* installing *source* package ‘git2r’ ...
** package ‘git2r’ successfully unpacked and MD5 sums checked
** using staged installation
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
Found pkg-config cflags and libs!
checking whether the libgit2 version will work in git2r... yes
checking whether the libgit2 function git_buf_dispose is available... yes
checking whether the libgit2 constant GIT_OBJECT_ANY is available... yes
checking whether the libgit2 function git_error_last is available... yes
checking whether the libgit2 function git_oid_is_zero is available... yes
----- Results of the git2r package configure -----

  PKG_CFLAGS:  -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES
  PKG_LIBS: -lgit2 

--------------------------------------------------
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘clang version 18.1.2’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/git2r/src'
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r.c -o git2r.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_S3.c -o git2r_S3.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_arg.c -o git2r_arg.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_blame.c -o git2r_blame.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_blob.c -o git2r_blob.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_branch.c -o git2r_branch.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_checkout.c -o git2r_checkout.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_clone.c -o git2r_clone.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_commit.c -o git2r_commit.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_config.c -o git2r_config.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_cred.c -o git2r_cred.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_diff.c -o git2r_diff.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_error.c -o git2r_error.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_graph.c -o git2r_graph.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_index.c -o git2r_index.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_libgit2.c -o git2r_libgit2.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_merge.c -o git2r_merge.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_note.c -o git2r_note.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_object.c -o git2r_object.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_odb.c -o git2r_odb.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_oid.c -o git2r_oid.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_push.c -o git2r_push.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_reference.c -o git2r_reference.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_reflog.c -o git2r_reflog.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_remote.c -o git2r_remote.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_repository.c -o git2r_repository.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_reset.c -o git2r_reset.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_revparse.c -o git2r_revparse.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_revwalk.c -o git2r_revwalk.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_signature.c -o git2r_signature.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_stash.c -o git2r_stash.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_status.c -o git2r_status.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_tag.c -o git2r_tag.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_transfer.c -o git2r_transfer.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DR_NO_REMAP -DSTRICT_R_HEADERS  -isystem /usr/local/clang18/include -I/usr/local/clang/include   -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c git2r_tree.c -o git2r_tree.o
/usr/local/clang18/bin/clang -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o git2r.so git2r.o git2r_S3.o git2r_arg.o git2r_blame.o git2r_blob.o git2r_branch.o git2r_checkout.o git2r_clone.o git2r_commit.o git2r_config.o git2r_cred.o git2r_diff.o git2r_error.o git2r_graph.o git2r_index.o git2r_libgit2.o git2r_merge.o git2r_note.o git2r_object.o git2r_odb.o git2r_oid.o git2r_push.o git2r_reference.o git2r_reflog.o git2r_remote.o git2r_repository.o git2r_reset.o git2r_revparse.o git2r_revwalk.o git2r_signature.o git2r_stash.o git2r_status.o git2r_tag.o git2r_transfer.o git2r_tree.o -lgit2
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/git2r/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/git2r/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/git2r/src'
installing to /data/gannet/ripley/R/packages/tests-clang/git2r.Rcheck/00LOCK-git2r/00new/git2r/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (git2r)