Installation issue on R-4.4.1/Ubuntu 18

[kodiweera]

Hi, I'm trying to install RMINC on R-4.4.1 on Ubuntu 18. I get the following error msg. Do you see what's wrong? hdf5 version: 1.8.18 and gcc version is 7. As a matter of fact, I tried installing with different versions of hdf5 and gcc versions, but no luck! I also tried the previous release and get the same error msg. Thanks for any suggestion.

.......................................................................................................................................................... In file included from /usr/share/R/include/R.h:78, from minc_reader.h:12, from modelling_functions.c:1: modelling_functions.c: In function ‘voxel_lm’: modellingfunctions.c:541:12: error: too few arguments to function ‘dpotri’ F77_CALL(dpotri)("Upper", &p, x, &n, &info);

after many lines..at the end of the day

/usr/lib/R/etc/Makeconf:195: recipe for target 'modelling_functions.o' failed make: *** [modelling_functions.o] Error 1 .........................................................................................................................................................

full output:

Installing package into ‘/home/brain/R/x86_64-pc-linux-gnu-library/4.4’ (as ‘lib’ is unspecified)

• installing source package ‘RMINC’ ... using staged installation checking for gcc... gcc 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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether we are using the GNU C++ compiler... yes checking whether g++ -std=gnu++17 accepts -g... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for a sed that does not truncate output... /bin/sed checking for gawk... gawk configure: Searching for libminc configure: MINC_TOOLKIT was specified configure: MINC_PATH set to /opt/minc/1.9.18 configure: override by setting the environment variable MINC_PATH configure: or by setting --with-build-path as a configure argument checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for h5cc... /usr/local/hdf5/bin/h5cc checking for HDF5 libraries... yes (version 1.8.18) checking hdf5.h usability... yes checking hdf5.h presence... yes checking for hdf5.h... yes checking for H5Fcreate in -lhdf5... yes checking for main in -lhdf5_hl... yes checking for matching HDF5 Fortran wrapper... /usr/local/hdf5/bin/h5fc checking for mifree_name in -lminc2... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for size_t... yes checking for error_at_line... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes configure: creating ./config.status config.status: creating src/Makevars libs using C compiler: ‘gcc (Ubuntu 8.4.0-1ubuntu1~18.04) 8.4.0’ using C++ compiler: ‘g++ (Ubuntu 8.4.0-1ubuntu1~18.04) 8.4.0’ using C++11 gcc -I"/usr/share/R/include" -DNDEBUG -I/opt/minc/1.9.18/include -I/usr/local/hdf5/include -I'/home/brain/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-y8QyKA/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RMINC_init.c -o RMINC_init.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/opt/minc/1.9.18/include -I/usr/local/hdf5/include -I'/home/brain/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-y8QyKA/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/opt/minc/1.9.18/include -I/usr/local/hdf5/include -I'/home/brain/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-y8QyKA/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c anat_summaries.cpp -o anat_summaries.o gcc -I"/usr/share/R/include" -DNDEBUG -I/opt/minc/1.9.18/include -I/usr/local/hdf5/include -I'/home/brain/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-y8QyKA/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c minc2_read.c -o minc2_read.o minc2_read.c: In function ‘read_voxel_from_files’: minc2_read.c:107:57: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘misize_t’ {aka ‘long long unsigned int’} [-Wformat=] if ( R_DEBUG_mincIO ) Rprintf("hSlab_count [0..3] = %d, %d, %d, %d\n", ~^ %lld hSlab_count[0], hSlab_count[1], hSlab_count[2], hSlab_count[3]);

  minc2_read.c:107:61: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘misize_t’ {aka ‘long long unsigned int’} [-Wformat=]
  if ( R_DEBUG_mincIO ) Rprintf("hSlab_count [0..3] = %d, %d, %d, %d\n",
                                                          ~^
                                                          %lld
      hSlab_count[0], hSlab_count[1], hSlab_count[2], hSlab_count[3]);

  minc2_read.c:107:65: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘misize_t’ {aka ‘long long unsigned int’} [-Wformat=] if ( R_DEBUG_mincIO ) Rprintf("hSlab_count [0..3] = %d, %d, %d, %d\n", ~^ %lld hSlab_count[0], hSlab_count[1], hSlab_count[2], hSlab_count[3]);

  minc2_read.c:107:69: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘misize_t’ {aka ‘long long unsigned int’} [-Wformat=]
  if ( R_DEBUG_mincIO ) Rprintf("hSlab_count [0..3] = %d, %d, %d, %d\n",
                                                                  ~^
                                                                  %lld
      hSlab_count[0], hSlab_count[1], hSlab_count[2], hSlab_count[3]);

  gcc -I"/usr/share/R/include" -DNDEBUG -I/opt/minc/1.9.18/include -I/usr/local/hdf5/include -I'/home/brain/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-y8QyKA/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c minc2_support.c -o minc2_support.o gcc -I"/usr/share/R/include" -DNDEBUG -I/opt/minc/1.9.18/include -I/usr/local/hdf5/include -I'/home/brain/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-y8QyKA/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c minc2_write.c -o minc2_write.o minc2_write.c: In function ‘write_volume’: minc2_write.c:156:55: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘misize_t’ {aka ‘long long unsigned int’} [-Wformat=] if ( R_DEBUG_mincIO ) Rprintf("hSlab_count [0..2] = %d, %d, %d\n", ~^ %lld hSlab_count[0], hSlab_count[1], hSlab_count[2]);

  minc2_write.c:156:59: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘misize_t’ {aka ‘long long unsigned int’} [-Wformat=]
  if ( R_DEBUG_mincIO ) Rprintf("hSlab_count [0..2] = %d, %d, %d\n",
                                                        ~^
                                                        %lld
  hSlab_count[0], hSlab_count[1], hSlab_count[2]);

  minc2_write.c:156:63: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘misize_t’ {aka ‘long long unsigned int’} [-Wformat=] if ( R_DEBUG_mincIO ) Rprintf("hSlab_count [0..2] = %d, %d, %d\n", ~^ %lld hSlab_count[0], hSlab_count[1], hSlab_count[2]);

  gcc -I"/usr/share/R/include" -DNDEBUG -I/opt/minc/1.9.18/include -I/usr/local/hdf5/include -I'/home/brain/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include'     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-y8QyKA/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c minc_anova.c -o minc_anova.o
  g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/opt/minc/1.9.18/include -I/usr/local/hdf5/include -I'/home/brain/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include'     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-y8QyKA/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -c minc_apply.cpp -o minc_apply.o
  minc_apply.cpp: In function ‘Rcpp::List rcpp_minc_apply(Rcpp::CharacterVector, bool, Rcpp::CharacterVector, double, double, Rcpp::RObject, bool, Rcpp::NumericVector, Rcpp::Function, Rcpp::List)’:
  minc_apply.cpp:92:11: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘misize_t’ {aka ‘long long unsigned int’} [-Wformat=]
  Rprintf("Number of slabs: %d\n", n_slabs[0] * n_slabs[1] * n_slabs[2]);
         ^~~~~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  minc_apply.cpp:99:16: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘misize_t’ {aka ‘long long unsigned int’} [-Wformat=]
      Rprintf("%d ", (i * n_slabs[1] * n_slabs[2]) +
              ^~~~~  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        (j * n_slabs[2]) +

    k);
    ~

  g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/opt/minc/1.9.18/include -I/usr/local/hdf5/include -I'/home/brain/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-y8QyKA/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c minc_cpp.cpp -o minc_cpp.o gcc -I"/usr/share/R/include" -DNDEBUG -I/opt/minc/1.9.18/include -I/usr/local/hdf5/include -I'/home/brain/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-y8QyKA/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c minc_reader.c -o minc_reader.o minc_reader.c: In function ‘minc2_apply’: minc_reader.c:436:27: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘misize_t’ {aka ‘long long unsigned int’} [-Wformat=] Rprintf("Volume sizes: %i %i %i\n", sizes[0], sizes[1], sizes[2]); ~^ ~~~~ %lli minc_reader.c:436:30: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘misize_t’ {aka ‘long long unsigned int’} [-Wformat=] Rprintf("Volume sizes: %i %i %i\n", sizes[0], sizes[1], sizes[2]); ~^ ~~~~ %lli minc_reader.c:436:33: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘misize_t’ {aka ‘long long unsigned int’} [-Wformat=] Rprintf("Volume sizes: %i %i %i\n", sizes[0], sizes[1], sizes[2]); ~^ ~~~~ %lli gcc -I"/usr/share/R/include" -DNDEBUG -I/opt/minc/1.9.18/include -I/usr/local/hdf5/include -I'/home/brain/R/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-y8QyKA/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c modelling_functions.c -o modelling_functions.o In file included from /usr/share/R/include/R.h:78, from minc_reader.h:12, from modelling_functions.c:1: modelling_functions.c: In function ‘voxel_lm’: modellingfunctions.c:541:12: error: too few arguments to function ‘dpotri’ F77_CALL(dpotri)("Upper", &p, x, &n, &info); ^~ /usr/share/R/include/R_ext/RS.h:77:22: note: in definition of macro ‘F77_CALL’

  define F77CALL(x) x ##

                ^

  /usr/share/R/include/R_ext/Lapack.h:854:10: note: declared here F77_NAME(dpotri)(const char uplo, const La_INT n, ^~ /usr/share/R/include/R_ext/RS.h:77:22: note: in definition of macro ‘F77_CALL’

  define F77CALL(x) x ##

                ^

  /usr/share/R/include/R_ext/Lapack.h:854:1: note: in expansion of macro ‘F77_NAME’ F77_NAME(dpotri)(const char uplo, const La_INT n, ^~~~ modelling_functions.c: In function ‘minc2_model’: modelling_functions.c:822:27: warning: format ‘%i’ expects argument of type ‘int’, but argument 2 has type ‘misize_t’ {aka ‘long long unsigned int’} [-Wformat=] Rprintf("Volume sizes: %i %i %i\n", sizes[0], sizes[1], sizes[2]); ~^ ~~~~ %lli modelling_functions.c:822:30: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘misize_t’ {aka ‘long long unsigned int’} [-Wformat=] Rprintf("Volume sizes: %i %i %i\n", sizes[0], sizes[1], sizes[2]); ~^ ~~~~ %lli modelling_functions.c:822:33: warning: format ‘%i’ expects argument of type ‘int’, but argument 4 has type ‘misize_t’ {aka ‘long long unsigned int’} [-Wformat=] Rprintf("Volume sizes: %i %i %i\n", sizes[0], sizes[1], sizes[2]); ~^ ~~~~ %lli /usr/lib/R/etc/Makeconf:195: recipe for target 'modelling_functions.o' failed make: *** [modelling_functions.o] Error 1 ERROR: compilation failed for package ‘RMINC’

• removing ‘/home/brain/R/x86_64-pc-linux-gnu-library/4.4/RMINC’ Warning message: In i.p(...) : installation of package ‘/tmp/RtmpRPacg7/file2a382cb896b9/RMINC_1.5.3.0.tar.gz’ had non-zero exit status

[yohanyee]

Hello, this appears to be a duplicate of issue #314 .

Can you try installing from the develop branch and let us know if that works?

[kodiweera]

Hi yohanyee, That worked! I installed it on both Ubuntu 18 and 20 runing R-4.4.1.

Here's what I did: git clone -b develop https://github.com/Mouse-Imaging-Centre/RMINC.git cd RMIN R CMD INSTALL .

Thanks you all for all your good work!

[yohanyee]

Great, glad to know it works.

Another way to install is via devtools in R:

devtools::install_github("Mouse-Imaging-Centre/RMINC@develop")