      |                   ^~~~~~~~~~~~~~~~
leaf_vector_utils.c:231:14: note: 'lv_offs' was declared here
  231 |         SEXP lv_offs, lv_vals, ans, ans_offs, ans_vals;
      |              ^~~~~~~
leaf_vector_utils.c: In function '_lv_apply_to_REALSXP':
leaf_vector_utils.c:374:20: warning: 'lv_vals' may be used uninitialized [-Wmaybe-uninitialized]
  374 |         in_Rtype = TYPEOF(lv_vals);
      |                    ^~~~~~~~~~~~~~~
leaf_vector_utils.c:368:23: note: 'lv_vals' was declared here
  368 |         SEXP lv_offs, lv_vals;
      |                       ^~~~~~~
leaf_vector_utils.c:373:16: warning: 'lv_offs' may be used uninitialized [-Wmaybe-uninitialized]
  373 |         offs = INTEGER(lv_offs);
      |                ^~~~~~~~~~~~~~~~
leaf_vector_utils.c:368:14: note: 'lv_offs' was declared here
  368 |         SEXP lv_offs, lv_vals;
      |              ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matrixStats_methods.c -o matrixStats_methods.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c randomSparseArray.c -o randomSparseArray.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c readSparseCSV.c -o readSparseCSV.o
In function 'load_csv_row_to_AEbufs',
    inlined from 'read_sparse_csv' at readSparseCSV.c:342:4,
    inlined from 'C_readSparseCSV_as_SVT_SparseMatrix' at readSparseCSV.c:402:11:
readSparseCSV.c:255:25: warning: 'vals_buf' may be used uninitialized [-Wmaybe-uninitialized]
  255 |                         load_csv_data_to_AEbufs(data, data_len, col_idx - 1,
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  256 |                                                 offs_buf, vals_buf);
      |                                                 ~~~~~~~~~~~~~~~~~~~
readSparseCSV.c: In function 'C_readSparseCSV_as_SVT_SparseMatrix':
readSparseCSV.c:307:27: note: 'vals_buf' was declared here
  307 |         IntAE *offs_buf, *vals_buf;
      |                           ^~~~~~~~
In function 'load_csv_row_to_AEbufs',
    inlined from 'read_sparse_csv' at readSparseCSV.c:342:4,
    inlined from 'C_readSparseCSV_as_SVT_SparseMatrix' at readSparseCSV.c:402:11:
readSparseCSV.c:255:25: warning: 'offs_buf' may be used uninitialized [-Wmaybe-uninitialized]
  255 |                         load_csv_data_to_AEbufs(data, data_len, col_idx - 1,
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  256 |                                                 offs_buf, vals_buf);
      |                                                 ~~~~~~~~~~~~~~~~~~~
readSparseCSV.c: In function 'C_readSparseCSV_as_SVT_SparseMatrix':
readSparseCSV.c:307:16: note: 'offs_buf' was declared here
  307 |         IntAE *offs_buf, *vals_buf;
      |                ^~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rowsum_methods.c -o rowsum_methods.o
In function 'rowsum_SVT_int',
    inlined from 'C_rowsum_SVT' at rowsum_methods.c:173:3:
rowsum_methods.c:109:25: warning: 'lv_vals' may be used uninitialized [-Wmaybe-uninitialized]
  109 |                         INTEGER(lv_vals), INTEGER(lv_offs), lv_len,
      |                         ^~~~~~~~~~~~~~~~
rowsum_methods.c: In function 'C_rowsum_SVT':
rowsum_methods.c:98:31: note: 'lv_vals' was declared here
   98 |         SEXP subSVT, lv_offs, lv_vals;
      |                               ^~~~~~~
In function 'rowsum_SVT_int',
    inlined from 'C_rowsum_SVT' at rowsum_methods.c:173:3:
rowsum_methods.c:109:43: warning: 'lv_offs' may be used uninitialized [-Wmaybe-uninitialized]
  109 |                         INTEGER(lv_vals), INTEGER(lv_offs), lv_len,
      |                                           ^~~~~~~~~~~~~~~~
rowsum_methods.c: In function 'C_rowsum_SVT':
rowsum_methods.c:98:22: note: 'lv_offs' was declared here
   98 |         SEXP subSVT, lv_offs, lv_vals;
      |                      ^~~~~~~
In function 'rowsum_SVT_double',
    inlined from 'C_rowsum_SVT' at rowsum_methods.c:168:3:
rowsum_methods.c:88:25: warning: 'lv_vals' may be used uninitialized [-Wmaybe-uninitialized]
   88 |                         REAL(lv_vals), INTEGER(lv_offs), lv_len,
      |                         ^~~~~~~~~~~~~
rowsum_methods.c: In function 'C_rowsum_SVT':
rowsum_methods.c:78:31: note: 'lv_vals' was declared here
   78 |         SEXP subSVT, lv_offs, lv_vals;
      |                               ^~~~~~~
In function 'rowsum_SVT_double',
    inlined from 'C_rowsum_SVT' at rowsum_methods.c:168:3:
rowsum_methods.c:88:40: warning: 'lv_offs' may be used uninitialized [-Wmaybe-uninitialized]
   88 |                         REAL(lv_vals), INTEGER(lv_offs), lv_len,
      |                                        ^~~~~~~~~~~~~~~~
rowsum_methods.c: In function 'C_rowsum_SVT':
rowsum_methods.c:78:22: note: 'lv_offs' was declared here
   78 |         SEXP subSVT, lv_offs, lv_vals;
      |                      ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sparseMatrix_utils.c -o sparseMatrix_utils.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/XVector/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test.c -o test.o
gcc -shared -s -static-libgcc -o SparseArray.dll tmp.def 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 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-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)

R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
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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: '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 0 | WARN 1 | SKIP 0 | PASS 5894 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 5894 ]
> 
> proc.time()
   user  system elapsed 
  35.57    4.04   39.65