+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /usr/pkg/bin/bmake stage-install BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/R-git2r-0.32.0/work.log
+ su pbulk -c '"$@"' make /usr/pkg/bin/bmake stage-install BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/R-git2r-0.32.0/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
===> Installing for R-git2r-0.32.0
=> Generating pre-install file lists
=> Creating installation directories
* 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 pkg-config is at least version 0.9.0... no
configure: package dependency requirement 'libgit2 >= 0.26.0' could not be satisfied.
-----------------------------------------------------------------------
Unable to find the libgit2 library on this system. Building 'git2r'
using the bundled source of the libgit2 library.
To build git2r with a system installation of libgit2, please install:
libgit2-dev (package on e.g. Debian and Ubuntu)
libgit2-devel (package on e.g. Fedora, CentOS and RHEL)
libgit2 (Homebrew package on OS X)
and try again.
If the libgit2 library is installed on your system but the git2r
configuration is unable to find it, you can specify the include and
lib path to libgit2 with:
given you downloaded a tar-gz archive:
R CMD INSTALL git2r-.tar.gz --configure-vars='INCLUDE_DIR=/path/to/include LIB_DIR=/path/to/lib'
or cloned the GitHub git2r repository into a directory:
R CMD INSTALL git2r/ --configure-vars='INCLUDE_DIR=/path/to/include LIB_DIR=/path/to/lib'
or download and install git2r in R using
install.packages('git2r', type='source', configure.vars='LIB_DIR=-L/path/to/libs INCLUDE_DIR=-I/path/to/headers')
On macOS, another possibility is to let the configuration
automatically download the libgit2 library from the Homebrew
package manager with:
R CMD INSTALL git2r-.tar.gz --configure-vars='autobrew=yes'
or
R CMD INSTALL git2r/ --configure-vars='autobrew=yes'
or
install.packages('git2r', type='source', configure.vars='autobrew=yes')
-----------------------------------------------------------------------
configure: attempting configuration of bundled libgit2
checking size of void*... 8
checking for gcc... cc -std=gnu11
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether cc -std=gnu11 accepts -g... yes
checking for cc -std=gnu11 option to enable C11 features... none needed
checking for library containing inflate... -lz
checking for library containing EVP_EncryptInit... no
configure: WARNING:
---------------------------------------------
Unable to find the OpenSSL library on this
system. Building a version without support
for https transport.
To build with https support, please install:
libssl-dev (package on e.g. Debian and Ubuntu)
openssl-devel (package on e.g. Fedora, CentOS and RHEL)
and try again.
If the OpenSSL library is installed on
your system but the git2r configuration
is unable to find it, you can specify
the include and lib path to OpenSSL with:
R CMD INSTALL git2r --configure-vars='LIBS=-L/path/to/libs CPPFLAGS=-I/path/to/headers'
---------------------------------------------
configure: WARNING:
---------------------------------------------
Unable to find the LibSSH2 (ver >= v1.8)
library on this system. Building git2r
without support for SSH transport.
To build with SSH support, please install:
libssh2-1-dev (package on e.g. Debian and Ubuntu)
libssh2-devel (package on e.g. Fedora, CentOS and RHEL)
libssh2 (Homebrew package on OS X)
and try again.
If the LibSSH2 library is installed on
your system but the git2r configuration
is unable to find it, you can specify
the include and lib path to LibSSH2 with:
R CMD INSTALL git2r --configure-vars='LIBS=-L/path/to/libs CPPFLAGS=-I/path/to/headers'
---------------------------------------------
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for struct stat.st_mtim... yes
checking for struct stat.st_mtimespec... no
checking for struct stat.st_mtime_nsec... no
checking for struct stat.st_mtim.tv_nsec... yes
checking for futimens... yes
checking for qsort_r... yes
checking for qsort_s... no
----- Results of the git2r package configure -----
HTTPS transport......................: no
LibSSH2 to enable the SSH transport..: no
--------------------------------------------------
configure: creating ./config.status
config.status: creating src/Makevars_libgit2
** libs
cc -std=gnu11 -I"/usr/pkg/lib/R/include" -DNDEBUG -I. -Ilibgit2/src/libgit2 -Ilibgit2/src/util -Ilibgit2/include -Ilibgit2/deps/http-parser -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/glib-2.0 -I/usr/pkg/include/gio-unix-2.0 -I/usr/pkg/lib/glib-2.0/include -I/usr/pkg/include/freetype2 -I/usr/pkg/include/harfbuzz -I/usr/pkg/include/ncurses -DLDAP_DEPRECATED -DGIT_ARCH_64 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DLIBGIT2_NO_FEATURES_H -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT_SHA1_COLLISIONDETECT=1 -DSHA1DC_NO_STANDARD_INCLUDES=1 -DSHA1DC_CUSTOM_INCLUDE_SHA1_C=\"common.h\" -DSHA1DC_CUSTOM_INCLUDE_UBC_CHECK_C=\"common.h\" -DGIT_USE_STAT_MTIM -DGIT_USE_NSEC -DHAVE_FUTIMENS -DHAVE_QSORT_R -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_HAVE_GIT_ERROR -DGIT2R_LIBGIT2_V0_99_0_RENAMES -DGIT_REGEX_REGCOMP -DTHREADSAFE=OFF -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/glib-2.0 -I/usr/pkg/include/gio-unix-2.0 -I/usr/pkg/lib/glib-2.0/include -I/usr/pkg/include/freetype2 -I/usr/pkg/include/harfbuzz -I/usr/pkg/include/ncurses -DLDAP_DEPRECATED -fpic -pipe -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/glib-2.0 -I/usr/pkg/include/gio-unix-2.0 -I/usr/pkg/lib/glib-2.0/include -I/usr/pkg/include/freetype2 -I/usr/pkg/include/harfbuzz -I/usr/pkg/include/ncurses -DLDAP_DEPRECATED -c libgit2/src/libgit2/annotated_commit.c -o libgit2/src/libgit2/annotated_commit.o
In file included from libgit2/src/libgit2/oid.h:14:0,
from libgit2/src/libgit2/refs.h:17,
from libgit2/src/libgit2/annotated_commit.c:10:
libgit2/src/util/hash.h:31:23: error: field 'sha256' has incomplete type
git_hash_sha256_ctx sha256;
^
*** Error code 1
Stop.
make: stopped in /home/pbulk/build/devel/R-git2r/work/git2r/src
ERROR: compilation failed for package 'git2r'
* removing '/home/pbulk/build/devel/R-git2r/work/.destdir/usr/pkg/lib/R/library/git2r'
*** Error code 1
Stop.
bmake[1]: stopped in /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/devel/R-git2r
*** Error code 1
Stop.
bmake: stopped in /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/devel/R-git2r