Attempting to compile rgl for r on arch linux x86_64. I copied just the error portion of the installation. This has occurred after I recently updated R. Any idea how to solve this?
g++ -I/usr/include/R/ -DNDEBUG -DHAVE_PNG_H -I/usr/include/libpng16 -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -c init.cpp -o init.o
In file included from /usr/include/freetype2/freetype.h:33:0,
from ext/ftgl/FTGL/ftgl.h:33,
from glgui.h:12,
from gui.h:10,
from rglview.h:11,
from Device.h:11,
from DeviceManager.h:9,
from init.cpp:6:
init.cpp: In function ‘SEXPREC* rgl::rgl_init(SEXP, SEXP, SEXP)’:
/usr/include/freetype2/config/ftconfig.h:369:26: error: expected primary-expression before ‘__typeof__’
#define TYPEOF( type ) (__typeof__ (type))
^
init.cpp:58:13: note: in expansion of macro ‘TYPEOF’
else if ( TYPEOF(initValue) == EXTPTRSXP ) {
^
/usr/include/freetype2/config/ftconfig.h:369:26: error: expected ‘)’ before ‘__typeof__’
#define TYPEOF( type ) (__typeof__ (type))
^
init.cpp:58:13: note: in expansion of macro ‘TYPEOF’
else if ( TYPEOF(initValue) == EXTPTRSXP ) {
^
init.cpp:61:3: error: expected ‘)’ before ‘else’
else if ( !isNull(initValue) )
^
/usr/lib64/R/etc/Makeconf:143: recipe for target 'init.o' failed
make: *** [init.o] Error 1
ERROR: compilation failed for package ‘rgl’
* removing ‘/home/user/R/x86_64-unknown-linux-gnu-library/3.2/rgl’
Warning in install.packages :
installation of package ‘rgl’ had non-zero exit status
Freetype is optional. Disabling it is the least hassles solution.
install.packages("rgl", repo="http://cran.r-project.org", configure.args="--disable-ftgl")
The issue is with freetype2 2.6. Downgrading to freetype2 2.5 allows rgl to compile properly.
For archlinux you can just run pacman -U /var/cache/pacman/pkg/freetype2-2.5.5-1-x86_64.pkg.tar.xz to downgrade to the older package.
For others who come looking I solved this on ubuntu by installing libfreetype6-dev
Get the binary from the repos:
sudo apt-get build-dep r-cran-rgl
or
Install OpenGL before building rgl from source.
Related
I am running MRO 3.5.0 on Win10, and trying to install a package image.CannyImage from bnosac/image on the github. But it keeps reporting fatal errors as following.
* installing *source* package 'image.CannyEdges' ...
** libs
c:/Rtools/mingw_64/bin/g++ -m64 -I"C:/PROGRA~1/MICROS~1/ROPEN~1/R-35~1.0/include" -DNDEBUG -I"C:/Users/eric1/Documents/R/win-library/3.5/Rcpp/include" -I"C:/swarm/workspace/External-R-3.5.0/vendor/extsoft/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
c:/Rtools/mingw_64/bin/gcc -m64 -I"C:/PROGRA~1/MICROS~1/ROPEN~1/R-35~1.0/include" -DNDEBUG -I"C:/Users/eric1/Documents/R/win-library/3.5/Rcpp/include" -I"C:/swarm/workspace/External-R-3.5.0/vendor/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c adsf.c -o adsf.o
c:/Rtools/mingw_64/bin/g++ -m64 -I"C:/PROGRA~1/MICROS~1/ROPEN~1/R-35~1.0/include" -DNDEBUG -I"C:/Users/eric1/Documents/R/win-library/3.5/Rcpp/include" -I"C:/swarm/workspace/External-R-3.5.0/vendor/extsoft/include" -O2 -Wall -mtune=core2 -c rcpp_canny.cpp -o rcpp_canny.o
In file included from rcpp_canny.cpp:13:0:
canny.h:8:19: fatal error: fftw3.h: No such file or directory
#include <fftw3.h>
^
compilation terminated.
make: *** [C:/PROGRA~1/MICROS~1/ROPEN~1/R-35~1.0/etc/x64/Makeconf:215: rcpp_canny.o] Error 1
ERROR: compilation failed for package 'image.CannyEdges'
* removing 'C:/Users/eric1/Documents/R/win-library/3.5/image.CannyEdges'
In R CMD INSTALL
Installation failed: Command failed (1)
^
compilation terminated.
Google says I can solve the issue by sudo apt-get remove libfftw3-dev. Unfortunately, I am on Windows, and some advised, apply lib /machine:i386 /def:libfftw3-3.def on cmd mode. Ouch, there is no such command or file called lib.exe on Win10.
Please advise, how I can solve this issue on my Win10+MRO system. Thanks.
Even though this question is already a bit old:
By now (Feb 2020) there are precompiled packages available that work also under Windows:
Canny Edges - Package
and more general:
List of all available packages
I have tried installing them and (at least for me) it worked.
I cannot install qpcR package, using this command in R:
install.packages("qpcR")
Apparently, everything looks fine initially:
Installing package into ‘/home/emanuel/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/qpcR_1.4-1.tar.gz'
Content type 'application/x-gzip' length 4303726 bytes (4.1 MB)
==================================================
downloaded 4.1 MB
* installing *source* package ‘qpcR’ ...
** package ‘qpcR’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack- protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c registerDynamicSymbol.c -o registerDynamicSymbol.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c smth.c -o smth.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o qpcR.so registerDynamicSymbol.o smth.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
And then things starts to going wrong:
usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'qpcR.so' failed
make: *** [qpcR.so] Error 1
ERROR: compilation failed for package ‘qpcR’
* removing ‘/home/emanuel/R/x86_64-pc-linux-gnu-library/3.4/qpcR’
Warning in install.packages :
installation of package ‘qpcR’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpOPiQkB/downloaded_packages’
Additional (maybe) relevant info:
Before the lines presented above, I was having trouble with another qpcR dependence, the rgl package, and I solved trying all the suggestions from another question: "Error in installing rgl package".
I made a brief search about: "-llpack", "-lblas", "qpcR.so" .Unfortunately nothing seems (to me at least) to be related to my specific problem.
I using Mint with these specifications: Linux version 4.8.0-53-generic (buildd#lgw01-56) (gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4) ) #56~16.04.1-Ubuntu
R version 3.4.4
R studio Version 1.1.453
Thanks in advance for any help!
satisfy the dependencies using this command in terminal.
sudo apt-get install libblas-dev liblapack-dev
hope this helps (Y)
I'm trying to install the following package in RStudio on Linux. I'm getting the follow error code. I don't really understand it. I was wondering if anyone could help me make sense of it.
Thanks,
Nick
> install.packages("PKI")
Installing package into ‘/home/nick/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/PKI_0.1-3.tar.gz'
Content type 'application/x-gzip' length 31058 bytes (30 KB)
==================================================
downloaded 30 KB
* installing *source* package ‘PKI’ ...
** package ‘PKI’ successfully unpacked and MD5 sums checked
** libs
gcc -I/usr/include/R/ -DNDEBUG -D_FORTIFY_SOURCE=2 -fpic -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -c asn1.c -o asn1.o
gcc -I/usr/include/R/ -DNDEBUG -D_FORTIFY_SOURCE=2 -fpic -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -c init.c -o init.o
gcc -I/usr/include/R/ -DNDEBUG -D_FORTIFY_SOURCE=2 -fpic -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -c pki-x509.c -o pki-x509.o
pki-x509.c: In function ‘PKI_extract_key’:
pki-x509.c:136:26: error: dereferencing pointer to incomplete type ‘EVP_PKEY {aka struct evp_pkey_st}’
if (EVP_PKEY_type(key->type) != EVP_PKEY_RSA)
^~
pki-x509.c: In function ‘get_cipher’:
pki-x509.c:244:40: error: dereferencing pointer to incomplete type ‘EVP_CIPHER_CTX {aka struct evp_cipher_ctx_st}’
ctx = (EVP_CIPHER_CTX*) malloc(sizeof(*ctx));
^~~~
pki-x509.c: In function ‘PKI_RSAkeygen’:
pki-x509.c:550:5: warning: ‘RSA_generate_key’ is deprecated [-Wdeprecated-declarations]
rsa = RSA_generate_key(bits, 65537, 0, 0);
^~~
In file included from /usr/include/openssl/rsa.h:13:0,
from pki.h:13,
from pki-x509.c:1:
/usr/include/openssl/rsa.h:193:1: note: declared here
DEPRECATEDIN_0_9_8(RSA *RSA_generate_key(int bits, unsigned long e, void
^
make: *** [/usr/lib64/R/etc/Makeconf:159: pki-x509.o] Error 1
ERROR: compilation failed for package ‘PKI’
* removing ‘/home/nick/R/x86_64-pc-linux-gnu-library/3.4/PKI’
Warning in install.packages :
installation of package ‘PKI’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpttDG6C/downloaded_packages’
I think I had the same problem recently.
I installed the package by downloading the most recent tarball (the .tar.gz file PKI_0.1-5.tar.gz) from the PKI RForge page and then running
install.packages(<tarball_path>, repos = NULL, type = "source").
EDIT: Actually, it's easier to run install.packages('PKI',,'http://www.rforge.net/') as written in small print at the bottom of the PKI RForge page
EDIT2: Looking at the news, it looks like version 0.1-4 (perhaps more stable) also fixes the problem and, well enough, it works on my system, while 0.1-3 doesn't (the one on CRAN currently).
I am trying to build a mapnik 2.2.0 RPM file on my RHEL/CENTOS 7 machine.
so I took the RPM SRC file from Fedora 22 which is mapnik-2.2.0-11.fc21.src.rpm ( I have the same result with mapnik-2.2.0-5.fc20.src.rpm )
when I am running the rpmbuild I receive the following error message:
Welcome to Mapnik...
scons: warning: Ignoring missing SConscript 'deps/agg/build.py'
File "/root/rpmbuild/BUILD/mapnik-v2.2.0/SConstruct", line 1799, in <module>
scons: warning: Ignoring missing SConscript 'deps/mapnik/build.py'
File "/root/rpmbuild/BUILD/mapnik-v2.2.0/SConstruct", line 1808, in <module>
scons: done reading SConscript files.
scons: Building targets ...
g++ -o bindings/python/mapnik_building_symbolizer.os -c -ansi -Wall -pthread -ftemplate-depth-300 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -fno-strict-aliasing -finline-functions -Wno-inline -Wno-parentheses -Wno-char-subscripts -fPIC -DHAVE_JPEG -DMAPNIK_USE_PROJ4 -DHAVE_PNG -DHAVE_TIFF -DBIGINT -DBOOST_REGEX_HAS_ICU -DLINUX -DMAPNIK_THREADSAFE -DNDEBUG -DHAVE_CAIRO -DHAVE_PYCAIRO -I. -Iinclude -I/usr/include/polyclipping -I/usr/include/agg2 -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/gdal -I/usr/include/python2.7 -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/libpng15 -I/usr/include/libdrm -I/usr/include/pycairo bindings/python/mapnik_building_symbolizer.cpp
In file included from include/mapnik/symbolizer.hpp:29:0,
from include/mapnik/building_symbolizer.hpp:29,
from bindings/python/mapnik_building_symbolizer.cpp:26:
include/mapnik/image_compositing.hpp:74:19: error: 'comp_op_grain_merge' is not a member of 'agg'
grain_merge = agg::comp_op_grain_merge,
^
include/mapnik/image_compositing.hpp:75:21: error: 'comp_op_grain_extract' is not a member of 'agg'
grain_extract = agg::comp_op_grain_extract,
^
scons: *** [bindings/python/mapnik_building_symbolizer.os] Error 1
scons: building terminated because of errors.
error: Bad exit status from /var/tmp/rpm-tmp.kuI6KW (%build)
RPM build errors:
Bad exit status from /var/tmp/rpm-tmp.kuI6KW (%build)
Mapnik normally comes with a heavily patched version of the AGG library right there in its source tree. The Fedora build however disables that in favour of having the Mapnik-AGG patches directly in its own AGG package (because they don't like duplicating system libraries elsewhere).
You either need an AGG library for CentOS that is feature-compatible with the patched Fedora version, or you have to modify your Mapnik build to disable the "system_agg" patch (and drop the "rm -rf boost deps" from the spec file).
I was trying to install the package videoplayR from github but failed to do the same. I tried two ways:
1. Using the installation guidance mentioned in README file.It gave the following error:
> install_github("sjmgarnier/videoplayR")
Downloading github repo sjmgarnier/videoplayR#master
Error in function (type, msg, asError = TRUE) :
2. Using R CMD SHLIB etc gives the following error while running R CMD check. It is a part of the install.out file:
* installing source package ‘videoplayR’ ...
** libs
g++ -I/usr/share/R/include -DNDEBUG -I"/home/nandy/R/x86_64-pc-linux-gnu-library/3.1/Rcpp/include" -I"/home/nandy/R/x86_64-pc-linux-gnu-library/3.1/RcppArmadillo/include" pkg-config --cflags opencv Rscript -e <p>'Rcpp:::CxxFlags()' -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG -I"/home/nandy/R/x86_64-pc-linux-gnu-library/3.1/Rcpp/include" -I"/home/nandy/R/x86_64-pc-linux-gnu-library/3.1/RcppArmadillo/include" pkg-config --cflags opencv Rscript -e <p>'Rcpp:::CxxFlags()' -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Video.cpp -o Video.o
Video.cpp: In member function ‘double Video::current_frame()’:
Video.cpp:42:25: error: ‘CV_CAP_PROP_POS_FRAMES’ was not declared in this scope
return(inputVideo.get(CV_CAP_PROP_POS_FRAMES));
^
Video.cpp: In member function ‘void Video::set_current_frame(int)’:
Video.cpp:46:18: error: ‘CV_CAP_PROP_POS_FRAMES’ was not declared in this scope
inputVideo.set(CV_CAP_PROP_POS_FRAMES, n);
^
Video.cpp: In member function ‘void Video::next_frame_cv()’:
Video.cpp:63:22: error: ‘CV_CAP_PROP_POS_FRAMES’ was not declared in this scope
if (inputVideo.get(CV_CAP_PROP_POS_FRAMES) == inputVideo.get(CV_CAP_PROP_FRAME_COUNT)) {
^
Video.cpp:63:64: error: ‘CV_CAP_PROP_FRAME_COUNT’ was not declared in this scope
if (inputVideo.get(CV_CAP_PROP_POS_FRAMES) == inputVideo.get(CV_CAP_PROP_FRAME_COUNT)) {
^
Video.cpp: In member function ‘void Video::get_frame_cv(int)’:
Video.cpp:76:27: error: ‘CV_CAP_PROP_FRAME_COUNT’ was not declared in this scope
if (n > inputVideo.get(CV_CAP_PROP_FRAME_COUNT)) {
^
Video.cpp:80:18: error: ‘CV_CAP_PROP_POS_FRAMES’ was not declared in this scope
inputVideo.set(CV_CAP_PROP_POS_FRAMES, n);
^
Video.cpp: In member function ‘int Video::length()’:
Video.cpp:91:25: error: ‘CV_CAP_PROP_FRAME_COUNT’ was not declared in this scope
return(inputVideo.get(CV_CAP_PROP_FRAME_COUNT));
^
I am guessing problem 2 is occurring due to version problem of OpenCV. Am I right? Is there any way out of this?
Looks similar to these 2 reported problems: https://github.com/hadley/devtools/issues/650 and https://github.com/hadley/devtools/issues/467. It seems that you need to update your system (Linux I presume) to the latest version of Curl.
I believe this is my fault. I forgot to exclude the compiled shared object videoplayR.so last time I committed changes to the GitHub repo. If you're using a different OS than mine (OSX Yosemite), it is most certainly the cause of the problem that you encountered. I fixed it and now it should compile nicely on your computer as well.
FYI I compiled and ran the package with both OpenCV 2.4.9 and 2.4.10, but it should work with any 2.4.X version of OpenCV (never tried the latest OpenCV 3.0 beta).