I am currently using CentOS Linux 7.4.1708 (Core). I have tried to install the package httpuv in R through various methods to no avail. It always ends with the error:
CC src/unix/libuv_la-procfs-exepath.lo
CC src/unix/libuv_la-proctitle.lo
CC src/unix/libuv_la-sysinfo-loadavg.lo
CC src/unix/libuv_la-sysinfo-memory.lo
CCLD libuv.la
libtool: error: require no space between '-L' and '-L/n/helmod/apps/centos7/Core/pcre/8.37-fasrc02/lib'
make[1]: *** [libuv.la] Error 1
make[1]: Leaving directory `/tmp/Rtmp5Dj7hL/R.INSTALL5c046d96dc92/httpuv/src/libuv'
make: *** [libuv/.libs/libuv.a] Error 2
ERROR: compilation failed for package ‘httpuv’
Does anyone have any thought as to what is going on here? Thanks.
The previous answer is partially correct in that it identifies libuv as the missing dependency.
In CentOS 7 you can add this with yum install libuv-devel, then attempt to install the package again with install.packages("httpuv") and provided that was your only issue, it should compile correctly.
The error says that there is a library error in libuv.la.
The cc and CCLD commands show that this is a compilation error - very likely from gcc thrown when trying to compile libuv.la.
In ubuntu linux, I would look in such cases:
$ apt search httpuv
# which gives:
# r-cran-httpuv
R packages with mostly need other system dependencies (libraries outside of R etc) mostly have a package in the apt repository.
Then you do simply:
$ sudo apt install r-cran-httpuv
And then every dependency problems are resolved (though it might be that R asks you to update/upgrade your package after the installation - which sometimes works but sometimes not).
I was looking if CentOS can use apt:
https://everyday-tech.com/apt-get-on-centos/
Another possibility for you would be to use conda which is great to solve such dependency problems. People have then similar to apt prepared for you conda-packages which provide all package dependencies.
$ conda install -c conda-forge r-httpuv
If you don't know conda, I highly recommend you this tutorial:
https://www.youtube.com/watch?v=YJC6ldI3hWk (from Corey Schafer who gives great - mainly Python - tutorials).
Related
I am working on Ubuntu 16.04 with R-version 3.4.2.
I want to install the R-Package "protolite" (more precisely, I want to install "tmap" where protolite is a prerequisite). I have libprotocol version 2.6.1 installed:
$ protoc --version
returns libprotoc 2.6.1.
When I type install.packages "protolite" , R gives me the warning:
Package protobuf was not found in the pkg-config search path.
Perhaps you should add the directory containing 'protobuf.pc'
to the PKG_CONFIG_PATH environment variable
No package 'protobuf' found
Later the installation fails with
/usr/bin/ld: cannot find -lprotobuf
collect2: error: ld returned 1 exit status
Since libprotocoll is installed, I searched for the pc file by
apt-file search protobuf.pc
which returned
libprotobuf-dev: /usr/lib/x86_64-linux-gnu/pkgconfig/protobuf.pc
So I added
export PKG_CONFIG_PATH=/usr/lib/x86_64-linux-gnu/pkgconfig
however, this did not resolve the issue. Can somebody help me out?
Note: I spent hours trying to install "tmap" by now, at first my problem was that I had installed libprotocol 3.2, which I had to delete to install tmap/protolite because the installation required libprotocol 2.6.1. So maybe this deletion/new installation brought some things in disorder on my computer.
Using
sudo apt-get install -y libprotobuf-dev protobuf-compiler
worked for me.
For anyone having the same problem. I checked with the Synaptic Package manager and found that not all libprotobuf versions were installed. In fact, just a lite version had been installed. Installing all "libprotobuf-dev 2.6.1-1.3 made it work.
I am having a tough time installing R-packages that are not available in the Anaconda repositories. My attempts so far can be found here How to install R-packages not in the conda repositories?.
Currently, I am trying to build the R-package rafalib for conda by following the instructions from this article under the heading Building a conda R package.
The first part works fine.
conda skeleton cran rafalib
Out:
Tip: install CacheControl to cache the CRAN metadata
Fetching metadata from http://cran.r-project.org/
Writing recipe for rafalib
Done
The build command runs into errors
conda build r-rafalib
Out:
Removing old build environment
Removing old work directory
BUILD START: r-rafalib-1.0.0-r3.2.2_0
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata: ......
Solving package specifications: .
Error: Packages missing in current linux-64 channels:
- r 3.2.2*
- r-rcolorbrewer
I have r 3.2.2-64bit installed via conda and it runs without problems. I also already have r-colorbrewer installed via conda and I can use that package without issues in R. Why am I getting these errors when trying to build a conda package?
I am on Linux (Antergos, an Arch derivative) with kernel 4.4.5-1-ARCH.
UPDATE 2015/04/19
Thanks to this answer, I found out that I could include the dependencies by building them separately in the same directory as the package I want to install. That didn't work for me, but I also read that I can include a channel in the build command with -c, just as when installing. So now I do:
conda build -c r r-rafalib
This gets passed all the dependency problems, but after fetching, extracting and linking packages, it fails. Here is the end of the error message.
Removing old work directory
Source cache directory is: /home/joel/anaconda2/conda-bld/src_cache
Downloading source to cache: rafalib_1.0.0.tar.gz
Downloading http://cran.r-project.org/src/contrib/rafalib_1.0.0.tar.gz
rafalib_1.0.0. 100% |#######################| Time: 0:00:00 4.87 MB/s
Success
Extracting download
Package: r-rafalib-1.0.0-r3.2.2_0
source tree in: /home/joel/anaconda2/conda-bld/work/rafalib
+ mv DESCRIPTION DESCRIPTION.old
+ grep -v '^Priority: ' DESCRIPTION.old
+ /home/joel/anaconda2/envs/_build/bin/R CMD INSTALL --build .
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
Command failed: /bin/bash -x -e /home/joel/drafts/r-rafalib/build.sh
The error sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook is the same as I encounter when using install.packages() as reported here.
There is some related discussion in this thread. I have tried to get around this error by installing different versions of ncurses, including this patched version, and I have tried to link the readline libraries, as suggested here, but I keep running into the same error. I'm quite lost at this point and any help to solve this would be greatly appreciated.
Although I started out with a different problem, the final solution turned out to be the same as I posted elsewhere How to install R-packages not in the conda repositories?. I am adding it here for completeness.
In the end, I got around the rl_event_hookproblems by following the approach recommended here and symlinking anaconda's libreadline to the system one:
mv ~/anaconda3/lib/libreadline.s.6.2 ~/anaconda3/lib/libreadline.s.6.2.bak
ln -s /usr/lib/libreadline.so.6.3 ~/anaconda3/lib/libreadline.s.6.2
I am still having troubles installing some dependency heavy R-packages due to failure to load shared objects when using install.packages() from withing R. However, simpler packages work fine and I can get most of the dependency heavy packages from anacondas R-repositories.
I recently needed to install R 3.2 to get a package from Bioconductor working, but after I installed, I get the following error:
[16:16:11 20] $ r
dyld: Library not loaded: /usr/local/lib/gcc/4.9/libgfortran.3.dylib
Referenced from: /usr/local/Cellar/r/3.2.0/R.framework/Versions/3.2/Resources/lib/libR.dylib
Reason: image not found
Trace/BPT trap: 5
Sure enough, brew was set to use gcc 5, so I told brew to use the 4.9 version
brew switch gcc 4.9
which got R running, but then R would fail in the middle of a package install (specifically when I ran biocLite('DESeq2').
Since then, I have tried a number of things, including trying to install gcc 4.8 (but I can't seem to get R to use it, even via ~/.R/Makevars). Even if 4.9 is not installed, R insists on calling the path shown above.
The windows version of R seems to say 4.9 does not work with 3.2:
R-devel temporarily used a new toolchain based on 4.9.2 gcc, put together by Duncan Murdoch using build scripts written by a contractor. However, there were too many incompatibilities with existing code, and this toolchain will not be used for R 3.2.0. See notes for details on building and testing the new toolchain.
Any help would be greatly appreciated!
Edit:
I tried installing from source, as suggested by #lmw., but it fails:
[11:27:55 2] $ brew install r --build-from-source
==> Installing r from homebrew/homebrew-science
==> Installing r dependency: gcc
==> Downloading http://ftpmirror.gnu.org/gcc/gcc-5.1.0/gcc-5.1.0.tar.bz2
######################################################################## 100.0%
curl: (28) Resolving timed out after 5542 milliseconds
Trying a mirror...
==> Downloading https://ftp.gnu.org/gnu/gcc/gcc-5.1.0/gcc-5.1.0.tar.bz2
######################################################################## 100.0%
==> Patching
patching file gcc/jit/Make-lang.in
==> ../configure --build=x86_64-apple-darwin14.3.0 --prefix=/usr/local/Cellar/gcc/5.1.0 --libdir=/usr/local/Cellar/gc
==> make bootstrap
==> make install
==> Caveats
GCC has been built with multilib support. Notably, OpenMP may not work:
https://gcc.gnu.org/bugzilla/show_bug.cgi?id=60670
If you need OpenMP support you may want to
brew reinstall gcc --without-multilib
==> Summary
🍺 /usr/local/Cellar/gcc/5.1.0: 1351 files, 248M, built in 32.5 minutes
==> Installing r
==> Using Homebrew-provided fortran compiler.
This may be changed by setting the FC environment variable.
==> Downloading http://cran.rstudio.com/src/base/R-3/R-3.2.0.tar.gz
######################################################################## 100.0%
==> Patching
patching file src/modules/lapack/vecLibg95c.c
==> ./configure --prefix=/usr/local/Cellar/r/3.2.0_1 --with-libintl-prefix=/usr/local/opt/gettext --enable-memory-pro
==> make
** installing vignettes
** testing if installed package can be loaded
* DONE (survival)
make[1]: *** [recommended-packages] Error 2
make: *** [stamp-recommended] Error 2
READ THIS: https://git.io/brew-troubleshooting
If reporting this issue please do so at (not Homebrew/homebrew):
https://github.com/homebrew/homebrew-science/issues
Edit 2:
Just for the fun of it, I tried installing r without the --build-from-source option, and it worked. See my solution below. (I think building from source may have fixed the issue with the gcc 5 upgrade, which got things working. I am not going to try it (things are finally working again...why screw with it?), but I wonder if I could remove the variables I set in ~/.R/Makevars (again, see solution below).
Rebuilding R from source fixes the same problem for me.
brew reinstall r --build-from-source
This was resolved by this commit, with new bottles for R. Make sure you brew update and brew upgrade r.
This is not a complete fix (it uses an older gcc version), but it get's me running again:
brew tap homebrew/homebrew-versions
brew install gcc48
brew install r
NOTE: I ran brew install r --build-from-source (reinstall did not work), which rebuilt something, but not r (it failed). It may be partially responsible for this working. Please let me know if it is! I'd like to give #lmw credit if his answer is the reason this worked.
Edit ~/.R/Makevars and add the following lines (edit paths as necessary):
CC=/usr/local/Cellar/gcc48/4.8.4/bin/gcc-4.8
CXX=/usr/local/Cellar/gcc48/4.8.4/bin/g++-4.8
CFLAGS=-std=c99
Run r.
(If you're trying to install bioconductor)
source("http://bioconductor.org/biocLite.R")
biocLite()
I am trying to install the packages rpanel and tkrplot on RStudio. After downloading and installing there I got this message:
downloaded 686 Kb
* installing *source* package ‘rpanel’ ...
** package ‘rpanel’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
Error in structure(.External(.C_dotTcl, ...), class = "tclObj") :
[tcl] can't find package BWidget.
Error : unable to load R code in package ‘rpanel’
ERROR: lazy loading failed for package ‘rpanel’
* removing ‘..../R/i686-pc-linux-gnu-library/3.0/rpanel’
Warning in install.packages :
installation of package ‘rpanel’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp1MdC0f/downloaded_packages’
I already installed BWidget on my own, but it didn't help.
Anyone any ideas about this problem and maybe can help me?
The system is Ubuntu 12.04.
Under windows 7 there is no problem and everything is working fine.
There are easier ways to install BWidgets. On my mac with Macports I did:
sudo port install BWidget
On Ubuntu you can probably install it with apt-get:
sudo apt-get install bwidget
"Stumbled across this while looking for an answer to the same question. Like an unfortunate number of library authors, the BWidgets people have assumed that the only people who need to use their libraries are planning to code with them. For those of us who've never used TCL, the installation instructions mean nothing.
From the a document called tuto-install-tkabber on the tkabber.jabber.ru website (irritating spam catcher won't let me post a URL), the answer is:
Install the BWidgets directory into the "lib" directory returned by:
whereis tcl
It should look something like: /usr/lib/tcl8.4"
from http://www.linuxquestions.org/questions/linux-software-2/where-to-install-bwidget-tcl-98583/ did the trick for me
Also I got BWidget from: http://sourceforge.net/projects/tcllib/files/BWidget/1.7.0/BWidget-1.7.0.zip/download
#Calimo's answer worked for me on Linux Mint 18.3 RStudio R 3.6.0. I would have commented in #Calimo's thread except for the stupid 50 reputation limit.
sudo apt-get install bwidget
Also works for Ubuntu 18 R 3.4.4 but if you get an X11 issue with rgl then this helped from #Ouistiti.
I had similar issues trying to get biotools working in Rstudio (on Ubuntu 16.04), where rpanel and tkrplot are required. Even after installing Bwidget per Calimo's answer, I got the error installation of package ‘tkrplot’ had non-zero exit status because tk.h: No such file or directory. If you look in the directory, this error is definitely correct. You need to get tk.h in there. I found out how to do so elsewhere on stackexchange:
Install tcl-dev package using apt or synaptic; tcl contains the
runtime, while tcl-devel contains header and development files. Do the
same with tk-dev
from:
https://stackoverflow.com/a/9649478/10405322
Thus,
sudo apt-get install tcl-dev
sudo apt-get install tk-dev
download BWidget from
http://sourceforge.net/project/showfiles.php?group_id=12883
once you get the archive BWidget-1.7.0.tar.gz move it to /usr/local/lib and install it with following code in terminal:
sudo mv /some_download_path/BWidget-1.7.0.tar.gz /usr/local/lib
cd /usr/loca/lib
sudo tar zxf BWidget-1.7.0.tar.gz
ok, done.
I suspect I am having a problem with my R installation, something that has to do with "--enable-R-shlib".
Can someone explain if this is something that I can fix using apt-get?
More specifically:
I am having trouble getting installing the RHive package.
I Installed R from scratch, following the instructions in (for example):
http://cran.ru.ac.za/bin/linux/ubuntu/
basically, just doing:
sudo apt-get update
sudo apt-get install r-base
sudo apt-get install r-base-dev
Next I opened R and installed rJava:
install.packages("rJava")
which worked fine.
Next I tried installing RHive:
install.packages("RHive")
at which point the installation fails with the following message:
* installing *source* package ‘Rserve’ ...
** package ‘Rserve’ successfully unpacked and MD5 sums checked
checking whether to compile the server... yes
configure: error: R was configured without --enable-R-shlib or --enable-R-static-lib
*** Rserve requires R (shared or static) library. ***
*** Please install R library or compile R with either --enable-R-shlib ***
*** or --enable-R-static-lib support ***
What Should I Do?
Also, I installed RStudio and this fails at startup with a related message:
"R shared library (/usr/local/lib64/R/lib/libR.so) not found. If this is a custom build of R, was it built with the --enable-R-shlib option"
All of which leads me to believe it is all related to the same problem. Weird thing is, I followed the same procedure on a different machine, and all seems to work fine...
I had the same problem.
In my case I changed R_HOME like this Sys.setenv(R_HOME="/usr/lib/R")
R, as well as r-cran-rjava and r-cran-rserve are available for Debian and Ubuntu as part of the basic distribution.
Can you not use those packages? They certainly work for me and many, many other people at least as far as RStudio is concerned -- I have not tried RHive myself.