Running ‘testthat.R’ [29m/56m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > # library("testthat")
  > # library("inDAGO")
  > 
  > testthat::test_check("inDAGO")
  Loading required package: inDAGO
  The following packages are not installed: ShortRead, rtracklayer, Rsamtools, HTSFilter.
  To enable all the features of inDAGO, install with:
    if (!requireNamespace('BiocManager', quietly=TRUE))
      install.packages('BiocManager')
    BiocManager::install(c("ShortRead", "rtracklayer", "Rsamtools", "HTSFilter"))
  
  'getOption("repos")' replaces Bioconductor standard repositories, see
  'help("repositories", package = "BiocManager")' for details.
  Replacement repositories:
      CRAN: file:///data/gannet/ripley/R
  Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable)
    (2026-03-06 r89558)
  Installing package(s) 'ShortRead'
  also installing the dependencies 'SparseArray', 'DelayedArray', 'SummarizedExperiment', 'Rsamtools', 'GenomicAlignments'
  
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SparseArray_1.11.10.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/DelayedArray_0.37.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SummarizedExperiment_1.41.1.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Rsamtools_2.27.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/GenomicAlignments_1.47.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/ShortRead_1.69.2.tar.gz'
  * installing *source* package ‘SparseArray’ ...
  ** this is package ‘SparseArray’ version ‘1.11.10’
  ** using staged installation
  ** libs
  using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
  make[1]: Entering directory '/tmp/RtmpjMtCOC/working_dir/RtmpadTu1B/R.INSTALL377f6e4e694dcd/SparseArray/src'
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o
  In file included from leaf_utils.h:6,
                   from ExtendableJaggedArray.c:8:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: ExtendableJaggedArray.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c IRanges_stubs.c -o IRanges_stubs.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c OPBufTree.c -o OPBufTree.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c R_init_SparseArray.c -o R_init_SparseArray.o
  In file included from leaf_utils.h:6,
                   from R_init_SparseArray.c:6:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: R_init_SparseArray.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c Rvector_utils.c -o Rvector_utils.o
  Rvector_utils.c: In function ‘_fill_Rvector_block_with_val’:
  Rvector_utils.c:245:43: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    245 |         _set_elts_to_val(TYPEOF(Rvector), DATAPTR(Rvector),
        |                                           ^~~~~~~
        |                                           DATAPTR_RO
  Rvector_utils.c:245:43: error: passing argument 2 of ‘_set_elts_to_val’ makes pointer from integer without a cast [-Wint-conversion]
    245 |         _set_elts_to_val(TYPEOF(Rvector), DATAPTR(Rvector),
        |                                           ^~~~~~~~~~~~~~~~
        |                                           |
        |                                           int
  Rvector_utils.c:99:45: note: expected ‘void *’ but argument is of type ‘int’
     99 | void _set_elts_to_val(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n,
        |                                       ~~~~~~^
  Rvector_utils.c: In function ‘_fill_Rvector_block_with_zeros’:
  Rvector_utils.c:263:34: error: passing argument 2 of ‘_set_elts_to_zero’ makes pointer from integer without a cast [-Wint-conversion]
    263 |         _set_elts_to_zero(Rtype, DATAPTR(Rvector), block_offset, block_len);
        |                                  ^~~~~~~~~~~~~~~~
        |                                  |
        |                                  int
  Rvector_utils.c:122:46: note: expected ‘void *’ but argument is of type ‘int’
    122 | void _set_elts_to_zero(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n)
        |                                        ~~~~~~^
  Rvector_utils.c: In function ‘_fill_Rvector_block_with_ones’:
  Rvector_utils.c:271:43: error: passing argument 2 of ‘_set_elts_to_one’ makes pointer from integer without a cast [-Wint-conversion]
    271 |         _set_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector),
        |                                           ^~~~~~~~~~~~~~~~
        |                                           |
        |                                           int
  Rvector_utils.c:137:45: note: expected ‘void *’ but argument is of type ‘int’
    137 | void _set_elts_to_one(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n)
        |                                       ~~~~~~^
  Rvector_utils.c: In function ‘_fill_Rvector_block_with_minus_one’:
  Rvector_utils.c:280:49: error: passing argument 2 of ‘_set_elts_to_minus_one’ makes pointer from integer without a cast [-Wint-conversion]
    280 |         _set_elts_to_minus_one(TYPEOF(Rvector), DATAPTR(Rvector),
        |                                                 ^~~~~~~~~~~~~~~~
        |                                                 |
        |                                                 int
  Rvector_utils.c:159:51: note: expected ‘void *’ but argument is of type ‘int’
    159 | void _set_elts_to_minus_one(SEXPTYPE Rtype, void *x,
        |                                             ~~~~~~^
  Rvector_utils.c: In function ‘_fill_Rvector_block_with_NA’:
  Rvector_utils.c:296:32: error: passing argument 2 of ‘_set_elts_to_NA’ makes pointer from integer without a cast [-Wint-conversion]
    296 |         _set_elts_to_NA(Rtype, DATAPTR(Rvector), block_offset, block_len);
        |                                ^~~~~~~~~~~~~~~~
        |                                |
        |                                int
  Rvector_utils.c:184:44: note: expected ‘void *’ but argument is of type ‘int’
    184 | void _set_elts_to_NA(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n)
        |                                      ~~~~~~^
  Rvector_utils.c: In function ‘_fill_Rvector_subset_with_zeros’:
  Rvector_utils.c:463:43: error: passing argument 2 of ‘_set_selected_elts_to_zero’ makes pointer from integer without a cast [-Wint-conversion]
    463 |         _set_selected_elts_to_zero(Rtype, DATAPTR(Rvector),
        |                                           ^~~~~~~~~~~~~~~~
        |                                           |
        |                                           int
  Rvector_utils.c:365:55: note: expected ‘void *’ but argument is of type ‘int’
    365 | void _set_selected_elts_to_zero(SEXPTYPE Rtype, void *x,
        |                                                 ~~~~~~^
  Rvector_utils.c: In function ‘_fill_Rvector_subset_with_ones’:
  Rvector_utils.c:473:52: error: passing argument 2 of ‘_set_selected_elts_to_one’ makes pointer from integer without a cast [-Wint-conversion]
    473 |         _set_selected_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector),
        |                                                    ^~~~~~~~~~~~~~~~
        |                                                    |
        |                                                    int
  Rvector_utils.c:397:54: note: expected ‘void *’ but argument is of type ‘int’
    397 | void _set_selected_elts_to_one(SEXPTYPE Rtype, void *x,
        |                                                ~~~~~~^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: Rvector_utils.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SBT_utils.c -o SBT_utils.o
  In file included from leaf_utils.h:6,
                   from SBT_utils.c:7:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SBT_utils.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o
  In file included from leaf_utils.h:6,
                   from SVT_SparseArray_class.c:9:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SVT_SparseArray_class.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o
  In file included from SparseArray_Arith_methods.c:7:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Arith_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o
  In file included from SparseArray_Compare_methods.c:7:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Compare_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o
  In file included from leaf_utils.h:6,
                   from SparseArray_Complex_methods.c:6:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Complex_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o
  In file included from SparseArray_Logic_methods.c:7:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Logic_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o
  In file included from SparseArray_Math_methods.c:7:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Math_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_abind.c -o SparseArray_abind.o
  In file included from leaf_utils.h:6,
                   from SparseArray_abind.c:11:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_abind.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_aperm.c -o SparseArray_aperm.o
  In file included from leaf_utils.h:6,
                   from SparseArray_aperm.c:16:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  SparseArray_aperm.c: In function ‘spray_integer_leaf’:
  SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    724 |                 nzvals_p = (const type *) DATAPTR(nzvals);              \
        |                            ^
  SparseArray_aperm.c:746:39: note: in expansion of macro ‘FUNDEF_spray_leaf’
    746 | static inline void spray_integer_leaf FUNDEF_spray_leaf(int)
        |                                       ^~~~~~~~~~~~~~~~~
  SparseArray_aperm.c: In function ‘spray_double_leaf’:
  SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    724 |                 nzvals_p = (const type *) DATAPTR(nzvals);              \
        |                            ^
  SparseArray_aperm.c:747:38: note: in expansion of macro ‘FUNDEF_spray_leaf’
    747 | static inline void spray_double_leaf FUNDEF_spray_leaf(double)
        |                                      ^~~~~~~~~~~~~~~~~
  SparseArray_aperm.c: In function ‘spray_complex_leaf’:
  SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    724 |                 nzvals_p = (const type *) DATAPTR(nzvals);              \
        |                            ^
  SparseArray_aperm.c:748:39: note: in expansion of macro ‘FUNDEF_spray_leaf’
    748 | static inline void spray_complex_leaf FUNDEF_spray_leaf(Rcomplex)
        |                                       ^~~~~~~~~~~~~~~~~
  SparseArray_aperm.c: In function ‘spray_raw_leaf’:
  SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    724 |                 nzvals_p = (const type *) DATAPTR(nzvals);              \
        |                            ^
  SparseArray_aperm.c:749:35: note: in expansion of macro ‘FUNDEF_spray_leaf’
    749 | static inline void spray_raw_leaf FUNDEF_spray_leaf(Rbyte)
        |                                   ^~~~~~~~~~~~~~~~~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_aperm.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o
  In file included from leaf_utils.h:6,
                   from SparseArray_dim_tuning.c:7:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_dim_tuning.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o
  In file included from SparseArray_matrixStats.c:15:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  SparseArray_matrixStats.c: In function ‘C_colStats_SVT’:
  SparseArray_matrixStats.c:275:26: error: passing argument 6 of ‘REC_colStats_SVT’ makes pointer from integer without a cast [-Wint-conversion]
    275 |                          DATAPTR(ans), ans_Rtype,
        |                          ^~~~~~~~~~~~
        |                          |
        |                          int
  SparseArray_matrixStats.c:203:23: note: expected ‘void *’ but argument is of type ‘int’
    203 |                 void *out, SEXPTYPE out_Rtype,
        |                 ~~~~~~^~~
  SparseArray_matrixStats.c: In function ‘C_rowStats_SVT’:
  SparseArray_matrixStats.c:1178:25: error: passing argument 8 of ‘SVT_rowMinsMaxs’ makes pointer from integer without a cast [-Wint-conversion]
   1178 |                         DATAPTR(ans), LENGTH(ans), ans_Rtype,
        |                         ^~~~~~~~~~~~
        |                         |
        |                         int
  SparseArray_matrixStats.c:966:23: note: expected ‘void *’ but argument is of type ‘int’
    966 |                 void *out, R_xlen_t out_len, SEXPTYPE out_Rtype,
        |                 ~~~~~~^~~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_matrixStats.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o
  In file included from leaf_utils.h:6,
                   from SparseArray_misc_methods.c:8:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_misc_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_subassignment.c -o SparseArray_subassignment.o
  In file included from leaf_utils.h:6,
                   from SparseArray_subassignment.c:13:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_subassignment.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_subsetting.c -o SparseArray_subsetting.o
  In file included from leaf_utils.h:6,
                   from SparseArray_subsetting.c:14:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  SparseArray_subsetting.c: In function ‘REC_subset_SVT_as_SVT’:
  SparseArray_subsetting.c:843:26: warning: comparison between pointer and integer
    843 |                 if (offs != i2 || ans_elt != subSVT)
        |                          ^~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_subsetting.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_summarization.c -o SparseArray_summarization.o
  In file included from leaf_utils.h:6,
                   from SparseArray_summarization.c:12:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_summarization.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseMatrix_mult.c -o SparseMatrix_mult.o
  In file included from SparseMatrix_mult.c:14:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  SparseMatrix_mult.c: At top level:
  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(
        |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseMatrix_mult.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec.c -o SparseVec.o
  In file included from SparseVec.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_Arith.c -o SparseVec_Arith.o
  In file included from SparseVec_Arith.h:6,
                   from SparseVec_Arith.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Arith.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_Compare.c -o SparseVec_Compare.o
  In file included from SparseVec_Compare.h:6,
                   from SparseVec_Compare.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Compare.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_Logic.c -o SparseVec_Logic.o
  In file included from SparseVec_Logic.h:6,
                   from SparseVec_Logic.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Logic.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_Math.c -o SparseVec_Math.o
  In file included from SparseVec_Math.h:6,
                   from SparseVec_Math.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Math.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_dotprod.c -o SparseVec_dotprod.o
  In file included from SparseVec_dotprod.h:4,
                   from SparseVec_dotprod.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_dotprod.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_subassignment.c -o SparseVec_subassignment.o
  In file included from SparseVec_subassignment.h:6,
                   from SparseVec_subassignment.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_subassignment.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_subsetting.c -o SparseVec_subsetting.o
  In file included from SparseVec_subsetting.h:6,
                   from SparseVec_subsetting.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_subsetting.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c XVector_stubs.c -o XVector_stubs.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c argcheck_utils.c -o argcheck_utils.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c coerceVector2.c -o coerceVector2.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c leaf_utils.c -o leaf_utils.o
  In file included from leaf_utils.h:6,
                   from leaf_utils.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  leaf_utils.c: In function ‘_make_leaf_from_two_arrays’:
  leaf_utils.c:132:24: error: passing argument 1 of ‘memcpy’ makes pointer from integer without a cast [-Wint-conversion]
    132 |                 memcpy(DATAPTR(ans_nzvals), nzvals_p, Rtype_size * nzcount);
        |                        ^~~~~~~~~~~~~~~~~~~
        |                        |
        |                        int
  In file included from /usr/include/features.h:524,
                   from /usr/include/bits/libc-header-start.h:33,
                   from /usr/include/string.h:26,
                   from /data/gannet/ripley/R/R-devel/include/R_ext/RS.h:34,
                   from /data/gannet/ripley/R/R-devel/include/Rdefines.h:38,
                   from leaf_utils.h:4:
  /usr/include/bits/string_fortified.h:26:1: note: expected ‘void *’ but argument is of type ‘int’
     26 | __NTH (memcpy (void *__restrict __dest, const void *__restrict __src,
        | ^~~~~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: leaf_utils.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c misc_utils.c -o misc_utils.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c randomSparseArray.c -o randomSparseArray.o
  In file included from leaf_utils.h:6,
                   from randomSparseArray.c:6:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: randomSparseArray.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c readSparseCSV.c -o readSparseCSV.o
  In file included from leaf_utils.h:6,
                   from readSparseCSV.c:10:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: readSparseCSV.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c rowsum_methods.c -o rowsum_methods.o
  In file included from leaf_utils.h:6,
                   from rowsum_methods.c:9:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: rowsum_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c sparseMatrix_utils.c -o sparseMatrix_utils.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c test.c -o test.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c thread_control.c -o thread_control.o
  make[1]: Target 'all' not remade because of errors.
  make[1]: Leaving directory '/tmp/RtmpjMtCOC/working_dir/RtmpadTu1B/R.INSTALL377f6e4e694dcd/SparseArray/src'
  ERROR: compilation failed for package ‘SparseArray’
  * removing ‘/data/gannet/ripley/R/packages/tests-devel/inDAGO.Rcheck/SparseArray’
  * installing *source* package ‘Rsamtools’ ...
  ** this is package ‘Rsamtools’ version ‘2.27.0’
  ** using staged installation
  ** libs
  using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
  using C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
  make[1]: Entering directory '/tmp/RtmpjMtCOC/working_dir/RtmpgDwZgd/R.INSTALL37899657c3e5a3/Rsamtools/src'
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c Biostrings_stubs.c -o Biostrings_stubs.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c IRanges_stubs.c -o IRanges_stubs.o
  g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c PileupBuffer.cpp -o PileupBuffer.o
  g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c PosCacheColl.cpp -o PosCacheColl.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c R_init_Rsamtools.c -o R_init_Rsamtools.o
  g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c ResultManager.cpp -o ResultManager.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c XVector_stubs.c -o XVector_stubs.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c as_bam.c -o as_bam.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bam.c -o bam.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bam_data.c -o bam_data.o
  g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c bam_mate_iter.cpp -o bam_mate_iter.o
  In file included from Template.h:9,
                   from BamIterator.h:10,
                   from BamRangeIterator.h:7,
                   from bam_mate_iter.cpp:1:
  BamRangeIterator.h: In member function ‘virtual void BamRangeIterator::finalize_inprogress(bamFile)’:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/samtools-1.7-compat.h:14:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
     14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
        |                                ~~~~~~~~~^~~~~~~~~~~~~~
  BamRangeIterator.h:138:16: note: in expansion of macro ‘bam_seek’
    138 |         (void) bam_seek(bfile, pos, SEEK_SET);
        |                ^~~~~~~~
  BamIterator.h: In constructor ‘BamIterator::BamIterator(bamFile, const bam_index_t*)’:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/samtools-1.7-compat.h:14:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
     14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
        |                                ~~~~~~~~~^~~~~~~~~~~~~~
  BamIterator.h:87:16: note: in expansion of macro ‘bam_seek’
     87 |         (void) bam_seek(bfile, 0, 0);
        |                ^~~~~~~~
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bam_plbuf.c -o bam_plbuf.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bam_sort.c -o bam_sort.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bambuffer.c -o bambuffer.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bamfile.c -o bamfile.o
  bamfile.c: In function ‘bamfile_isincomplete’:
  bamfile.c:168:20: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
    168 |             (void) bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
        |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  In function ‘_bam_tryindexload’,
      inlined from ‘_bamfile_open_r’ at bamfile.c:89:24,
      inlined from ‘bamfile_open’ at bamfile.c:127:17:
  bamfile.c:29:17: warning: ‘cfile’ may be used uninitialized [-Wmaybe-uninitialized]
     29 |         index = hts_idx_load2(file, indexname);
        |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  bamfile.c: In function ‘bamfile_open’:
  bamfile.c:73:17: note: ‘cfile’ was declared here
     73 |     const char *cfile;
        |                 ^~~~~
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bcffile.c -o bcffile.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bedidx.c -o bedidx.o
  In file included from bedidx.c:1:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/bedidx.c: In function ‘bed_hash_regions’:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/bedidx.c:537:97: warning: format ‘%p’ expects argument of type ‘void *’, but argument 4 has type ‘reghash_t *’ {aka ‘struct kh_reg_s *’} [-Wformat=]
    537 |             fprintf(stderr, "Error when inserting region='%s' in the bed hash table at address=%p!\n", regs[i], h);
        |                                                                                                ~^               ~
        |                                                                                                 |               |
        |                                                                                                 void *          reghash_t * {aka struct kh_reg_s *}
  /data/gannet/ripley/R/test-dev/Rhtslib/include/bedidx.c:542:103: warning: format ‘%p’ expects argument of type ‘void *’, but argument 4 has type ‘reghash_t *’ {aka ‘struct kh_reg_s *’} [-Wformat=]
    542 |             fprintf(stderr, "Error when inserting region='%s' in the temporary hash table at address=%p!\n", regs[i], t);
        |                                                                                                      ~^               ~
        |                                                                                                       |               |
        |                                                                                                       void *          reghash_t * {aka struct kh_reg_s *}
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c encode.c -o encode.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c fafile.c -o fafile.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c idxstats.c -o idxstats.o
  In file included from bamfile.h:5,
                   from idxstats.c:1:
  idxstats.c: In function ‘idxstats_bamfile’:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/samtools-1.7-compat.h:14:32: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
     14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
        |                                ^~~~~~~~~~~~~~~~~~~~~~~
  idxstats.c:20:12: note: in expansion of macro ‘bam_seek’
     20 |     (void) bam_seek(fp, 0, 0);
        |            ^~~~~~~~
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c io_sam.c -o io_sam.o
  In file included from io_sam.c:9:
  io_sam.c: In function ‘_tmpl_PhredQuality’:
  utilities.h:55:5: error: implicit declaration of function ‘SET_TYPEOF’; did you mean ‘TYPEOF’? [-Wimplicit-function-declaration]
     55 |     SET_TYPEOF(T, LANGSXP);                     \
        |     ^~~~~~~~~~
  io_sam.c:88:5: note: in expansion of macro ‘NEW_CALL’
     88 |     NEW_CALL(s, t, "PhredQuality", nmspc, 2);
        |     ^~~~~~~~
  In file included from io_sam.c:3:
  io_sam.c: In function ‘_scan_bam_all’:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/samtools-1.7-compat.h:14:32: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
     14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
        |                                ^~~~~~~~~~~~~~~~~~~~~~~
  io_sam.c:302:12: note: in expansion of macro ‘bam_seek’
    302 |     (void) bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
        |            ^~~~~~~~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: io_sam.o] Error 1
  g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
  g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c pileup.cpp -o pileup.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c pileupbam.c -o pileupbam.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c sam_opts.c -o sam_opts.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c sam_utils.c -o sam_utils.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c samtools_patch.c -o samtools_patch.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c scan_bam_data.c -o scan_bam_data.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c tabixfile.c -o tabixfile.o
  tabixfile.c: In function ‘index_tabix’:
  tabixfile.c:190:5: warning: ‘bgzf_is_bgzf’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
    190 |     if (bgzf_is_bgzf(fn) != 1)
        |     ^~
  In file included from tabixfile.c:3:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/htslib/bgzf.h:270:9: note: declared here
    270 |     int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
        |         ^~~~~~~~~~~~
  tabixfile.c: In function ‘scan_tabix’:
  tabixfile.c:371:22: warning: ISO C forbids conversion of object pointer to function pointer type [-Wpedantic]
    371 |     SCAN_FUN *scan = (SCAN_FUN *) R_ExternalPtrAddr(fun);
        |                      ^
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c tagfilter.c -o tagfilter.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c utilities.c -o utilities.o
  In file included from utilities.c:3:
  utilities.c: In function ‘_as_PhredQuality’:
  utilities.h:55:5: error: implicit declaration of function ‘SET_TYPEOF’; did you mean ‘TYPEOF’? [-Wimplicit-function-declaration]
     55 |     SET_TYPEOF(T, LANGSXP);                     \
        |     ^~~~~~~~~~
  utilities.c:184:5: note: in expansion of macro ‘NEW_CALL’
    184 |     NEW_CALL(s, t, "PhredQuality", nmspc, 2);
        |     ^~~~~~~~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: utilities.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c zip_compression.c -o zip_compression.o
  make[1]: Target 'all' not remade because of errors.
  make[1]: Leaving directory '/tmp/RtmpjMtCOC/working_dir/RtmpgDwZgd/R.INSTALL37899657c3e5a3/Rsamtools/src'
  ERROR: compilation failed for package ‘Rsamtools’
  * removing ‘/data/gannet/ripley/R/packages/tests-devel/inDAGO.Rcheck/Rsamtools’
  ERROR: dependency ‘SparseArray’ is not available for package ‘DelayedArray’
  Perhaps try a variation of:
  install.packages('SparseArray')
  * removing ‘/data/gannet/ripley/R/packages/tests-devel/inDAGO.Rcheck/DelayedArray’
  ERROR: dependency ‘DelayedArray’ is not available for package ‘SummarizedExperiment’
  Perhaps try a variation of:
  install.packages('DelayedArray')
  * removing ‘/data/gannet/ripley/R/packages/tests-devel/inDAGO.Rcheck/SummarizedExperiment’
  ERROR: dependencies ‘SummarizedExperiment’, ‘Rsamtools’ are not available for package ‘GenomicAlignments’
  Perhaps try a variation of:
  install.packages(c('SummarizedExperiment', 'Rsamtools'))
  * removing ‘/data/gannet/ripley/R/packages/tests-devel/inDAGO.Rcheck/GenomicAlignments’
  ERROR: dependencies ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘ShortRead’
  Perhaps try a variation of:
  install.packages(c('Rsamtools', 'GenomicAlignments'))
  * removing ‘/data/gannet/ripley/R/packages/tests-devel/inDAGO.Rcheck/ShortRead’
  
  The downloaded source packages are in
  	'/tmp/RtmpjMtCOC/working_dir/RtmpWs5AyV/downloaded_packages'
  Old packages: 'ANCOMBC', 'BiocNeighbors', 'Biostrings', 'DAPAR', 'DAPARdata',
    'MSnbase', 'WIPF', 'bluster', 'scpi', 'xcms', 'Fletcher2013b',
    'GenomicScores', 'RTCGA', 'RTN', 'bsseq', 'bsseqData', 'geneplast', 'mia',
    'viper'
  'getOption("repos")' replaces Bioconductor standard repositories, see
  'help("repositories", package = "BiocManager")' for details.
  Replacement repositories:
      CRAN: file:///data/gannet/ripley/R
  Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable)
    (2026-03-06 r89558)
  Installing package(s) 'rtracklayer'
  also installing the dependencies 'SparseArray', 'DelayedArray', 'SummarizedExperiment', 'Rsamtools', 'GenomicAlignments'
  
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SparseArray_1.11.10.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/DelayedArray_0.37.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SummarizedExperiment_1.41.1.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Rsamtools_2.27.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/GenomicAlignments_1.47.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/rtracklayer_1.71.3.tar.gz'
  * installing *source* package ‘SparseArray’ ...
  ** this is package ‘SparseArray’ version ‘1.11.10’
  ** using staged installation
  ** libs
  using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
  make[1]: Entering directory '/tmp/RtmpjMtCOC/working_dir/Rtmp9u6zfi/R.INSTALL38b2bf57db8071/SparseArray/src'
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o
  In file included from leaf_utils.h:6,
                   from ExtendableJaggedArray.c:8:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: ExtendableJaggedArray.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c IRanges_stubs.c -o IRanges_stubs.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c OPBufTree.c -o OPBufTree.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c R_init_SparseArray.c -o R_init_SparseArray.o
  In file included from leaf_utils.h:6,
                   from R_init_SparseArray.c:6:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: R_init_SparseArray.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c Rvector_utils.c -o Rvector_utils.o
  Rvector_utils.c: In function ‘_fill_Rvector_block_with_val’:
  Rvector_utils.c:245:43: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    245 |         _set_elts_to_val(TYPEOF(Rvector), DATAPTR(Rvector),
        |                                           ^~~~~~~
        |                                           DATAPTR_RO
  Rvector_utils.c:245:43: error: passing argument 2 of ‘_set_elts_to_val’ makes pointer from integer without a cast [-Wint-conversion]
    245 |         _set_elts_to_val(TYPEOF(Rvector), DATAPTR(Rvector),
        |                                           ^~~~~~~~~~~~~~~~
        |                                           |
        |                                           int
  Rvector_utils.c:99:45: note: expected ‘void *’ but argument is of type ‘int’
     99 | void _set_elts_to_val(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n,
        |                                       ~~~~~~^
  Rvector_utils.c: In function ‘_fill_Rvector_block_with_zeros’:
  Rvector_utils.c:263:34: error: passing argument 2 of ‘_set_elts_to_zero’ makes pointer from integer without a cast [-Wint-conversion]
    263 |         _set_elts_to_zero(Rtype, DATAPTR(Rvector), block_offset, block_len);
        |                                  ^~~~~~~~~~~~~~~~
        |                                  |
        |                                  int
  Rvector_utils.c:122:46: note: expected ‘void *’ but argument is of type ‘int’
    122 | void _set_elts_to_zero(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n)
        |                                        ~~~~~~^
  Rvector_utils.c: In function ‘_fill_Rvector_block_with_ones’:
  Rvector_utils.c:271:43: error: passing argument 2 of ‘_set_elts_to_one’ makes pointer from integer without a cast [-Wint-conversion]
    271 |         _set_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector),
        |                                           ^~~~~~~~~~~~~~~~
        |                                           |
        |                                           int
  Rvector_utils.c:137:45: note: expected ‘void *’ but argument is of type ‘int’
    137 | void _set_elts_to_one(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n)
        |                                       ~~~~~~^
  Rvector_utils.c: In function ‘_fill_Rvector_block_with_minus_one’:
  Rvector_utils.c:280:49: error: passing argument 2 of ‘_set_elts_to_minus_one’ makes pointer from integer without a cast [-Wint-conversion]
    280 |         _set_elts_to_minus_one(TYPEOF(Rvector), DATAPTR(Rvector),
        |                                                 ^~~~~~~~~~~~~~~~
        |                                                 |
        |                                                 int
  Rvector_utils.c:159:51: note: expected ‘void *’ but argument is of type ‘int’
    159 | void _set_elts_to_minus_one(SEXPTYPE Rtype, void *x,
        |                                             ~~~~~~^
  Rvector_utils.c: In function ‘_fill_Rvector_block_with_NA’:
  Rvector_utils.c:296:32: error: passing argument 2 of ‘_set_elts_to_NA’ makes pointer from integer without a cast [-Wint-conversion]
    296 |         _set_elts_to_NA(Rtype, DATAPTR(Rvector), block_offset, block_len);
        |                                ^~~~~~~~~~~~~~~~
        |                                |
        |                                int
  Rvector_utils.c:184:44: note: expected ‘void *’ but argument is of type ‘int’
    184 | void _set_elts_to_NA(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n)
        |                                      ~~~~~~^
  Rvector_utils.c: In function ‘_fill_Rvector_subset_with_zeros’:
  Rvector_utils.c:463:43: error: passing argument 2 of ‘_set_selected_elts_to_zero’ makes pointer from integer without a cast [-Wint-conversion]
    463 |         _set_selected_elts_to_zero(Rtype, DATAPTR(Rvector),
        |                                           ^~~~~~~~~~~~~~~~
        |                                           |
        |                                           int
  Rvector_utils.c:365:55: note: expected ‘void *’ but argument is of type ‘int’
    365 | void _set_selected_elts_to_zero(SEXPTYPE Rtype, void *x,
        |                                                 ~~~~~~^
  Rvector_utils.c: In function ‘_fill_Rvector_subset_with_ones’:
  Rvector_utils.c:473:52: error: passing argument 2 of ‘_set_selected_elts_to_one’ makes pointer from integer without a cast [-Wint-conversion]
    473 |         _set_selected_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector),
        |                                                    ^~~~~~~~~~~~~~~~
        |                                                    |
        |                                                    int
  Rvector_utils.c:397:54: note: expected ‘void *’ but argument is of type ‘int’
    397 | void _set_selected_elts_to_one(SEXPTYPE Rtype, void *x,
        |                                                ~~~~~~^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: Rvector_utils.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SBT_utils.c -o SBT_utils.o
  In file included from leaf_utils.h:6,
                   from SBT_utils.c:7:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SBT_utils.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o
  In file included from leaf_utils.h:6,
                   from SVT_SparseArray_class.c:9:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SVT_SparseArray_class.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o
  In file included from SparseArray_Arith_methods.c:7:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Arith_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o
  In file included from SparseArray_Compare_methods.c:7:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Compare_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o
  In file included from leaf_utils.h:6,
                   from SparseArray_Complex_methods.c:6:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Complex_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o
  In file included from SparseArray_Logic_methods.c:7:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Logic_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o
  In file included from SparseArray_Math_methods.c:7:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Math_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_abind.c -o SparseArray_abind.o
  In file included from leaf_utils.h:6,
                   from SparseArray_abind.c:11:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_abind.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_aperm.c -o SparseArray_aperm.o
  In file included from leaf_utils.h:6,
                   from SparseArray_aperm.c:16:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  SparseArray_aperm.c: In function ‘spray_integer_leaf’:
  SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    724 |                 nzvals_p = (const type *) DATAPTR(nzvals);              \
        |                            ^
  SparseArray_aperm.c:746:39: note: in expansion of macro ‘FUNDEF_spray_leaf’
    746 | static inline void spray_integer_leaf FUNDEF_spray_leaf(int)
        |                                       ^~~~~~~~~~~~~~~~~
  SparseArray_aperm.c: In function ‘spray_double_leaf’:
  SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    724 |                 nzvals_p = (const type *) DATAPTR(nzvals);              \
        |                            ^
  SparseArray_aperm.c:747:38: note: in expansion of macro ‘FUNDEF_spray_leaf’
    747 | static inline void spray_double_leaf FUNDEF_spray_leaf(double)
        |                                      ^~~~~~~~~~~~~~~~~
  SparseArray_aperm.c: In function ‘spray_complex_leaf’:
  SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    724 |                 nzvals_p = (const type *) DATAPTR(nzvals);              \
        |                            ^
  SparseArray_aperm.c:748:39: note: in expansion of macro ‘FUNDEF_spray_leaf’
    748 | static inline void spray_complex_leaf FUNDEF_spray_leaf(Rcomplex)
        |                                       ^~~~~~~~~~~~~~~~~
  SparseArray_aperm.c: In function ‘spray_raw_leaf’:
  SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    724 |                 nzvals_p = (const type *) DATAPTR(nzvals);              \
        |                            ^
  SparseArray_aperm.c:749:35: note: in expansion of macro ‘FUNDEF_spray_leaf’
    749 | static inline void spray_raw_leaf FUNDEF_spray_leaf(Rbyte)
        |                                   ^~~~~~~~~~~~~~~~~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_aperm.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o
  In file included from leaf_utils.h:6,
                   from SparseArray_dim_tuning.c:7:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_dim_tuning.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o
  In file included from SparseArray_matrixStats.c:15:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  SparseArray_matrixStats.c: In function ‘C_colStats_SVT’:
  SparseArray_matrixStats.c:275:26: error: passing argument 6 of ‘REC_colStats_SVT’ makes pointer from integer without a cast [-Wint-conversion]
    275 |                          DATAPTR(ans), ans_Rtype,
        |                          ^~~~~~~~~~~~
        |                          |
        |                          int
  SparseArray_matrixStats.c:203:23: note: expected ‘void *’ but argument is of type ‘int’
    203 |                 void *out, SEXPTYPE out_Rtype,
        |                 ~~~~~~^~~
  SparseArray_matrixStats.c: In function ‘C_rowStats_SVT’:
  SparseArray_matrixStats.c:1178:25: error: passing argument 8 of ‘SVT_rowMinsMaxs’ makes pointer from integer without a cast [-Wint-conversion]
   1178 |                         DATAPTR(ans), LENGTH(ans), ans_Rtype,
        |                         ^~~~~~~~~~~~
        |                         |
        |                         int
  SparseArray_matrixStats.c:966:23: note: expected ‘void *’ but argument is of type ‘int’
    966 |                 void *out, R_xlen_t out_len, SEXPTYPE out_Rtype,
        |                 ~~~~~~^~~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_matrixStats.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o
  In file included from leaf_utils.h:6,
                   from SparseArray_misc_methods.c:8:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_misc_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_subassignment.c -o SparseArray_subassignment.o
  In file included from leaf_utils.h:6,
                   from SparseArray_subassignment.c:13:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_subassignment.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_subsetting.c -o SparseArray_subsetting.o
  In file included from leaf_utils.h:6,
                   from SparseArray_subsetting.c:14:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  SparseArray_subsetting.c: In function ‘REC_subset_SVT_as_SVT’:
  SparseArray_subsetting.c:843:26: warning: comparison between pointer and integer
    843 |                 if (offs != i2 || ans_elt != subSVT)
        |                          ^~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_subsetting.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_summarization.c -o SparseArray_summarization.o
  In file included from leaf_utils.h:6,
                   from SparseArray_summarization.c:12:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_summarization.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseMatrix_mult.c -o SparseMatrix_mult.o
  In file included from SparseMatrix_mult.c:14:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  SparseMatrix_mult.c: At top level:
  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(
        |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseMatrix_mult.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec.c -o SparseVec.o
  In file included from SparseVec.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_Arith.c -o SparseVec_Arith.o
  In file included from SparseVec_Arith.h:6,
                   from SparseVec_Arith.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Arith.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_Compare.c -o SparseVec_Compare.o
  In file included from SparseVec_Compare.h:6,
                   from SparseVec_Compare.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Compare.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_Logic.c -o SparseVec_Logic.o
  In file included from SparseVec_Logic.h:6,
                   from SparseVec_Logic.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Logic.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_Math.c -o SparseVec_Math.o
  In file included from SparseVec_Math.h:6,
                   from SparseVec_Math.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Math.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_dotprod.c -o SparseVec_dotprod.o
  In file included from SparseVec_dotprod.h:4,
                   from SparseVec_dotprod.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_dotprod.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_subassignment.c -o SparseVec_subassignment.o
  In file included from SparseVec_subassignment.h:6,
                   from SparseVec_subassignment.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_subassignment.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_subsetting.c -o SparseVec_subsetting.o
  In file included from SparseVec_subsetting.h:6,
                   from SparseVec_subsetting.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_subsetting.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c XVector_stubs.c -o XVector_stubs.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c argcheck_utils.c -o argcheck_utils.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c coerceVector2.c -o coerceVector2.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c leaf_utils.c -o leaf_utils.o
  In file included from leaf_utils.h:6,
                   from leaf_utils.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  leaf_utils.c: In function ‘_make_leaf_from_two_arrays’:
  leaf_utils.c:132:24: error: passing argument 1 of ‘memcpy’ makes pointer from integer without a cast [-Wint-conversion]
    132 |                 memcpy(DATAPTR(ans_nzvals), nzvals_p, Rtype_size * nzcount);
        |                        ^~~~~~~~~~~~~~~~~~~
        |                        |
        |                        int
  In file included from /usr/include/features.h:524,
                   from /usr/include/bits/libc-header-start.h:33,
                   from /usr/include/string.h:26,
                   from /data/gannet/ripley/R/R-devel/include/R_ext/RS.h:34,
                   from /data/gannet/ripley/R/R-devel/include/Rdefines.h:38,
                   from leaf_utils.h:4:
  /usr/include/bits/string_fortified.h:26:1: note: expected ‘void *’ but argument is of type ‘int’
     26 | __NTH (memcpy (void *__restrict __dest, const void *__restrict __src,
        | ^~~~~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: leaf_utils.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c misc_utils.c -o misc_utils.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c randomSparseArray.c -o randomSparseArray.o
  In file included from leaf_utils.h:6,
                   from randomSparseArray.c:6:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: randomSparseArray.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c readSparseCSV.c -o readSparseCSV.o
  In file included from leaf_utils.h:6,
                   from readSparseCSV.c:10:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: readSparseCSV.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c rowsum_methods.c -o rowsum_methods.o
  In file included from leaf_utils.h:6,
                   from rowsum_methods.c:9:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: rowsum_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c sparseMatrix_utils.c -o sparseMatrix_utils.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c test.c -o test.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c thread_control.c -o thread_control.o
  make[1]: Target 'all' not remade because of errors.
  make[1]: Leaving directory '/tmp/RtmpjMtCOC/working_dir/Rtmp9u6zfi/R.INSTALL38b2bf57db8071/SparseArray/src'
  ERROR: compilation failed for package ‘SparseArray’
  * removing ‘/data/gannet/ripley/R/packages/tests-devel/inDAGO.Rcheck/SparseArray’
  * installing *source* package ‘Rsamtools’ ...
  ** this is package ‘Rsamtools’ version ‘2.27.0’
  ** using staged installation
  ** libs
  using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
  using C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
  make[1]: Entering directory '/tmp/RtmpjMtCOC/working_dir/RtmpkY1DbF/R.INSTALL38baed33d6e269/Rsamtools/src'
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c Biostrings_stubs.c -o Biostrings_stubs.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c IRanges_stubs.c -o IRanges_stubs.o
  g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c PileupBuffer.cpp -o PileupBuffer.o
  g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c PosCacheColl.cpp -o PosCacheColl.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c R_init_Rsamtools.c -o R_init_Rsamtools.o
  g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c ResultManager.cpp -o ResultManager.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c XVector_stubs.c -o XVector_stubs.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c as_bam.c -o as_bam.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bam.c -o bam.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bam_data.c -o bam_data.o
  g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c bam_mate_iter.cpp -o bam_mate_iter.o
  In file included from Template.h:9,
                   from BamIterator.h:10,
                   from BamRangeIterator.h:7,
                   from bam_mate_iter.cpp:1:
  BamRangeIterator.h: In member function ‘virtual void BamRangeIterator::finalize_inprogress(bamFile)’:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/samtools-1.7-compat.h:14:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
     14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
        |                                ~~~~~~~~~^~~~~~~~~~~~~~
  BamRangeIterator.h:138:16: note: in expansion of macro ‘bam_seek’
    138 |         (void) bam_seek(bfile, pos, SEEK_SET);
        |                ^~~~~~~~
  BamIterator.h: In constructor ‘BamIterator::BamIterator(bamFile, const bam_index_t*)’:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/samtools-1.7-compat.h:14:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
     14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
        |                                ~~~~~~~~~^~~~~~~~~~~~~~
  BamIterator.h:87:16: note: in expansion of macro ‘bam_seek’
     87 |         (void) bam_seek(bfile, 0, 0);
        |                ^~~~~~~~
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bam_plbuf.c -o bam_plbuf.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bam_sort.c -o bam_sort.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bambuffer.c -o bambuffer.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bamfile.c -o bamfile.o
  bamfile.c: In function ‘bamfile_isincomplete’:
  bamfile.c:168:20: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
    168 |             (void) bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
        |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  In function ‘_bam_tryindexload’,
      inlined from ‘_bamfile_open_r’ at bamfile.c:89:24,
      inlined from ‘bamfile_open’ at bamfile.c:127:17:
  bamfile.c:29:17: warning: ‘cfile’ may be used uninitialized [-Wmaybe-uninitialized]
     29 |         index = hts_idx_load2(file, indexname);
        |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  bamfile.c: In function ‘bamfile_open’:
  bamfile.c:73:17: note: ‘cfile’ was declared here
     73 |     const char *cfile;
        |                 ^~~~~
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bcffile.c -o bcffile.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bedidx.c -o bedidx.o
  In file included from bedidx.c:1:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/bedidx.c: In function ‘bed_hash_regions’:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/bedidx.c:537:97: warning: format ‘%p’ expects argument of type ‘void *’, but argument 4 has type ‘reghash_t *’ {aka ‘struct kh_reg_s *’} [-Wformat=]
    537 |             fprintf(stderr, "Error when inserting region='%s' in the bed hash table at address=%p!\n", regs[i], h);
        |                                                                                                ~^               ~
        |                                                                                                 |               |
        |                                                                                                 void *          reghash_t * {aka struct kh_reg_s *}
  /data/gannet/ripley/R/test-dev/Rhtslib/include/bedidx.c:542:103: warning: format ‘%p’ expects argument of type ‘void *’, but argument 4 has type ‘reghash_t *’ {aka ‘struct kh_reg_s *’} [-Wformat=]
    542 |             fprintf(stderr, "Error when inserting region='%s' in the temporary hash table at address=%p!\n", regs[i], t);
        |                                                                                                      ~^               ~
        |                                                                                                       |               |
        |                                                                                                       void *          reghash_t * {aka struct kh_reg_s *}
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c encode.c -o encode.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c fafile.c -o fafile.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c idxstats.c -o idxstats.o
  In file included from bamfile.h:5,
                   from idxstats.c:1:
  idxstats.c: In function ‘idxstats_bamfile’:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/samtools-1.7-compat.h:14:32: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
     14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
        |                                ^~~~~~~~~~~~~~~~~~~~~~~
  idxstats.c:20:12: note: in expansion of macro ‘bam_seek’
     20 |     (void) bam_seek(fp, 0, 0);
        |            ^~~~~~~~
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c io_sam.c -o io_sam.o
  In file included from io_sam.c:9:
  io_sam.c: In function ‘_tmpl_PhredQuality’:
  utilities.h:55:5: error: implicit declaration of function ‘SET_TYPEOF’; did you mean ‘TYPEOF’? [-Wimplicit-function-declaration]
     55 |     SET_TYPEOF(T, LANGSXP);                     \
        |     ^~~~~~~~~~
  io_sam.c:88:5: note: in expansion of macro ‘NEW_CALL’
     88 |     NEW_CALL(s, t, "PhredQuality", nmspc, 2);
        |     ^~~~~~~~
  In file included from io_sam.c:3:
  io_sam.c: In function ‘_scan_bam_all’:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/samtools-1.7-compat.h:14:32: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
     14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
        |                                ^~~~~~~~~~~~~~~~~~~~~~~
  io_sam.c:302:12: note: in expansion of macro ‘bam_seek’
    302 |     (void) bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
        |            ^~~~~~~~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: io_sam.o] Error 1
  g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
  g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c pileup.cpp -o pileup.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c pileupbam.c -o pileupbam.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c sam_opts.c -o sam_opts.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c sam_utils.c -o sam_utils.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c samtools_patch.c -o samtools_patch.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c scan_bam_data.c -o scan_bam_data.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c tabixfile.c -o tabixfile.o
  tabixfile.c: In function ‘index_tabix’:
  tabixfile.c:190:5: warning: ‘bgzf_is_bgzf’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
    190 |     if (bgzf_is_bgzf(fn) != 1)
        |     ^~
  In file included from tabixfile.c:3:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/htslib/bgzf.h:270:9: note: declared here
    270 |     int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
        |         ^~~~~~~~~~~~
  tabixfile.c: In function ‘scan_tabix’:
  tabixfile.c:371:22: warning: ISO C forbids conversion of object pointer to function pointer type [-Wpedantic]
    371 |     SCAN_FUN *scan = (SCAN_FUN *) R_ExternalPtrAddr(fun);
        |                      ^
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c tagfilter.c -o tagfilter.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c utilities.c -o utilities.o
  In file included from utilities.c:3:
  utilities.c: In function ‘_as_PhredQuality’:
  utilities.h:55:5: error: implicit declaration of function ‘SET_TYPEOF’; did you mean ‘TYPEOF’? [-Wimplicit-function-declaration]
     55 |     SET_TYPEOF(T, LANGSXP);                     \
        |     ^~~~~~~~~~
  utilities.c:184:5: note: in expansion of macro ‘NEW_CALL’
    184 |     NEW_CALL(s, t, "PhredQuality", nmspc, 2);
        |     ^~~~~~~~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: utilities.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c zip_compression.c -o zip_compression.o
  make[1]: Target 'all' not remade because of errors.
  make[1]: Leaving directory '/tmp/RtmpjMtCOC/working_dir/RtmpkY1DbF/R.INSTALL38baed33d6e269/Rsamtools/src'
  ERROR: compilation failed for package ‘Rsamtools’
  * removing ‘/data/gannet/ripley/R/packages/tests-devel/inDAGO.Rcheck/Rsamtools’
  ERROR: dependency ‘SparseArray’ is not available for package ‘DelayedArray’
  Perhaps try a variation of:
  install.packages('SparseArray')
  * removing ‘/data/gannet/ripley/R/packages/tests-devel/inDAGO.Rcheck/DelayedArray’
  ERROR: dependency ‘DelayedArray’ is not available for package ‘SummarizedExperiment’
  Perhaps try a variation of:
  install.packages('DelayedArray')
  * removing ‘/data/gannet/ripley/R/packages/tests-devel/inDAGO.Rcheck/SummarizedExperiment’
  ERROR: dependencies ‘SummarizedExperiment’, ‘Rsamtools’ are not available for package ‘GenomicAlignments’
  Perhaps try a variation of:
  install.packages(c('SummarizedExperiment', 'Rsamtools'))
  * removing ‘/data/gannet/ripley/R/packages/tests-devel/inDAGO.Rcheck/GenomicAlignments’
  ERROR: dependencies ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’
  Perhaps try a variation of:
  install.packages(c('Rsamtools', 'GenomicAlignments'))
  * removing ‘/data/gannet/ripley/R/packages/tests-devel/inDAGO.Rcheck/rtracklayer’
  
  The downloaded source packages are in
  	'/tmp/RtmpjMtCOC/working_dir/RtmpWs5AyV/downloaded_packages'
  Old packages: 'ANCOMBC', 'BiocNeighbors', 'Biostrings', 'DAPAR', 'DAPARdata',
    'MSnbase', 'WIPF', 'bluster', 'scpi', 'xcms', 'Fletcher2013b',
    'GenomicScores', 'RTCGA', 'RTN', 'bsseq', 'bsseqData', 'geneplast', 'mia',
    'viper'
  'getOption("repos")' replaces Bioconductor standard repositories, see
  'help("repositories", package = "BiocManager")' for details.
  Replacement repositories:
      CRAN: file:///data/gannet/ripley/R
  Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable)
    (2026-03-06 r89558)
  Installing package(s) 'Rsamtools'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Rsamtools_2.27.0.tar.gz'
  Content type 'application/x-gzip' length 1908006 bytes (1.8 MB)
  ==================================================
  downloaded 1.8 MB
  
  * installing *source* package ‘Rsamtools’ ...
  ** this is package ‘Rsamtools’ version ‘2.27.0’
  ** using staged installation
  ** libs
  using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
  using C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
  make[1]: Entering directory '/tmp/RtmpjMtCOC/working_dir/RtmpANqRa9/R.INSTALL39e346488de84d/Rsamtools/src'
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c Biostrings_stubs.c -o Biostrings_stubs.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c IRanges_stubs.c -o IRanges_stubs.o
  g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c PileupBuffer.cpp -o PileupBuffer.o
  g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c PosCacheColl.cpp -o PosCacheColl.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c R_init_Rsamtools.c -o R_init_Rsamtools.o
  g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c ResultManager.cpp -o ResultManager.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c XVector_stubs.c -o XVector_stubs.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c as_bam.c -o as_bam.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bam.c -o bam.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bam_data.c -o bam_data.o
  g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c bam_mate_iter.cpp -o bam_mate_iter.o
  In file included from Template.h:9,
                   from BamIterator.h:10,
                   from BamRangeIterator.h:7,
                   from bam_mate_iter.cpp:1:
  BamRangeIterator.h: In member function ‘virtual void BamRangeIterator::finalize_inprogress(bamFile)’:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/samtools-1.7-compat.h:14:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
     14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
        |                                ~~~~~~~~~^~~~~~~~~~~~~~
  BamRangeIterator.h:138:16: note: in expansion of macro ‘bam_seek’
    138 |         (void) bam_seek(bfile, pos, SEEK_SET);
        |                ^~~~~~~~
  BamIterator.h: In constructor ‘BamIterator::BamIterator(bamFile, const bam_index_t*)’:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/samtools-1.7-compat.h:14:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
     14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
        |                                ~~~~~~~~~^~~~~~~~~~~~~~
  BamIterator.h:87:16: note: in expansion of macro ‘bam_seek’
     87 |         (void) bam_seek(bfile, 0, 0);
        |                ^~~~~~~~
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bam_plbuf.c -o bam_plbuf.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bam_sort.c -o bam_sort.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bambuffer.c -o bambuffer.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bamfile.c -o bamfile.o
  bamfile.c: In function ‘bamfile_isincomplete’:
  bamfile.c:168:20: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
    168 |             (void) bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
        |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  In function ‘_bam_tryindexload’,
      inlined from ‘_bamfile_open_r’ at bamfile.c:89:24,
      inlined from ‘bamfile_open’ at bamfile.c:127:17:
  bamfile.c:29:17: warning: ‘cfile’ may be used uninitialized [-Wmaybe-uninitialized]
     29 |         index = hts_idx_load2(file, indexname);
        |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  bamfile.c: In function ‘bamfile_open’:
  bamfile.c:73:17: note: ‘cfile’ was declared here
     73 |     const char *cfile;
        |                 ^~~~~
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bcffile.c -o bcffile.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c bedidx.c -o bedidx.o
  In file included from bedidx.c:1:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/bedidx.c: In function ‘bed_hash_regions’:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/bedidx.c:537:97: warning: format ‘%p’ expects argument of type ‘void *’, but argument 4 has type ‘reghash_t *’ {aka ‘struct kh_reg_s *’} [-Wformat=]
    537 |             fprintf(stderr, "Error when inserting region='%s' in the bed hash table at address=%p!\n", regs[i], h);
        |                                                                                                ~^               ~
        |                                                                                                 |               |
        |                                                                                                 void *          reghash_t * {aka struct kh_reg_s *}
  /data/gannet/ripley/R/test-dev/Rhtslib/include/bedidx.c:542:103: warning: format ‘%p’ expects argument of type ‘void *’, but argument 4 has type ‘reghash_t *’ {aka ‘struct kh_reg_s *’} [-Wformat=]
    542 |             fprintf(stderr, "Error when inserting region='%s' in the temporary hash table at address=%p!\n", regs[i], t);
        |                                                                                                      ~^               ~
        |                                                                                                       |               |
        |                                                                                                       void *          reghash_t * {aka struct kh_reg_s *}
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c encode.c -o encode.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c fafile.c -o fafile.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c idxstats.c -o idxstats.o
  In file included from bamfile.h:5,
                   from idxstats.c:1:
  idxstats.c: In function ‘idxstats_bamfile’:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/samtools-1.7-compat.h:14:32: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
     14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
        |                                ^~~~~~~~~~~~~~~~~~~~~~~
  idxstats.c:20:12: note: in expansion of macro ‘bam_seek’
     20 |     (void) bam_seek(fp, 0, 0);
        |            ^~~~~~~~
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c io_sam.c -o io_sam.o
  In file included from io_sam.c:9:
  io_sam.c: In function ‘_tmpl_PhredQuality’:
  utilities.h:55:5: error: implicit declaration of function ‘SET_TYPEOF’; did you mean ‘TYPEOF’? [-Wimplicit-function-declaration]
     55 |     SET_TYPEOF(T, LANGSXP);                     \
        |     ^~~~~~~~~~
  io_sam.c:88:5: note: in expansion of macro ‘NEW_CALL’
     88 |     NEW_CALL(s, t, "PhredQuality", nmspc, 2);
        |     ^~~~~~~~
  In file included from io_sam.c:3:
  io_sam.c: In function ‘_scan_bam_all’:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/samtools-1.7-compat.h:14:32: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
     14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
        |                                ^~~~~~~~~~~~~~~~~~~~~~~
  io_sam.c:302:12: note: in expansion of macro ‘bam_seek’
    302 |     (void) bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
        |            ^~~~~~~~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: io_sam.o] Error 1
  g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
  g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c pileup.cpp -o pileup.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c pileupbam.c -o pileupbam.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c sam_opts.c -o sam_opts.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c sam_utils.c -o sam_utils.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c samtools_patch.c -o samtools_patch.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c scan_bam_data.c -o scan_bam_data.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c tabixfile.c -o tabixfile.o
  tabixfile.c: In function ‘index_tabix’:
  tabixfile.c:190:5: warning: ‘bgzf_is_bgzf’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
    190 |     if (bgzf_is_bgzf(fn) != 1)
        |     ^~
  In file included from tabixfile.c:3:
  /data/gannet/ripley/R/test-dev/Rhtslib/include/htslib/bgzf.h:270:9: note: declared here
    270 |     int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
        |         ^~~~~~~~~~~~
  tabixfile.c: In function ‘scan_tabix’:
  tabixfile.c:371:22: warning: ISO C forbids conversion of object pointer to function pointer type [-Wpedantic]
    371 |     SCAN_FUN *scan = (SCAN_FUN *) R_ExternalPtrAddr(fun);
        |                      ^
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c tagfilter.c -o tagfilter.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c utilities.c -o utilities.o
  In file included from utilities.c:3:
  utilities.c: In function ‘_as_PhredQuality’:
  utilities.h:55:5: error: implicit declaration of function ‘SET_TYPEOF’; did you mean ‘TYPEOF’? [-Wimplicit-function-declaration]
     55 |     SET_TYPEOF(T, LANGSXP);                     \
        |     ^~~~~~~~~~
  utilities.c:184:5: note: in expansion of macro ‘NEW_CALL’
    184 |     NEW_CALL(s, t, "PhredQuality", nmspc, 2);
        |     ^~~~~~~~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: utilities.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet/ripley/R/test-dev/Rhtslib/include' -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I'/data/gannet/ripley/R/test-dev/Biostrings/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c zip_compression.c -o zip_compression.o
  make[1]: Target 'all' not remade because of errors.
  make[1]: Leaving directory '/tmp/RtmpjMtCOC/working_dir/RtmpANqRa9/R.INSTALL39e346488de84d/Rsamtools/src'
  ERROR: compilation failed for package ‘Rsamtools’
  * removing ‘/data/gannet/ripley/R/packages/tests-devel/inDAGO.Rcheck/Rsamtools’
  
  The downloaded source packages are in
  	'/tmp/RtmpjMtCOC/working_dir/RtmpWs5AyV/downloaded_packages'
  Old packages: 'ANCOMBC', 'BiocNeighbors', 'Biostrings', 'DAPAR', 'DAPARdata',
    'MSnbase', 'WIPF', 'bluster', 'scpi', 'xcms', 'Fletcher2013b',
    'GenomicScores', 'RTCGA', 'RTN', 'bsseq', 'bsseqData', 'geneplast', 'mia',
    'viper'
  'getOption("repos")' replaces Bioconductor standard repositories, see
  'help("repositories", package = "BiocManager")' for details.
  Replacement repositories:
      CRAN: file:///data/gannet/ripley/R
  Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable)
    (2026-03-06 r89558)
  Installing package(s) 'HTSFilter'
  also installing the dependencies 'SparseArray', 'DelayedArray', 'SummarizedExperiment', 'DESeq2'
  
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SparseArray_1.11.10.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/DelayedArray_0.37.0.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SummarizedExperiment_1.41.1.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/DESeq2_1.51.6.tar.gz'
  trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/HTSFilter_1.51.0.tar.gz'
  * installing *source* package ‘SparseArray’ ...
  ** this is package ‘SparseArray’ version ‘1.11.10’
  ** using staged installation
  ** libs
  using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
  make[1]: Entering directory '/tmp/RtmpjMtCOC/working_dir/RtmpLvtsxg/R.INSTALL3a95c74041c393/SparseArray/src'
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o
  In file included from leaf_utils.h:6,
                   from ExtendableJaggedArray.c:8:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: ExtendableJaggedArray.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c IRanges_stubs.c -o IRanges_stubs.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c OPBufTree.c -o OPBufTree.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c R_init_SparseArray.c -o R_init_SparseArray.o
  In file included from leaf_utils.h:6,
                   from R_init_SparseArray.c:6:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: R_init_SparseArray.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c Rvector_utils.c -o Rvector_utils.o
  Rvector_utils.c: In function ‘_fill_Rvector_block_with_val’:
  Rvector_utils.c:245:43: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    245 |         _set_elts_to_val(TYPEOF(Rvector), DATAPTR(Rvector),
        |                                           ^~~~~~~
        |                                           DATAPTR_RO
  Rvector_utils.c:245:43: error: passing argument 2 of ‘_set_elts_to_val’ makes pointer from integer without a cast [-Wint-conversion]
    245 |         _set_elts_to_val(TYPEOF(Rvector), DATAPTR(Rvector),
        |                                           ^~~~~~~~~~~~~~~~
        |                                           |
        |                                           int
  Rvector_utils.c:99:45: note: expected ‘void *’ but argument is of type ‘int’
     99 | void _set_elts_to_val(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n,
        |                                       ~~~~~~^
  Rvector_utils.c: In function ‘_fill_Rvector_block_with_zeros’:
  Rvector_utils.c:263:34: error: passing argument 2 of ‘_set_elts_to_zero’ makes pointer from integer without a cast [-Wint-conversion]
    263 |         _set_elts_to_zero(Rtype, DATAPTR(Rvector), block_offset, block_len);
        |                                  ^~~~~~~~~~~~~~~~
        |                                  |
        |                                  int
  Rvector_utils.c:122:46: note: expected ‘void *’ but argument is of type ‘int’
    122 | void _set_elts_to_zero(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n)
        |                                        ~~~~~~^
  Rvector_utils.c: In function ‘_fill_Rvector_block_with_ones’:
  Rvector_utils.c:271:43: error: passing argument 2 of ‘_set_elts_to_one’ makes pointer from integer without a cast [-Wint-conversion]
    271 |         _set_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector),
        |                                           ^~~~~~~~~~~~~~~~
        |                                           |
        |                                           int
  Rvector_utils.c:137:45: note: expected ‘void *’ but argument is of type ‘int’
    137 | void _set_elts_to_one(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n)
        |                                       ~~~~~~^
  Rvector_utils.c: In function ‘_fill_Rvector_block_with_minus_one’:
  Rvector_utils.c:280:49: error: passing argument 2 of ‘_set_elts_to_minus_one’ makes pointer from integer without a cast [-Wint-conversion]
    280 |         _set_elts_to_minus_one(TYPEOF(Rvector), DATAPTR(Rvector),
        |                                                 ^~~~~~~~~~~~~~~~
        |                                                 |
        |                                                 int
  Rvector_utils.c:159:51: note: expected ‘void *’ but argument is of type ‘int’
    159 | void _set_elts_to_minus_one(SEXPTYPE Rtype, void *x,
        |                                             ~~~~~~^
  Rvector_utils.c: In function ‘_fill_Rvector_block_with_NA’:
  Rvector_utils.c:296:32: error: passing argument 2 of ‘_set_elts_to_NA’ makes pointer from integer without a cast [-Wint-conversion]
    296 |         _set_elts_to_NA(Rtype, DATAPTR(Rvector), block_offset, block_len);
        |                                ^~~~~~~~~~~~~~~~
        |                                |
        |                                int
  Rvector_utils.c:184:44: note: expected ‘void *’ but argument is of type ‘int’
    184 | void _set_elts_to_NA(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n)
        |                                      ~~~~~~^
  Rvector_utils.c: In function ‘_fill_Rvector_subset_with_zeros’:
  Rvector_utils.c:463:43: error: passing argument 2 of ‘_set_selected_elts_to_zero’ makes pointer from integer without a cast [-Wint-conversion]
    463 |         _set_selected_elts_to_zero(Rtype, DATAPTR(Rvector),
        |                                           ^~~~~~~~~~~~~~~~
        |                                           |
        |                                           int
  Rvector_utils.c:365:55: note: expected ‘void *’ but argument is of type ‘int’
    365 | void _set_selected_elts_to_zero(SEXPTYPE Rtype, void *x,
        |                                                 ~~~~~~^
  Rvector_utils.c: In function ‘_fill_Rvector_subset_with_ones’:
  Rvector_utils.c:473:52: error: passing argument 2 of ‘_set_selected_elts_to_one’ makes pointer from integer without a cast [-Wint-conversion]
    473 |         _set_selected_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector),
        |                                                    ^~~~~~~~~~~~~~~~
        |                                                    |
        |                                                    int
  Rvector_utils.c:397:54: note: expected ‘void *’ but argument is of type ‘int’
    397 | void _set_selected_elts_to_one(SEXPTYPE Rtype, void *x,
        |                                                ~~~~~~^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: Rvector_utils.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SBT_utils.c -o SBT_utils.o
  In file included from leaf_utils.h:6,
                   from SBT_utils.c:7:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SBT_utils.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o
  In file included from leaf_utils.h:6,
                   from SVT_SparseArray_class.c:9:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SVT_SparseArray_class.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o
  In file included from SparseArray_Arith_methods.c:7:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Arith_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o
  In file included from SparseArray_Compare_methods.c:7:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Compare_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o
  In file included from leaf_utils.h:6,
                   from SparseArray_Complex_methods.c:6:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Complex_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o
  In file included from SparseArray_Logic_methods.c:7:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Logic_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o
  In file included from SparseArray_Math_methods.c:7:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Math_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_abind.c -o SparseArray_abind.o
  In file included from leaf_utils.h:6,
                   from SparseArray_abind.c:11:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_abind.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_aperm.c -o SparseArray_aperm.o
  In file included from leaf_utils.h:6,
                   from SparseArray_aperm.c:16:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  SparseArray_aperm.c: In function ‘spray_integer_leaf’:
  SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    724 |                 nzvals_p = (const type *) DATAPTR(nzvals);              \
        |                            ^
  SparseArray_aperm.c:746:39: note: in expansion of macro ‘FUNDEF_spray_leaf’
    746 | static inline void spray_integer_leaf FUNDEF_spray_leaf(int)
        |                                       ^~~~~~~~~~~~~~~~~
  SparseArray_aperm.c: In function ‘spray_double_leaf’:
  SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    724 |                 nzvals_p = (const type *) DATAPTR(nzvals);              \
        |                            ^
  SparseArray_aperm.c:747:38: note: in expansion of macro ‘FUNDEF_spray_leaf’
    747 | static inline void spray_double_leaf FUNDEF_spray_leaf(double)
        |                                      ^~~~~~~~~~~~~~~~~
  SparseArray_aperm.c: In function ‘spray_complex_leaf’:
  SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    724 |                 nzvals_p = (const type *) DATAPTR(nzvals);              \
        |                            ^
  SparseArray_aperm.c:748:39: note: in expansion of macro ‘FUNDEF_spray_leaf’
    748 | static inline void spray_complex_leaf FUNDEF_spray_leaf(Rcomplex)
        |                                       ^~~~~~~~~~~~~~~~~
  SparseArray_aperm.c: In function ‘spray_raw_leaf’:
  SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
    724 |                 nzvals_p = (const type *) DATAPTR(nzvals);              \
        |                            ^
  SparseArray_aperm.c:749:35: note: in expansion of macro ‘FUNDEF_spray_leaf’
    749 | static inline void spray_raw_leaf FUNDEF_spray_leaf(Rbyte)
        |                                   ^~~~~~~~~~~~~~~~~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_aperm.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o
  In file included from leaf_utils.h:6,
                   from SparseArray_dim_tuning.c:7:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_dim_tuning.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o
  In file included from SparseArray_matrixStats.c:15:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  SparseArray_matrixStats.c: In function ‘C_colStats_SVT’:
  SparseArray_matrixStats.c:275:26: error: passing argument 6 of ‘REC_colStats_SVT’ makes pointer from integer without a cast [-Wint-conversion]
    275 |                          DATAPTR(ans), ans_Rtype,
        |                          ^~~~~~~~~~~~
        |                          |
        |                          int
  SparseArray_matrixStats.c:203:23: note: expected ‘void *’ but argument is of type ‘int’
    203 |                 void *out, SEXPTYPE out_Rtype,
        |                 ~~~~~~^~~
  SparseArray_matrixStats.c: In function ‘C_rowStats_SVT’:
  SparseArray_matrixStats.c:1178:25: error: passing argument 8 of ‘SVT_rowMinsMaxs’ makes pointer from integer without a cast [-Wint-conversion]
   1178 |                         DATAPTR(ans), LENGTH(ans), ans_Rtype,
        |                         ^~~~~~~~~~~~
        |                         |
        |                         int
  SparseArray_matrixStats.c:966:23: note: expected ‘void *’ but argument is of type ‘int’
    966 |                 void *out, R_xlen_t out_len, SEXPTYPE out_Rtype,
        |                 ~~~~~~^~~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_matrixStats.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o
  In file included from leaf_utils.h:6,
                   from SparseArray_misc_methods.c:8:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_misc_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_subassignment.c -o SparseArray_subassignment.o
  In file included from leaf_utils.h:6,
                   from SparseArray_subassignment.c:13:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_subassignment.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_subsetting.c -o SparseArray_subsetting.o
  In file included from leaf_utils.h:6,
                   from SparseArray_subsetting.c:14:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  SparseArray_subsetting.c: In function ‘REC_subset_SVT_as_SVT’:
  SparseArray_subsetting.c:843:26: warning: comparison between pointer and integer
    843 |                 if (offs != i2 || ans_elt != subSVT)
        |                          ^~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_subsetting.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseArray_summarization.c -o SparseArray_summarization.o
  In file included from leaf_utils.h:6,
                   from SparseArray_summarization.c:12:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_summarization.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseMatrix_mult.c -o SparseMatrix_mult.o
  In file included from SparseMatrix_mult.c:14:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  SparseMatrix_mult.c: At top level:
  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(
        |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseMatrix_mult.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec.c -o SparseVec.o
  In file included from SparseVec.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_Arith.c -o SparseVec_Arith.o
  In file included from SparseVec_Arith.h:6,
                   from SparseVec_Arith.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Arith.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_Compare.c -o SparseVec_Compare.o
  In file included from SparseVec_Compare.h:6,
                   from SparseVec_Compare.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Compare.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_Logic.c -o SparseVec_Logic.o
  In file included from SparseVec_Logic.h:6,
                   from SparseVec_Logic.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Logic.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_Math.c -o SparseVec_Math.o
  In file included from SparseVec_Math.h:6,
                   from SparseVec_Math.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Math.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_dotprod.c -o SparseVec_dotprod.o
  In file included from SparseVec_dotprod.h:4,
                   from SparseVec_dotprod.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_dotprod.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_subassignment.c -o SparseVec_subassignment.o
  In file included from SparseVec_subassignment.h:6,
                   from SparseVec_subassignment.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_subassignment.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c SparseVec_subsetting.c -o SparseVec_subsetting.o
  In file included from SparseVec_subsetting.h:6,
                   from SparseVec_subsetting.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_subsetting.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c XVector_stubs.c -o XVector_stubs.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c argcheck_utils.c -o argcheck_utils.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c coerceVector2.c -o coerceVector2.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c leaf_utils.c -o leaf_utils.o
  In file included from leaf_utils.h:6,
                   from leaf_utils.c:4:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  leaf_utils.c: In function ‘_make_leaf_from_two_arrays’:
  leaf_utils.c:132:24: error: passing argument 1 of ‘memcpy’ makes pointer from integer without a cast [-Wint-conversion]
    132 |                 memcpy(DATAPTR(ans_nzvals), nzvals_p, Rtype_size * nzcount);
        |                        ^~~~~~~~~~~~~~~~~~~
        |                        |
        |                        int
  In file included from /usr/include/features.h:524,
                   from /usr/include/bits/libc-header-start.h:33,
                   from /usr/include/string.h:26,
                   from /data/gannet/ripley/R/R-devel/include/R_ext/RS.h:34,
                   from /data/gannet/ripley/R/R-devel/include/Rdefines.h:38,
                   from leaf_utils.h:4:
  /usr/include/bits/string_fortified.h:26:1: note: expected ‘void *’ but argument is of type ‘int’
     26 | __NTH (memcpy (void *__restrict __dest, const void *__restrict __src,
        | ^~~~~
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: leaf_utils.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c misc_utils.c -o misc_utils.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c randomSparseArray.c -o randomSparseArray.o
  In file included from leaf_utils.h:6,
                   from randomSparseArray.c:6:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: randomSparseArray.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c readSparseCSV.c -o readSparseCSV.o
  In file included from leaf_utils.h:6,
                   from readSparseCSV.c:10:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: readSparseCSV.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c rowsum_methods.c -o rowsum_methods.o
  In file included from leaf_utils.h:6,
                   from rowsum_methods.c:9:
  SparseVec.h: In function ‘toSparseVec’:
  SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                     ^~~~~~~
        |                                     DATAPTR_RO
  SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion]
    125 |                         sv.nzvals = DATAPTR(nzvals);
        |                                   ^
  make[1]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: rowsum_methods.o] Error 1
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c sparseMatrix_utils.c -o sparseMatrix_utils.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c test.c -o test.o
  gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/S4Vectors/include' -I'/data/gannet/ripley/R/test-dev/IRanges/include' -I'/data/gannet/ripley/R/test-dev/XVector/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c thread_control.c -o thread_control.o
  make[1]: Target 'all' not remade because of errors.
  make[1]: Leaving directory '/tmp/RtmpjMtCOC/working_dir/RtmpLvtsxg/R.INSTALL3a95c74041c393/SparseArray/src'
  ERROR: compilation failed for package ‘SparseArray’
  * removing ‘/data/gannet/ripley/R/packages/tests-devel/inDAGO.Rcheck/SparseArray’
  ERROR: dependency ‘SparseArray’ is not available for package ‘DelayedArray’
  Perhaps try a variation of:
  install.packages('SparseArray')
  * removing ‘/data/gannet/ripley/R/packages/tests-devel/inDAGO.Rcheck/DelayedArray’
  ERROR: dependency ‘DelayedArray’ is not available for package ‘SummarizedExperiment’
  Perhaps try a variation of:
  install.packages('DelayedArray')
  * removing ‘/data/gannet/ripley/R/packages/tests-devel/inDAGO.Rcheck/SummarizedExperiment’
  ERROR: dependency ‘SummarizedExperiment’ is not available for package ‘DESeq2’
  Perhaps try a variation of:
  install.packages('SummarizedExperiment')
  * removing ‘/data/gannet/ripley/R/packages/tests-devel/inDAGO.Rcheck/DESeq2’
  ERROR: dependency ‘DESeq2’ is not available for package ‘HTSFilter’
  Perhaps try a variation of:
  install.packages('DESeq2')
  * removing ‘/data/gannet/ripley/R/packages/tests-devel/inDAGO.Rcheck/HTSFilter’
  
  The downloaded source packages are in
  	'/tmp/RtmpjMtCOC/working_dir/RtmpWs5AyV/downloaded_packages'
  Old packages: 'ANCOMBC', 'BiocNeighbors', 'Biostrings', 'DAPAR', 'DAPARdata',
    'MSnbase', 'PubChemR', 'WIPF', 'bluster', 'rPDBapi', 'scpi', 'xcms',
    'Fletcher2013b', 'GenomicScores', 'RTCGA', 'RTN', 'bsseq', 'bsseqData',
    'geneplast', 'mia', 'viper'
  Saving _problems/test-inDAGO_shiny-26.R
  [ FAIL 1 | WARN 18 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-inDAGO_shiny.R:26:3'): Shiny app is generated ──────────────────
  Error in `inDAGO()`: The following packages are not installed: ShortRead, rtracklayer, Rsamtools, HTSFilter.
  To enable all the features of inDAGO install with:
    if (!requireNamespace('BiocManager', quietly=TRUE))
      install.packages('BiocManager')
    BiocManager::install(c("ShortRead", "rtracklayer", "Rsamtools", "HTSFilter"))
  
  Backtrace:
      ▆
   1. ├─testthat::expect_s3_class(inDAGO(), "shiny.appobj") at test-inDAGO_shiny.R:26:3
   2. │ └─testthat::quasi_label(enquo(object))
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─inDAGO::inDAGO()
  
  [ FAIL 1 | WARN 18 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted