publicmatt
commented
1 year ago 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/.
pkyle
samskyjyyyyy
I'm using the following R version on Ubuntu 20.02:
I installed renv:
When I try to run
renv::restore()I get the following error:I've tried reinstall gfortran, per some other issues I found here, but that doesn't help.