I am on Apple M1. I tried to install a special package (Vienna RNA Package, precompiled binary package, https://www.tbi.univie.ac.at/RNA/#pack_macosx).
Installation is finished, but when I type the following
$ RNAduplex
I get the following:
dyld: Library not loaded: /usr/local/opt/mpfr/lib/libmpfr.4.dylib
Referenced from: /usr/local/bin/RNAfold
Reason: image not found
Abort trap: 6
Mpfr is installed via homebrew, but only the most recent version (4.1.0). I guess I need to install the previous version (3.1.6), but I don't get it work.
I tried to install it from https://www.mpfr.org/mpfr-3.1.6/ downloaded from https://www.mpfr.org/mpfr-3.1.6/.
When I do
./configure
I get
configure: error: gmp.h can't be found, or is unusable.
even though gmp is already installed via homebrew (present at /opt/homebrew/Cellar/gmp/).
Any advice on this?
Looking forward to any comments!
Best,
Stefanie
The config.log file may give more information about the error, but I suppose that gmp.h isn't in the include search path. You can try something similar, by compiling:
#include <gmp.h>
int main (void) { return 0; }
You will probably get an error as well.
So you may need to add the directory where gmp.h has been installed to the CPATH or C_INCLUDE_PATH environment variable. You will need to do something similar for the library. Another solution is to use the --with-gmp=... configure option with the GMP installation directory. See the INSTALL file for more information.
Related
I have a general question about how to effectively load any kind of external package into R. I have found that many sources detailing this information are simply insufficient, but I will leave out mentioning those respective URLs. I have successfully loaded external packages into R before, but I am having difficulties loading the fgui package.
In my specific case, I cannot load the library fgui into R Studio. First I download directly from CRAN with the command:
install.packages("fgui", lib="~/Documents/R_dir")
This works fine for me. My working directory is set to ~/Documents/R_dir
The next command I use is:
library("fgui", lib.loc="~/Documents/R_dir")
The error I get is:
Error : .onLoad failed in loadNamespace() for 'tcltk', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/tcltk/libs/tcltk.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/library/tcltk/libs/tcltk.so, 10): Library not loaded: /opt/X11/lib/libX11.6.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/tcltk/libs/tcltk.so
Reason: image not found
Error: package or namespace load failed for ‘fgui’
I have examined the thread "Error when trying to load library(ggplot2) in R" but it did not answer my question.
Please help me with any suggestions to get the package fgui to work properly in R Studio and feel free to address the more general issue of effectively loading external packages into R.
tcltk is not a typical package. It's probably already installed on your system and it cannot be installed using the usual install.packages procedure because it is not on CRAN (just like the base packages that come with R, like stats, etc.). Also, tcltk2 is not the same as tcltk; that is a package that expands upon (and depends on) the functionality of tcltk.
So, start with this:
> capabilities("tcltk")
tcltk
TRUE
If that comes back FALSE it means that your R was not built with tcltk support. You don't say what OS you're using, so it's a little bit difficult to help you.
That said, if you're on Linux, you need to rebuild R with tcltk support. This should be relatively straightforward. Basically, make sure Tcl and tk are available on your system in a standard location (something like sudo apt-get install tcl8.5-dev tk8.5-dev) and then rebuild R per usual procedures.
If you're on Mac OS, you're encountering the same error that John Fox describes here in relation to Rcmdr. In short, it's probably one of two things:
A file permission issue related to the directory where you have Tcl installed. To quote Fox: "You can verify the source of this problem by issuing the following command at the R command prompt:
system("ls -ld /usr/local /usr/local/lib /usr/local/lib/libtcl*")
# ls: /usr/local/lib: Permission denied
# ls: /usr/local/lib/libtcl*: Permission denied
# drwx------ 8 root wheel 272 Sep 24 10:21 /usr/local
If the output of the system command looks like the above, you should go to Terminal and do the following: sudo chmod -R a+rX /usr/local and enter your password to change directory permissions.
You have an out-dated version of X-Windows. Try running Mac OS Software Update.
It may also be solvable by creating a symbolic link as described in this answer.
This should never come up on Windows, unless you built R from source without tcl/tk support.
On Arch Linux, tk is a separate package from tcl and both need to be installed:
sudo pacman -S tcl tk
This is given that the output from capabilities("tcltk") with R is TRUE (which means your R is compiled with tcltk support as noted previously in the answers here, this should be the case if you installed it from the arch repos).
The official installation instructions for R say:
Note: the use of X11 (including tcltk) requires XQuartz to be
installed since it is no longer part of OS X. Always re-install
XQuartz when upgrading your OS X to a new major version.
So: Simply (re)install XQuartz if you want to use the tcltk package in R.
delete the X11 file on location : /opt
delete the X11 on application unitiltiy
reinstall X11 again
Problem solved...
For Mac-OS users:
I struggled with this problem recently and found that R-3.1.2 has a bug, which assumes that otool is installed when it is not.
R-3.0.0 (and later) ships with Tck/Tk 8.6.0, so you shouldn't need to install that.
Simply upgrading to a more recent version of R (3.4.2) fixed the problem for me.
I had the same issue and went down a rabbit hole before discovering a simple fix. If you install R from bianry it will include tcltk by default. Just run the installer with the default installation. You can get the .dmg here: https://cran.r-project.org/bin/macosx/
Easiest answer for Mac users:
1- Install tcl-tk using brew:
brew install tcl-tk
2- Run the following code:
ln -s /usr/local/Cellar/tcl-tk/$version/lib/libtcl8.6.dylib /usr/local/lib/libtcl8.6.dylib
ln -s /usr/local/Cellar/tcl-tk/$version/lib/libtk8.6.dylib /usr/local/lib/libtk8.6.dylib
Problem solved!
Trying to compile R-3.3.2 on Debian Jessie, all dependencies are installed. However the ./configure script complains about the zlib/bzip2 library versions not matching with the minimum requirement.
Minimum version required:
zlib: 1.2.6 (installed version: 1.2.11)
bzip2: 1.0.6 (installed version: 1.0.6)
After looking at the parts of configure script checking the library versions, it seems that it compares versions with strcmp or strncmp. Since "1.2.11" is lexicographically smaller that "1.2.6" it return a non-zero value indicating that the match failed. Besides, it just compares the first 5 characters which is also not what it is intented. So, it's a bug in configure script. Changing the script fixed the issue.
For zlib, find this line:
exit(strncmp(ZLIB_VERSION, "1.2.5", 5) < 0);
Change it to:
exit(ZLIB_VERNUM < 0x1250);
I had some issues installing R myself, specifically with the error
checking for BZ2_bzlibVersion in -lbz2... no
I had to install libbz2-dev to get that error to go away.
Unfortunately, I came across a few more issues while running ./configure and had to do a little more digging to find out how to solve it.
Discussion on issue
After reading that, I had realized I had to install a couple packages like libcurl4-openssl-dev, libpcre3, and liblzma-dev to finally finish the configuration.
The cited link suggested
At this stage you could have as well tried to install R 3.2.0RC ...
R-devel has not yet diverged much.
Personally, I think that installing an older version to resolve dependency issues reeks of laziness, but that's just my two cents.
I am trying to built a wireshark plugin code on my RHEL5 Virtual machine and while I am trying to compile it, I am getting the below error.
On ./configure command , below is the error message I receive and the make file is not being generated.
checking for Qt5Core - version >= 4.6.0... no
checking for QtCore - version >= 4.6.0... no
configure: error: Qt is not available
Please advise on how to go about this error. I have looked up for various rpm files and tried installing them but none works!
Try installing below packages as stated in this answer. Worked for me.
libqt4-dev (4:4.8.2+dfsg-11)
libqt4-dev-bin (4:4.8.2+dfsg-11)
libqt4-opengl-dev (4:4.8.2+dfsg-11)
libqtwebkit-dev (2.2.1-5)
qt4-linguist-tools (4:4.8.2+dfsg-11)
qt4-qmake (4:4.8.2+dfsg-11)
The error message you post is telling you that you need a version of Qt greater than or equal to 4.6.0. Since you are building software against Qt you will need the developer version of the package. There seems to be packages named qt47-devel that should be suitable.
I'm trying to import data (.ods file) and I know how to import .csv, .xls etc. but I strand all the time. I tried it with the package Gnumeric but R tells me that the required program 'ssconvert' cannot be found.
I wrote a package called readODS
which has a function read.ods that returns ods files as data.frames
(a list of data.frames, one per sheet)
It is available on CRAN, see here!
Source and bug reports here:
https://github.com/chainsawriot/readODS
I had the exact problem on Ubuntu Linux. It's frustratingly obvious:
sudo apt-get install gnumeric
As it happens, I had a bunch of obsolete packages, and went thru a bunch to update them. The gnumeric library requires the XML library, and my installation of XML library was built on 2.14, and my R wouldn't load anything built before 3.0. I don't think that is your issue, but if this solution above doesn't work, maybe you could also check that your packages are up-to-date. Anything I installed via sudo had to be removed via sudo, or I got permissions errors.
It's frustratingly obvious, because the error message is
Error in read.gnumeric.sheet(file = fname, head = TRUE, sheet.name = "Sheet1") :
Required program 'ssconvert' not found.
To emphasize it, the package documentation at http://cran.at.r-project.org/web/packages/gnumeric/gnumeric.pdf says
Requires an external program, 'ssconvert' (normally installed with 'gnumeric' (http://projects.gnome.org/gnumeric/) in 'PATH'.
How do you get ssconvert? Again, frustratingly obvious: it's normally installed with gnumeric. Go to the command line, and type ssconvert, and it'll remind you that:
user#Computer:~$ ssconvert
The program 'ssconvert' is currently not installed. You can install it by typing:
sudo apt-get install gnumeric
I checked, ssconvert isn't in the dependency packages (like gnumeric-common), it's in gnumeric proper, so you have to install the complete gnumeric package:
sudo apt-get install gnumeric
I haven't tried it but the ROpenOffice package looks like it might do the job: http://www.omegahat.org/ROpenOffice/
I have spent a lot of time trying to solve this, but still no luck. I am trying to get Rgraphviz to work with R 2.14.1 on a Max OS X Lion
These are the steps I took in order to install and use Rgraphviz on Mac OS X Lion:
Installed graphviz via: sudo port install graphviz
Checked that the installation was successful : pkg-config --modversion libgvc
Result: 2.28.0 <- That means its OK
Under R 2.14.1
source("http://www.bioconductor.org/biocLite.R")
biocLite("Rgraphviz")
Whenever I try to use the library I get the following error
Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details:
call: value[[3L]](cond)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so':
dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so, 6): Library not loaded: /usr/local/lib/libgvc.5.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so
Check that (1) graphviz is installed on your system; (2) the installed version of
graphviz matches '2.26.3'; this is the version used to build this Rgraphviz
package; (3) graphviz is accessible to R, e.g., the path to the graphviz 'bin'
directory is in the system 'PATH' variable. See additional instructions in the
'README' file of the Rgraphviz 'source' distribution, available at
Some things I notice
The graphviz suggested in the "help" file is 2.26.3 and the graphviz installed by Mac Ports is 2.28.0, but as it is a newer version I don't think this makes a difference, and besides I can not find v 2.26.3
Suggestion number (3) seems to be the key, but I can't find/don't have a bin directory under graphbiz
Also when I run a locate Rgraphviz.so there are no results.
Any clue towards a solution will be much appreciated,
Thanks a lot!
Thanks for the final answer, the installation seems to work for me! (I still have to check that the package runs properly). Just a quick observation: Graphviz was installed in /usr/local on my machine so that the above command had to be entered as follows:
sudo R CMD INSTALL --configure-args='--with-graphviz=/usr/local' Rgraphviz_1.32.0.tar.gz
One more fail point. If you used Fink to install graphviz, you may still, like me, encounter separate build errors even after you use the configure arguments to point to graphviz, which now look like:
R CMD INSTALL --configure-args='--with-graphviz=/sw' Rgraphviz_1.34.0.tar.gz
The installation will fail during build errors for LL_funcs.c because it is looking for libraries that do not install unless you ALSO install graphviz-dev. You will see this:
In file included from LL_funcs.c:1:
common.h:31:17: error: gvc.h: No such file or directory
common.h:32:22: error: gvplugin.h: No such file or directory
common.h:35:20: error: gvcext.h: No such file or directory
common.h:39:20: error: gvcjob.h: No such file or directory
followed by many more build errors of course. Just be sure to
fink install graphviz-dev