I'm trying to install biocneighbors from bioconductor. Unfortunately I recieve the following error:
* installing *source* package ‘BiocNeighbors’ ...
** libs
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG -I"/home/m3hdad/R/Rcpp/include" -
ric -O2 -pipe -fstack-protector-strong -fno-plt -c annoy_stubs.cpp -o annoy_stub
In file included from annoy_stubs.cpp:2:
annoy.h:13:10: fatal error: annoylib.h: No such file or directory
#include "annoylib.h"
^~~~~~~~~~~~
compilation terminated.
I do not understand if I have to provide the file for the algorithm "annoy" or it should be included in the source code.
I am using Arch linux.
That would be RcppAnnoy for which I am maintainer.
And BiocNeighbors has a LinkingTo: on it as it should.
So something is wrong/weird at your end as every LinkingTo: turns to a -I... as we see e.g. in your quote on the other LinkingTo: it has -- for Rcpp.
Related
I am trying to install RcppMP in MacOS.
However, when I type:
remotes::install_github("Thell/RcppMP",dependencies = T)
I get the following error:
* installing *source* package ‘RcppMP’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/RcppMP.h:7:
In file included from ../inst/include/RcppMP_RcppExports.h:7:
../inst/include/RcppMP_types.hpp:15:10: fatal error: 'mpreal.h' file not found
#include <mpreal.h>
^~~~~~~~~~
1 error generated.
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘RcppMP’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppMP’
Warning message:
In i.p(...) :
installation of package ‘/var/folders/pq/hxwd9my563q_qpy4rbrlgkmw0000gn/T//RtmpIdnyiB/file2184610d74ea/RcppMP_0.1.1.tar.gz’ had non-zero exit status
My ~/.R/Makevars file contain the following specifications:
CC=/usr/local/opt/llvm/bin/clang
CXX=/usr/local/opt/llvm/bin/clang++
CXX1X=/usr/local/opt/llvm/bin/clang++
LDFLAGS=-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib
CXXFLAGS=-I/usr/local/opt/llvm/include
FLIBS=-L/usr/local/Cellar/gcc/11.3.0_1/lib/gcc/11
This was a bit more complicated than I thought; this package requires mpfr, gmp and the very-similarly-named mpfrc++. The steps that worked for me are:
Install gmp and mpfr via homebrew
Download and unzip "mpfrc++-3.6.8.zip" from
http://www.holoborodko.com/pavel/mpfr/#download
Copy the mpreal header file ("mpreal.h") to
/usr/local/include (sudo cp ./mpreal.h /usr/local/include/) or, in your case, perhaps sudo cp ./mpreal.h /usr/local/opt/llvm/include would make more sense
Install/compile RcppMP
(remotes::install_github("Thell/RcppMP",dependencies = TRUE))
I got some warnings but no errors, and the package loaded (library(RcppMP)), so I'm relatively confident it installed successfully. If you find otherwise, please let me know and I'll look into it further.
I am trying to submit a package to CRAN that fails during the pretest
process on Debian.
I use some C++ code that interfaces to the nlopt optimization
library with Rcpp/RcppArmadillo (using <nlopt.hpp>). Thus, my package requires a system version of nlopt that can be installed via the deb package libnlopt-dev (I added this to the SystemRequirements field).
I use a configure script and pkg-config to retrieve the (hopefully)
appropriate compiler flags which I then send to src/Makevars
NLOPT_LIBS=`pkg-config --libs ${PKG_CONFIG_NAME}`
NLOPT_FLAG=`pkg-config --cflags ${PKG_CONFIG_NAME}`
This approach works on my system (Ubuntu 18.04, R 3.5.2) and on Travis
(linux and mac OS), but fails on the Debian CRAN server :
https://win-builder.r-project.org/incoming_pretest/PLNmodels_0.7_20190119_161032/Debian/00install.out
I added some verbosity to check that the flags were correctly exported
on CRAN servers, and they seems alright to me: at least, a version of
nlopt is found on the system (see below, NLOPT_LIBS=-lnlopt -lm).
However, the <nlopt.hpp> is not found latter on...
Any help would be greatly appreciated. Thank for taking the time to read this.
* installing *source* package ‘PLNmodels’ ...
Using NLOPT_LIBS=-lnlopt -lm
Using NLOPT_FLAG=
** libs
g++-8 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -fopenmp
-I"/home/hornik/lib/R/Library/3.6/x86_64-linux-gnu/Rcpp/include"
-I"/home/hornik/lib/R/Library/3.6/x86_64-linux-gnu/RcppArmadillo/include"
-I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic
-mtune=native -c RcppExports.cpp -o RcppExports.o
g++-8 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -fopenmp
-I"/home/hornik/lib/R/Library/3.6/x86_64-linux-gnu/Rcpp/include"
-I"/home/hornik/lib/R/Library/3.6/x86_64-linux-gnu/RcppArmadillo/include"
-I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic
-mtune=native -c call_nlopt_PLN_VE.cpp -o call_nlopt_PLN_VE.o
In file included from call_nlopt_PLN_VE.cpp:6:
utils.h:5:10: fatal error: nlopt.hpp: No such file or directory
#include <nlopt.hpp>
^~~~~~~~~~~
compilation terminated.
make: *** [/home/hornik/tmp/R/etc/Makeconf:173: call_nlopt_PLN_VE.o] Error 1
ERROR: compilation failed for package ‘PLNmodels’
* removing ‘/srv/hornik/tmp/CRAN/PLNmodels.Rcheck/PLNmodels’
The C++ interface for nlopt has migrated to a separate package in Debian, c.f. https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=855600. So it looks like that particular CRAN machine uses either Debian Testing or Stable + Backports and has only libnlopt-dev but not libnlopt-cxx-dev installed. You will have to contact the CRAN maintainers to install this dependency.
BTW, ideally such errors should be cought in the configure script, i.e. you should try to compile a simple program that requires nlopt.hpp.
You asked the same question here on r-package-devel and I had no good answer for you.
In essence, you have fine variation within one required upstream package. That is very delicate. I cannot think of anything but what #Ralf suggested: test for it.
Or maybe you just fail in communicating the requirements of your package to CRAN. But that would be an even simpler question, and when the wrong version is encountered, you are bound to fail installation.
So overall, my recommendation is the same as previously: work with Jelmer, and wait for him to release an updated nloptr release. Until then, all solutions are bound to be fudges as you cannot control what version of nloptr your package may encounter.
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 am writing an R package that has Fortran source code. In short, my problem is when I try to install the package I get the error "gfortran -m32: not found" however, I am able compile my code using gfortran -m32 when I'm not installing the package.
Detailed Version:
I have installed the newest version of R(3.1.1) along with the newest version of Rtools(31) and renamed my path variables accordingly (C:\Rtools\bin;C:\Rtools\gcc-4.6.3\bin;C:\Program Files\R\R-3.1.1\bin\x64;C:\msys;C:\Program Files (x86)\SSH Secure Shell;C:\Program Files\MiKTeX 2.9\miktex\bin).
For testing purposes, I downloaded the PropClust package from CRAN which has Fortran source code.
When I type "R CMD INSTALL PropClust_1.4.tar.gz" after building it, I get the following error:
* installing *source* package 'PropClust' ...
** libs
*** arch - i386
C:/PROGRA~1/R/R-31~1.1/etc/i386/Makeconf:202: warning: overriding recipe for target `.m.o'
C:/PROGRA~1/R/R-31~1.1/etc/i386/Makeconf:195: warning: ignoring old recipe for target `.m.o'
gfortran -m32 -O3 -mtune=core2 -c PropClustParallelTrials.f90 -o PropClustParallelTrials.o
gcc -m32 -I"C:/PROGRA~1/R/R-31~1.1/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c minWhichMin.c -o minWhichMin.o
gfortran -m32 -shared -s -static-libgcc -o PropClust.dll tmp.def PropClustParallelTrials.o minWhichMin.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-31~1.1/bin/i386 -lR
gfortran -m32: not found
C:/PROGRA~1/R/R-31~1.1/etc/i386/Makeconf:202: warning: overriding recipe for target `.m.o'
C:/PROGRA~1/R/R-31~1.1/etc/i386/Makeconf:195: warning: ignoring old recipe for target `.m.o'
cygwin warning:
MS-DOS style path detected: C:/PROGRA~1/R/R-31~1.1/bin/i386/Rterm.exe
Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-31~1.1/bin/i386/Rterm.exe
CYGWIN environment variable option "nodosfilewarning" turns off this warning.
Consult the user's guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
no DLL was created
ERROR: compilation failed for package 'PropClust'
* removing 'C:/Users/kamicz/Documents/IsotopeR/PropClust.Rcheck/PropClust'
Although it says "gfortran -m32: not found" I have compiled my code in the same window with the same options(gfortran -m32 -O3 -mtne=core2 -c a.f90 -o a.out) with no problems. Has anyone had this problem before? I am running Windows 7 64-bit if that matters.
I had a similar problem : R was invoking gfortran-4.8 - an unrecognized command on my system - instead of gfortran. This problem was fixed upon creating the file ~/.R/Makevars within my home directory. Here are the contents of Makevars which points to the appropriate gfortran installation:
F77 = gfortran
FC = gfortran
FLIBS = -L/usr/local/gfortran/lib
I am trying to install the package called topicmodels in R and I have not had success. Here's what I have tried...
Action:
Install the package using install.packages("topicmodels")
Result:
package ‘topicmodels’ is available as a source package but not as a binary
Warning in install.packages :
package ‘topicmodels’ is not available (for R version 3.1.0)
So there I said okay let's install from source
Action:
install.packages("/Users/my_name/Downloads/topicmodels_0.2-1.tar.gz",repos=NULL,type="source")
Result:
* installing *source* package ‘topicmodels’ ...
** package ‘topicmodels’ successfully unpacked and MD5 sums checked
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c cokus.c -o cokus.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c common.c -o common.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c ctm.c -o ctm.o
ctm.c:29:10: fatal error: 'gsl/gsl_rng.h' file not found
include gsl/gsl_rng.h
1 error generated.
make: *** [ctm.o] Error 1
ERROR: compilation failed for package ‘topicmodels’
* removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/topicmodels’
Warning in install.packages :
installation of package ‘/Users/me/Downloads/topicmodels_0.2-1.tar.gz’ had non-zero exit status
So then I researched this gsl thing and came upon this link. And for the moment I thought all of my problems were gone and when I finally follow these directions. I get the following error (in the terminal)...
Warning in untar2(tarfile, files, list, exdir, restore_times) :
using pax extended headers
ERROR: cannot extract package from ‘topicmodels.tar.gz’
First of all you have to install gsl. Once you have that installed you can try to install the R package. You can download gsl from here (there you can pick the latest version gsl-latest.tar.gz). Once it's been downloaded, install it by doing the following:
Decompress the downloaded file (in my case the "latest" file contained this version: gsl-1.16)
Open the "Terminal"
Then (using the Terminal), move inside the folder that you created on step 1. In my case I had the file on the folder called "Downloads", so I moved to the newly created folder by doing:
cd Downloads/gsl-1.16
Once you are within that folder run the following commands (in order):
./configure
make
sudo make install
After doing it you won't get the previous error saying fatal error: 'gsl/gsl_rng.h' file not found, so you can try again the installation.
Now go back to your R environment (e.g., RStudio) to try again to install the package by doing:
install.packages("PATH_TO_TOPIC_MODELS.tar.gz", repos=NULL, type="source").
I had the same problem, and after doing this I got the R package correctly installed, I hope it also works in your case.
If you already using homebrew. It is better and faster to fix with variables than installing gsl manually from source.
Install gsl with homebrew brew install gsl
Edit ~/.R/Makevars and add.
PKG_LIBS=-L/usr/local/opt/gettext/lib
CFLAGS=-I/usr/local/opt/gsl/include
LDFLAGS=-L/usr/local/opt/gsl/lib -lgsl -lgslcblas
If you are using Linux based on Debian, that's my solution:
Using terminal run sudo apt install gsl-bin libgsl-dbg libgsl-dev libgsl25 libgslcblas0;
Then, using R console, run install.packages("topicmodels",dependencies =T);
Enjoy!!