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've been attempting to install R-3.1.3 from source on
# cat /etc/*release*
NAME="Amazon Linux AMI"
VERSION="2015.09"
ID="amzn"
ID_LIKE="rhel fedora"
VERSION_ID="2015.09"
PRETTY_NAME="Amazon Linux AMI 2015.09"
ANSI_COLOR="0;33"
CPE_NAME="cpe:/o:amazon:linux:2015.09:ga"
HOME_URL="http://aws.amazon.com/amazon-linux-ami/"
Amazon Linux AMI release 2015.09
cpe:/o:amazon:linux:2015.09:ga
And after ./configure && make installation fails with the following error
gcc -std=gnu99 -shared -fopenmp -L/usr/local/lib64 -o libRlapack.so
dlamch.o dlapack.o cmplx.o -L../../../lib -lRblas -lgfortran -lm -lquadmath
/usr/bin/ld: /usr/lib/gcc/x86_64-amazon-linux/4.8.3/libgfortran.a(string_intrinsics.o): relocation R_X86_64_32S against `.bss.zero_length_string' can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-amazon-linux/4.8.3/libgfortran.a: could not read symbols: Bad value
collect2: error: ld returned 1 exit status
make[4]: *** [libRlapack.so] Error 1
Naturally I learn about -fPIC on how to recompile with -fPIC and R_X86_64_32S on What do R_X86_64_32S and R_X86_64_64 relocation mean?
I then make the change in the CFLAGS
# ./configure 'CFLAGS=-g -O2 -fPIC' --with-x=no --enable-shared
I know it worked because configure prints the values it set,
C compiler: gcc -std=gnu99 -g -O2 -fPIC
Fortran 77 compiler: gfortran -g -O2
Nevertheless same error occurs.
I've tested this on Centos65, and Centos71 and Ubuntu1404 all work, but my VPC won't, please help
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'm trying to install the deldir package in R via install.packages("deldir",type = 'source') but am getting the following error message (this is OSX Mavericks):
* installing *source* package ‘deldir’ ...
** package ‘deldir’ successfully unpacked and MD5 sums checked
** libs
gfortran-4.8 -fPIC -g -O2 -c acchk.f -o acchk.o
make: gfortran-4.8: No such file or directory
make: *** [acchk.o] Error 1
ERROR: compilation failed for package ‘deldir’
gfortran 4.8 does seem to be available on my system, however:
> gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin13/4.8.2/lto-wrapper
Target: x86_64-apple-darwin13
Configured with: ../gcc-4.8.2/configure --prefix=/usr/local/gfortran --with-gmp=/Users/fx/devel/gcc/deps-static/x86_64 --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin13
Thread model: posix
gcc version 4.8.2 (GCC)
After symlinking gfortran-4.8 to gfortran I get a bit further but fail nonetheless:
* installing *source* package ‘deldir’ ...
** package ‘deldir’ successfully unpacked and MD5 sums checked
** libs
gfortran-4.8 -fPIC -g -O2 -c acchk.f -o acchk.o
gfortran-4.8 -fPIC -g -O2 -c addpt.f -o addpt.o
gfortran-4.8 -fPIC -g -O2 -c adjchk.f -o adjchk.o
gfortran-4.8 -fPIC -g -O2 -c binsrt.f -o binsrt.o
gfortran-4.8 -fPIC -g -O2 -c circen.f -o circen.o
gfortran-4.8 -fPIC -g -O2 -c cross.f -o cross.o
gfortran-4.8 -fPIC -g -O2 -c delet.f -o delet.o
gfortran-4.8 -fPIC -g -O2 -c delet1.f -o delet1.o
gfortran-4.8 -fPIC -g -O2 -c delout.f -o delout.o
gfortran-4.8 -fPIC -g -O2 -c delseg.f -o delseg.o
gfortran-4.8 -fPIC -g -O2 -c dirout.f -o dirout.o
gfortran-4.8 -fPIC -g -O2 -c dirseg.f -o dirseg.o
gfortran-4.8 -fPIC -g -O2 -c dldins.f -o dldins.o
gfortran-4.8 -fPIC -g -O2 -c initad.f -o initad.o
gfortran-4.8 -fPIC -g -O2 -c insrt.f -o insrt.o
gfortran-4.8 -fPIC -g -O2 -c insrt1.f -o insrt1.o
gfortran-4.8 -fPIC -g -O2 -c intri.f -o intri.o
gfortran-4.8 -fPIC -g -O2 -c locn.f -o locn.o
gfortran-4.8 -fPIC -g -O2 -c master.f -o master.o
gfortran-4.8 -fPIC -g -O2 -c mnnd.f -o mnnd.o
gfortran-4.8 -fPIC -g -O2 -c pred.f -o pred.o
gfortran-4.8 -fPIC -g -O2 -c qtest.f -o qtest.o
gfortran-4.8 -fPIC -g -O2 -c qtest1.f -o qtest1.o
gfortran-4.8 -fPIC -g -O2 -c stoke.f -o stoke.o
gfortran-4.8 -fPIC -g -O2 -c succ.f -o succ.o
gfortran-4.8 -fPIC -g -O2 -c swap.f -o swap.o
gfortran-4.8 -fPIC -g -O2 -c testeq.f -o testeq.o
gfortran-4.8 -fPIC -g -O2 -c triar.f -o triar.o
gfortran-4.8 -fPIC -g -O2 -c trifnd.f -o trifnd.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o deldir.so acchk.o addpt.o adjchk.o binsrt.o circen.o cross.o delet.o delet1.o delout .o delseg.o dirout.o dirseg.o dldins.o initad.o insrt.o insrt1.o intri.o locn.o master.o mnnd.o pred.o qtest.o qtest1.o stoke.o succ.o swap.o testeq.o triar.o trifnd.o -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 - lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [deldir.so] Error 1
ERROR: compilation failed for package ‘deldir’
Note that /usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.3 exists, /usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 does not
sessionInfo():
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
Sys.getenv():
> Sys.getenv()
__CF_USER_TEXT_ENCODING
"0x1F5:0:0"
__CHECKFIX1436934
"1"
Apple_PubSub_Socket_Render
"/tmp/launch-jCxLku/Render"
DISPLAY
":0"
DYLD_FALLBACK_LIBRARY_PATH
"/Users/<myusername>/lib:/usr/local/lib:/usr/lib::/Library/Frameworks/R.framework/Resources/lib"
EDITOR
"vi"
GIT_ASKPASS
"rpostback-askpass"
HOME
"/Users/<myusername>"
LANG
"en_US.UTF-8"
LC_CTYPE
"en_US.UTF-8"
LN_S
"ln -s"
LOGNAME
"<myusername>"
MAKE
"make"
PAGER
"/usr/bin/less"
PATH
"/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin"
R_BROWSER
"/usr/bin/open"
R_BZIPCMD
"/usr/bin/bzip2"
R_DOC_DIR
"/Library/Frameworks/R.framework/Resources/doc"
R_GZIPCMD
"/usr/bin/gzip"
R_HOME
"/Library/Frameworks/R.framework/Resources"
R_INCLUDE_DIR
"/Library/Frameworks/R.framework/Resources/include"
R_LIBS_SITE
""
R_LIBS_USER
"~/Library/R/3.1/library"
R_PAPERSIZE
"a4"
R_PDFVIEWER
"/usr/bin/open"
R_PLATFORM
"x86_64-apple-darwin13.1.0"
R_PRINTCMD
"lpr"
R_QPDF
"/Library/Frameworks/R.framework/Resources/bin/qpdf"
R_RD4PDF
"times,inconsolata,hyper"
R_SESSION_TMPDIR
"/var/folders/jf/ds4sdyys44xckz_7f9zhrvsh0000gn/T//RtmpXaPpYF"
R_SHARE_DIR
"/Library/Frameworks/R.framework/Resources/share"
R_SYSTEM_ABI
"osx,gcc,gxx,gfortran,?"
R_TEXI2DVICMD
"/usr/bin/texi2dvi"
R_UNZIPCMD
"/usr/bin/unzip"
R_ZIPCMD
"/usr/bin/zip"
RS_RPOSTBACK_PATH
"/Applications/RStudio.app/Contents/MacOS/rpostback"
RS_SHARED_SECRET
<removed>
RSTUDIO
"1"
RSTUDIO_PANDOC
"/Applications/RStudio.app/Contents/MacOS/pandoc"
RSTUDIO_SESSION_PORT
"10153"
RSTUDIO_USER_IDENTITY
"<myusername>"
SED
"/usr/bin/sed"
SHELL
"/bin/bash"
SSH_AUTH_SOCK
"/tmp/launch-Shnu2H/Listeners"
TAR
"/usr/bin/tar"
TMPDIR
"/var/folders/jf/ds4sdyys44xckz_7f9zhrvsh0000gn/T/"
USER
"<myusername>"
I was getting the same error when installing the igraph package in R on Manjaro Linux.
It was due to the absence of a Fortran compiler (gfortran I think). I found out that gfortran package is named as gcc-fortran in Manjaro repo and many other (GNU) Linux repos. So, I just installed gcc-fortran package and then restarted RStudio and igraph package installed without any issues.
I found a solution here: https://support.rstudio.com/hc/communities/public/questions/201688563-Problem-with-Mac-Yosemite-Beta-and-RStudio-not-finding-TeX-distribution
It turns out that Adam Maxwell noted that Yosemite beta has a significant bug in passing environment variables to subprocesses.
After installing gfortran as in OS X package installation depends on gfortran-4.8 .
This works: create an alias in your .bash_profile
alias fixrs="launchctl setenv PATH /usr/texbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin"
Then close and open the terminal.
And execute the fixrs command in the terminal before launching RStudio.
Then I could build igraph successfully.
I was using a linux machine and RStudio server. I had a similar problem. I knew already that gfortran was on the machine thanks to the system administrator.
To solve, in the shell, I typed which gfortran, which gave me a path.
Then, following this SO posting, I entered the following in the shell to create a new Makevars file
# create a file called ~/.R/Makevars:
mkdir -p ~/.R
touch ~/.R/Makevars
Then, in that new file, I wrote the following
F77 = /usr/local/bin/gfortran #this was the path that I got from typing which gfortran in the shell
FC = $F77
FLIBS = -L/usr/local/bin/gfortran
From there, I was able to install the package that wasn't compiling properly (in my case vegan instead of igraph using install.packages("vegan")
I had your same problem (in OS X Yosemite), and (unfortunately) painstakingly recreated your symlink "partial solution". Finally, I was able to solve the issue by forgetting about linking or aliasing and just downgrading to gfortran-4.8.
I had installed the newer version with brew, so for me this entailed uninstalling
brew uninstall gcc
and then following the instructions here to install 4.8.2, i.e.
curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /
It still threw up some warnings but at least I got a successful installation of deldir, which I needed to run pgirmess.
I tried the instructions of building latest QT5-Alpha(http://qt-project.org/wiki/Qt-5-Alpha
http://qt-project.org/wiki/Building_Qt_5_from_Git)
from GIT,but facing compilation in wayland files
Ubuntu Linux 11.10
__make[4]: Entering directory `/home/xyz/build/newqt5/qt5/qtwayland/src/plugins/platforms/wayland'
g++ -c -pipe -g -fvisibility=hidden -fvisibility-inlines-hidden -D_REENTRANT -Wall -W -fPIC -DQT_NO_LIBUDEV -DQ_PLATFORM_WAYLAND -DQT_NO_WAYLAND_XKB -DQT_WAYLAND_GL_SUPPORT -DQT_WAYLAND_WINDOWMANAGER_SUPPORT -DQ_FONTCONFIGDATABASE -DQT_COMPILES_IN_HARFBUZZ -DQT_PLUGIN -DQT_GUI_LIB -DQT_CORE_LIB -I/home/xyz/build/newqt5/qt5/qtbase/mkspecs/linux-g++ -I. -I/home/xyz/build/newqt5/qt5/qtbase/include/QtCore/5.0.0 -I/home/xyz/build/newqt5/qt5/qtbase/include/QtCore/5.0.0/QtCore -I/home/xyz/build/newqt5/qt5/qtbase/include/QtCore -I/home/xyz/build/newqt5/qt5/qtbase/include/QtGui/5.0.0 -I/home/xyz/build/newqt5/qt5/qtbase/include/QtGui/5.0.0/QtGui -I/home/xyz/build/newqt5/qt5/qtbase/include/QtGui -I/home/xyz/build/newqt5/qt5/qtbase/include/QtPlatformSupport/5.0.0 -I/home/xyz/build/newqt5/qt5/qtbase/include/QtPlatformSupport/5.0.0/QtPlatformSupport -I/home/xyz/build/newqt5/qt5/qtbase/include/QtPlatformSupport -I/home/xyz/build/newqt5/qt5/qtbase/include -I../../../shared -Igl_integration/xcomposite_share -I.moc/debug-shared -o .obj/debug-shared/qwaylandintegration.o qwaylandintegration.cpp
In file included from qwaylandshmwindow.h:45:0,
from qwaylandintegration.cpp:46:
qwaylandwindow.h:112:18: error: ‘wl_callback_listener’ does not name a type
make[4]: *** [.obj/debug-shared/qwaylandintegration.o] Error 1_
Any pointers to overcome this?
Download the alpha source package here: http://releases.qt-project.org/qt5.0/alpha/ and use the steps in README file.
The master in git is NOT what was released as alpha. The build scripts are different. You have to wait for them to add alpha tag to pull it from git. But why not just grab the gz file?