Renv fails to install Matrix package

[publicmatt]

I'm using the following R version on Ubuntu 20.02:

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

I installed renv:

> renv::init( bare = TRUE)

renv: Project Environments for R

Welcome to renv! It looks like this is your first time using renv.
This is a one-time message, briefly describing some of renv's functionality.

renv will write to files within the active project folder, including:

  - A folder 'renv' in the project directory, and
  - A lockfile called 'renv.lock' in the project directory.

In particular, projects using renv will normally use a private, per-project
R library, in which new packages will be installed. This project library is
isolated from other R libraries on your system.

In addition, renv will update files within your project directory, including:

  - .gitignore
  - .Rbuildignore
  - .Rprofile

Finally, renv maintains a local cache of data on the filesystem, located at:

  - "~/.cache/R/renv"

This path can be customized: please see the documentation in `?renv::paths`.

Please read the introduction vignette with `vignette("renv")` for more information.
You can browse the package documentation online at https://rstudio.github.io/renv/.
Do you want to proceed? [y/N]: y
* "~/.cache/R/renv" has been created.
* Project '~/gcam' loaded. [renv 0.17.3]
* The project is currently out-of-sync.
* Use `renv::status()` for more details.
* renv activated -- please restart the R session.

When I try to run renv::restore() I get the following error:

> renv::restore()
The following package(s) will be updated:

# CRAN ===============================
- Matrix            [1.5-4.1 -> 1.2-18]
- lattice            [0.21-8 -> 0.20-45]
- BH                  [* -> 1.72.0-3]

[...]

Installing Matrix [1.2-18] ...
	FAILED
Error installing package 'Matrix':
==================================

* installing to library ‘/tmp/RtmpZPdCcC/renv-staging-77407636e62c’
* installing *source* package ‘Matrix’ ...
** package ‘Matrix’ successfully unpacked and MD5 sums checked
** using staged installation
  Cleaning up after installing the Matrix package
( cd Lib ; make clean )
make[1]: Entering directory '/tmp/RtmpZPdCcC/renv-package-774023612b87/Matrix/src/CHOLMOD/Lib'
make[1]: Leaving directory '/tmp/RtmpZPdCcC/renv-package-774023612b87/Matrix/src/CHOLMOD/Lib'
( cd Source ; make clean )
make[1]: Entering directory '/tmp/RtmpZPdCcC/renv-package-774023612b87/Matrix/src/COLAMD/Source'
make[1]: Leaving directory '/tmp/RtmpZPdCcC/renv-package-774023612b87/Matrix/src/COLAMD/Source'
( cd Source ; make clean )
make[1]: Entering directory '/tmp/RtmpZPdCcC/renv-package-774023612b87/Matrix/src/AMD/Source'
make[1]: Leaving directory '/tmp/RtmpZPdCcC/renv-package-774023612b87/Matrix/src/AMD/Source'
** libs
using C compiler: ‘gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0’
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-rAnobU/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c CHMfactor.c -o CHMfactor.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-rAnobU/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Csparse.c -o Csparse.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-rAnobU/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c TMatrix_as.c -o TMatrix_as.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-rAnobU/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Tsparse.c -o Tsparse.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-rAnobU/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c init.c -o init.o
In file included from /usr/share/R/include/R.h:78,
                 from Mutils.h:12,
                 from init.c:1:
dgeMatrix.h:43:15: error: conflicting types for ‘dgesdd_’
   43 | void F77_NAME(dgesdd)(const char *jobz,
      |               ^~~~~~
/usr/share/R/include/R_ext/RS.h:77:22: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x) x ## _
      |                      ^
dgeMatrix.h:43:6: note: in expansion of macro ‘F77_NAME’
   43 | void F77_NAME(dgesdd)(const char *jobz,
      |      ^~~~~~~~
/usr/share/R/include/R_ext/Lapack.h:2404:10: note: previous declaration of ‘dgesdd_’ was here
 2404 | F77_NAME(dgesdd)(const char* jobz,
      |          ^~~~~~
/usr/share/R/include/R_ext/RS.h:77:22: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x) x ## _
      |                      ^
/usr/share/R/include/R_ext/Lapack.h:2404:1: note: in expansion of macro ‘F77_NAME’
 2404 | F77_NAME(dgesdd)(const char* jobz,
      | ^~~~~~~~
make: *** [/usr/lib/R/etc/Makeconf:191: init.o] Error 1
ERROR: compilation failed for package ‘Matrix’
* removing ‘/tmp/RtmpZPdCcC/renv-staging-77407636e62c/Matrix’
Error: install of package 'Matrix' failed
Traceback (most recent calls last):
13: renv::restore()
12: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
11: renv_install(records)
10: renv_install_staged(records)
 9: renv_install_default(records)
 8: handler(package, renv_install_impl(record))
 7: renv_install_impl(record)
 6: withCallingHandlers(renv_install_package_local(record), error = function(e) {
        vwritef("\tFAILED")
        writef(e$output)
    })
 5: renv_install_package_local(record)
 4: renv_install_package_local_impl(package, path)
 3: r_cmd_install(package, path)
 2: r_exec_error(package, output, "install")
 1: stop(error)

I've tried reinstall gfortran, per some other issues I found here, but that doesn't help.

[publicmatt]

Bump. I'm still having this issue, even with the latest rocker/tidyverse docker image. I'm using the following Dockerfile:

FROM rocker/tidyverse:4.3

COPY ./ /gcamdata

WORKDIR /gcamdata

RUN R -e 'install.packages( "https://cran.r-project.org/src/contrib/Archive/renv/renv_0.12.5.tar.gz", repos = NULL, type = "source" )'
RUN R -e 'renv::consent(provided = TRUE)'
RUN R -e 'renv::init( bare = TRUE)'
RUN R -e 'renv::restore()'
RUN R -e 'renv::activate()'

RUN R -e 'driver_drake()'

Which outputs the following error:

#0 103.4 Installing Matrix [1.2-18] ...
#0 105.8        FAILED
#0 105.8 Error: install of package 'Matrix' failed
#0 105.8 Error installing package 'Matrix':
#0 105.8 ==================================
#0 105.8
#0 105.8 * installing to library ‘/tmp/RtmppIjktx/renv-staging-7288eba9d’
#0 105.8 * installing *source* package ‘Matrix’ ...
#0 105.8 ** package ‘Matrix’ successfully unpacked and MD5 sums checked
#0 105.8 ** using staged installation
#0 105.8   Cleaning up after installing the Matrix package
#0 105.8 ( cd Lib ; make clean )
#0 105.8 make[1]: Entering directory '/tmp/RtmppIjktx/renv-package-727f80d04/Matrix/src/CHOLMOD/Lib'
#0 105.8 make[1]: Leaving directory '/tmp/RtmppIjktx/renv-package-727f80d04/Matrix/src/CHOLMOD/Lib'
#0 105.8 ( cd Source ; make clean )
#0 105.8 make[1]: Entering directory '/tmp/RtmppIjktx/renv-package-727f80d04/Matrix/src/COLAMD/Source'
#0 105.8 make[1]: Leaving directory '/tmp/RtmppIjktx/renv-package-727f80d04/Matrix/src/COLAMD/Source'
#0 105.8 ( cd Source ; make clean )
#0 105.8 make[1]: Entering directory '/tmp/RtmppIjktx/renv-package-727f80d04/Matrix/src/AMD/Source'
#0 105.8 make[1]: Leaving directory '/tmp/RtmppIjktx/renv-package-727f80d04/Matrix/src/AMD/Source'
#0 105.8 ** libs
#0 105.8 using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’
#0 105.8 gcc -I"/usr/local/lib/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c CHMfactor.c -o CHMfactor.o
#0 105.8 gcc -I"/usr/local/lib/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Csparse.c -o Csparse.o
#0 105.8 gcc -I"/usr/local/lib/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c TMatrix_as.c -o TMatrix_as.o
#0 105.8 gcc -I"/usr/local/lib/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Tsparse.c -o Tsparse.o
#0 105.8 gcc -I"/usr/local/lib/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config  -I/usr/local/include    -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
#0 105.8 In file included from /usr/local/lib/R/include/R.h:78,
#0 105.8                  from Mutils.h:12,
#0 105.8                  from init.c:1:
#0 105.8 dgeMatrix.h:43:15: error: conflicting types for ‘dgesdd_’; have ‘void(const char *, const int *, const int *, double *, const int *, double *, double *, const int *, double *, const int *, double *, const int *, int *, int *)’
#0 105.8    43 | void F77_NAME(dgesdd)(const char *jobz,
#0 105.8       |               ^~~~~~
#0 105.8 /usr/local/lib/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
#0 105.8    77 | # define F77_CALL(x)    x ## _
#0 105.8       |                         ^
#0 105.8 dgeMatrix.h:43:6: note: in expansion of macro ‘F77_NAME’
#0 105.8    43 | void F77_NAME(dgesdd)(const char *jobz,
#0 105.8       |      ^~~~~~~~
#0 105.8 /usr/local/lib/R/include/R_ext/Lapack.h:2404:10: note: previous declaration of ‘dgesdd_’ with type ‘void(const char *, const int *, const int *, double *, const int *, double *, double *, const int *, double *, const int *, double *, const int *, int *, int *, size_t)’ {aka ‘void(const char *, const int *, const int *, double *, const int *, double *, double *, const int *, double *, const int *, double *, const int *, int *, int *, long unsigned int)’}
#0 105.8  2404 | F77_NAME(dgesdd)(const char* jobz,
#0 105.8       |          ^~~~~~
#0 105.8 /usr/local/lib/R/include/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
#0 105.8    77 | # define F77_CALL(x)    x ## _
#0 105.8       |                         ^
#0 105.8 /usr/local/lib/R/include/R_ext/Lapack.h:2404:1: note: in expansion of macro ‘F77_NAME’
#0 105.8  2404 | F77_NAME(dgesdd)(const char* jobz,
#0 105.8       | ^~~~~~~~
#0 105.8 make: *** [/usr/local/lib/R/etc/Makeconf:191: init.o] Error 1
#0 105.8 ERROR: compilation failed for package ‘Matrix’
#0 105.8 * removing ‘/tmp/RtmppIjktx/renv-staging-7288eba9d/Matrix’
#0 105.8 Traceback (most recent calls last):

Inside the container, I checked the versions of gfortran, gcc, g++, gmake and R:

root@844ff8c0566d:/gcamdata# gfortran --version
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

root@844ff8c0566d:/gcamdata# g++ --version
g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

root@844ff8c0566d:/gcamdata# gcc --version
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

root@844ff8c0566d:/gcamdata# gmake --version
GNU Make 4.3
Built for x86_64-pc-linux-gnu
Copyright (C) 1988-2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
root@844ff8c0566d:/gcamdata# make --version
GNU Make 4.3
Built for x86_64-pc-linux-gnu
Copyright (C) 1988-2020 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
root@844ff8c0566d:/gcamdata#
exit
❯ d run -it publicmatt/gcamdata /bin/bash
root@7e4688e11af0:/gcamdata# R --version
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.

[publicmatt]

Any help with this issue would be appreciated!

[publicmatt]

Bump! Setting up gcamdata has been a struggle on our machines. Is there a docker image used internally that could be made available to the public?

[pkyle]

I don't use renv, so can't comment on how to get it working, but it can be de-activated by running, from R:
renv::deactivate()
At that point you'll need to manage the package versions yourself. If you're installing fresh to a new workspace, all will default to the latest version. Given the tidyverse team's practice of pushing regular updates that cause code that worked in prior editions to fail in later ones, this isn't ideal, but it's only a few packages that tend to cause problems. Here are the ones I'm using locally, in case that helps. The devtools::install_version() function is helpful for specifying versions.
[1] compiler_4.2.2 pillar_1.8.1 prettyunits_1.1.1 remotes_2.4.2 tools_4.2.2 bit_4.0.4 [7] pkgbuild_1.3.1 pkgload_1.3.1 memoise_2.0.1 lifecycle_1.0.3 tibble_3.1.8 pkgconfig_2.0.3 [13] rlang_1.1.0 cli_3.4.1 rstudioapi_0.14 parallel_4.2.2 fastmap_1.1.0 stringr_1.5.0 [19] withr_2.5.0 dplyr_1.0.10 generics_0.1.3 desc_1.4.2 fs_1.5.2 vctrs_0.6.2 [25] devtools_2.3.1 hms_1.1.2 bit64_4.0.5 rprojroot_2.0.3 tidyselect_1.2.0 data.table_1.14.4 [31] glue_1.6.2 R6_2.5.1 processx_3.8.0 fansi_1.0.3 vroom_1.6.0 sessioninfo_1.2.2 [37] callr_3.7.3 tidyr_1.3.0 purrr_1.0.1 readr_2.1.3 tzdb_0.3.0 magrittr_2.0.3 [43] ps_1.7.2 ellipsis_0.3.2 usethis_1.6.0 assertthat_0.2.1 utf8_1.2.2 stringi_1.7.8 [49] cachem_1.0.6 crayon_1.5.2 brio_1.1.3

[samskyjyyyyy]

when i run renv:restore(), i got error that:
Error installing package 'git2r':

• installing to library 'C:/Users/pro16/AppData/Local/Temp/RtmpeyEYlu/renv-library-4aac312813e9'

• installing source package 'git2r' ...
  ** 成功将'git2r'程序包解包并MD5和检查
  ** using staged installation

  ---

  WARNING: this package has a configure script
  It probably needs manual configuration

  ---

** libs
rm -f git2r.dll 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
"C:/PROGRA1/R/R-361.1/bin/x64/Rscript.exe" "../tools/winlibs.R" 1.4.2-fixed
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r.c -o git2r.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_S3.c -o git2r_S3.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_arg.c -o git2r_arg.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_blame.c -o git2r_blame.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_blob.c -o git2r_blob.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_branch.c -o git2r_branch.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_checkout.c -o git2r_checkout.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_clone.c -o git2r_clone.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_commit.c -o git2r_commit.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_config.c -o git2r_config.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_cred.c -o git2r_cred.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_diff.c -o git2r_diff.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_error.c -o git2r_error.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_graph.c -o git2r_graph.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_index.c -o git2r_index.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_libgit2.c -o git2r_libgit2.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_merge.c -o git2r_merge.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_note.c -o git2r_note.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_object.c -o git2r_object.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_odb.c -o git2r_odb.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_oid.c -o git2r_oid.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_push.c -o git2r_push.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_reference.c -o git2r_reference.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_reflog.c -o git2r_reflog.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_remote.c -o git2r_remote.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_repository.c -o git2r_repository.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_reset.c -o git2r_reset.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_revparse.c -o git2r_revparse.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_revwalk.c -o git2r_revwalk.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_signature.c -o git2r_signature.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_stash.c -o git2r_stash.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_status.c -o git2r_status.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_tag.c -o git2r_tag.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_transfer.c -o git2r_transfer.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -I"C:/PROGRA1/R/R-361.1/include" -DNDEBUG -I../windows/libgit2-1.4.2-fixed/include -DR_NO_REMAP -DSTRICT_R_HEADERS -DGIT2R_HAVE_BUF_DISPOSE -DGIT2R_HAVE_OBJECT_ANY -DGIT2R_LIBGIT2_V0_99_0_RENAMES -O2 -Wall -std=gnu99 -mtune=generic -c git2r_tree.c -o git2r_tree.o
C:/RBuildTools/3.5/mingw_64/bin/gcc -shared -s -static-libgcc -o git2r.dll git2r-win.def 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 -L../windows/libgit2-1.4.2-fixed/lib/x64 -lgit2 -lssh2 -lz -lssl -lcrypto -lwinhttp -lws2_32 -lcrypt32 -lole32 -lrpcrt4 -LC:/PROGRA1/R/R-361.1/bin/x64 -lR
../windows/libgit2-1.4.2-fixed/lib/x64/libgit2.a(diff_print.c.obj):(.text+0x13b7): undefined reference to __imp___acrt_iob_func' ../windows/libgit2-1.4.2-fixed/lib/x64/libgit2.a(signature.c.obj):(.text+0x45f): undefined reference to __imp__difftime64'
../windows/libgit2-1.4.2-fixed/lib/x64/libgit2.a(signature.c.obj):(.text+0x593): undefined reference to __imp__difftime64' ../windows/libgit2-1.4.2-fixed/lib/x64/libgit2.a(winhttp.c.obj):(.text+0xf94): undefined reference to __stdio_common_vswprintf_s'
../windows/libgit2-1.4.2-fixed/lib/x64/libgit2.a(util.c.obj):(.text+0x4a): undefined reference to __imp___acrt_iob_func' ../windows/libgit2-1.4.2-fixed/lib/x64/libgit2.a(util.c.obj):(.text+0x95): undefined reference to __imp___acrt_iob_func'
../windows/libgit2-1.4.2-fixed/lib/x64/libgit2.a(util.c.obj):(.text+0xe5): undefined reference to __imp___acrt_iob_func' ../windows/libgit2-1.4.2-fixed/lib/x64/libgit2.a(util.c.obj):(.text+0x135): undefined reference to __imp___acrt_iob_func'
../windows/libgit2-1.4.2-fixed/lib/x64/libgit2.a(util.c.obj):(.text+0x185): undefined reference to __imp___acrt_iob_func' ../windows/libgit2-1.4.2-fixed/lib/x64/libgit2.a(util.c.obj):(.text+0x1d5): more undefined references to __imp___acrt_iob_func' follow
../windows/libgit2-1.4.2-fixed/lib/x64/libssh2.a(session.o):(.text+0xa96): undefined reference to __imp__difftime64' ../windows/libgit2-1.4.2-fixed/lib/x64/libcrypto.a(e_capi.o):(.text+0x3700): undefined reference to __imp___acrt_iob_func'
../windows/libgit2-1.4.2-fixed/lib/x64/libcrypto.a(eng_openssl.o):(.text+0x12): undefined reference to __imp___acrt_iob_func' ../windows/libgit2-1.4.2-fixed/lib/x64/libcrypto.a(eng_openssl.o):(.text+0x266): undefined reference to __imp___acrt_iob_func'
../windows/libgit2-1.4.2-fixed/lib/x64/libcrypto.a(ui_openssl.o):(.text+0x19): undefined reference to __imp___acrt_iob_func' ../windows/libgit2-1.4.2-fixed/lib/x64/libcrypto.a(ui_openssl.o):(.text+0x174): undefined reference to __imp___acrt_iob_func'
../windows/libgit2-1.4.2-fixed/lib/x64/libcrypto.a(ui_openssl.o):(.text+0x197): more undefined references to __imp___acrt_iob_func' follow C:/RBuildTools/3.5/mingw_64/bin/../lib/gcc/x86_64-w64-mingw32/4.9.3/../../../../x86_64-w64-mingw32/lib/../lib/libiconv.a(localcharset.o):localcharset.c:(.text+0x8): undefined reference to __imp_GetACP'
collect2.exe: error: ld returned 1 exit status
make: *** [C:/PROGRA1/R/R-361.1/share/make/winshlib.mk:13: git2r.dll] Error 1
ERROR: compilation failed for package 'git2r'

• removing 'C:/Users/pro16/AppData/Local/Temp/RtmpeyEYlu/renv-library-4aac312813e9/git2r'
  错误: install of package 'git2r' failed
  此外: Warning messages:
  1: The 'rmarkdown' package is required to parse dependencies within R Markdown files.
  Consider installing it with install.packages("rmarkdown").
  2: The 'knitr' package is required to parse dependencies within multi-mode files.
  Consider installing it with install.packages("knitr").