Installation issue on R-4.4.1/Ubuntu 18 #324
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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? |
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Hi yohanyee, Here's what I did: Thanks you all for all your good work! |
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Great, glad to know it works. Another way to install is via devtools in R:
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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’:
modelling_functions.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)
** 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) 8.4.0’18.04) 8.4.0’using C++ compiler: ‘g++ (Ubuntu 8.4.0-1ubuntu1
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’:
modelling_functions.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 F77_CALL(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 F77_CALL(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’
Warning message:
In i.p(...) :
installation of package ‘/tmp/RtmpRPacg7/file2a382cb896b9/RMINC_1.5.3.0.tar.gz’ had non-zero exit status
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