I just started working through R for everyone and I'm having trouble installing the RODBC package. I've seen that a lot of other people have had trouble doing this on Macs as well. (I'm currently running 10.10.5 Yosemite.)
Originally I was having trouble with the program finding the sql.h and sql.ext headers, but I've finally managed to work through that.
Now, however, when I run
install.packages("RODBC")
or
install.packages("~/Downloads/RODBC_1.3-12.tar", repos = NULL, type = "source"),
I get this:
clang: error: no such file or directory: '/usr/local/lib/libcairo.a'
clang: error: no such file or directory: '/usr/local/lib/libpixman-1.a'
clang: error: no such file or directory: '/usr/local/lib/libfreetype.a'
clang: error: no such file or directory: '/usr/local/lib/libfontconfig.a'
clang: error: no such file or directory: '/usr/local/lib/libreadline.a'
make: *** [RODBC.so] Error 1
ERROR: compilation failed for package ‘RODBC’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RODBC’
Warning in install.packages :
installation of package ‘/Users/John/Downloads/RODBC_1.3-12.tar’ had non-zero exit status
And I've come to an impasse. I can't seem to find much in the way of advice on getting through this and I really don't understand what it means. I could really use some help!
I had the same problem while using Microsoft R Open 3.2.4, in OSX 10.11.6.
To solve it I just did brew install cairo.
After that I got a different error:
clang: error: no such file or directory: '/usr/local/lib/libreadline.a'
This was solved with brew link --force readline.
I then went again with install.packages("RODBC",type = "source"), and it worked for me.
Related
I am trying to install minfi in R:
BiocManager::install("minfi")
but the installation stops during the compiling of HDF5Array with the following errors:
gcc: error: "/usr/lib64/R/library/Rhdf5lib/lib/libhdf5.a": No such file or
directory
gcc: error: "/usr/lib64/R/library/Rhdf5lib/lib/libsz.a": No such file or
directory
make: *** [HDF5Array.so] Error 1
ERROR: compilation failed for package ‘HDF5Array’
I've already installed rhdf5 and Rhdf5lib package plus the files R "can't see" actually exist in the exact directory (/usr/lib64/R/library/Rhdf5lib/lib/) where it supposedly "searches" for them.
ls /usr/lib64/R/library/Rhdf5lib/lib/
libhdf5.a libhdf5_cpp.a libsz.a
My R version is 3.6.0, my GCC version is 4.8.5 20150623 (Red Hat 4.8.5-39) and my CentOS distribution is 7.6.1810
I would appreciate any suggestions.
Thank you.
I met the same problem.
http://bioconductor.org/checkResults/release/bioc-LATEST/HDF5Array/ mentions that "HDF5Array(1.12.2)" failed to be installed. So wait for improvements.
There is a way: installing an older version of "HDF5Array".
url<-"https://bioconductor.org/packages/3.8/bioc/src/contrib/HDF5Array_1.10.1.tar.gz"
install.packages(url,repos=NULL,type="source")
BiocManager::install("minfi")
I am new to R (so your patience and support is appreciated)! I looked up this issue, but still could not find a solution that worked. I am trying to install the "party" package in R. However, I keep receiving the following error messages:
> **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: *** [party.so] Error 1 ERROR:
> compilation failed for package ‘party’
> * removing ‘/Users/md3389/Library/R/3.3/library/party’ **Warning in install.packages : installation of package ‘party’ had non-zero exit
> status**
>
> The downloaded source packages are in
> ‘/private/var/folders/fw/wxx2bzj51f7c7p6ptk_g1tyw0000gn/T/RtmpmZHUu9/downloaded_packages’
I successfully installed "mvtnorm" and "multcomp" as suggested on a similar thread here: [Error installing PARTY package in R
However, I still could not install PARTY, so I checked this thread: error install packages("party") - R studio IDE
The above thread led me to https://www.r-bloggers.com/installing-r-on-os-x/
However, I am wondering if there is a more simple solution that does not require me downloading additional software that will force me to update my version of Mac OS X to 10.13.6 or later. I currently have OS X Yosemite (version 10.10.5) and am nervous about updating, since I have heard mixed reviews.
Could someone please advise? I am trying to install "party" for a course assignment, and the "non-zero exit status" and "ld" warnings should not be what I am wasting time on! :-(
Thank you so much!
While installing "car" package in Rstudio in Ubuntu, I faced an error saying that dependencies "nloptr","lme4" and one more, are not installed.
So I started installing "nloptr" but I faced this error-
configure: Need to download and build NLopt
trying URL 'http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz'
Error in download.file(url = "http://ab-initio.mit.edu/nlopt/nlopt-
2.4.2.tar.gz", :
cannot open URL 'http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz'
Execution halted
/bin/tar: This does not look like a tar archive
gzip: stdin: unexpected end of file
/bin/tar: Child returned status 1
/bin/tar: Error is not recoverable: exiting now
Warning message:
In untar(tarfile = "nlopt-2.4.2.tar.gz") :
'/bin/tar -xf 'nlopt-2.4.2.tar.gz'' returned error code 2
configure: Starting to install library to
/tmp/RtmpSeLv7g/R.INSTALL18a67910d582/nloptr/nlopt-2.4.2
./configure: line 3325: cd: nlopt-2.4.2: No such file or directory
System hangs after last line and when I restart after some time, "nloptr" is not installed and hence I am unable to install "car" package.
Please help me. Thanks in advance.
I was encountering the same problem under R (pure R 3.2.3 on Linux Debian). I was first blocked by another issue during the same installation : the installation process failed to lock directory ~/.../R/x86_64.../3.2 and suggested to remove ~/.../R/x86_64.../3.2/00LOCK-nloptr . I did it, restart the car package installation, and then it blocked at the same point: it needs nlopt.h.
So, I installed libnlopt-dev (sudo apt-get install libnlopt-dev) and re-restart the car installation ... and then it worked.
Ok, this is under linux, but perhaps should you try to focus on installing something about NLOPT under windows.
Good luck.
I have exactly the same problem as the poster here, unfortunately no solution is provided on that link.
I built and installed IPOPT (version 3.12.6) on Windows 7 (64bit) with Cygwin, but I cannot seem to get the R interface to work. All commands (configure, make, make install, make test) were executed without error.
When I try to build the R interface from RStudio, I tried using both the code in the "build" folder as well as the code in the main directory. I get the following errors:
`>install.packages("C:/cygwin64/home/Ipopt-3.12.6/build/Ipopt/contrib/RInterface",
repos=NULL, type="source")
Error:
cygwin64/home/Ipopt-3.12.6/build/Ipopt/contrib/RInterface/DESCRIPTION'
Not using the build directory:
`>install.packages("C:/cygwin64/home/Ipopt-3.12.6/Ipopt/contrib/RInterface", repos=NULL, type="source")
Error:
installing source package 'ipoptr' ...
** libs
*** arch - i386 Warning: running command 'make -f "Makevars.win" -f "C:/Users/~1/DOCUME~1/R/R-33~1.1/etc/i386/Makeconf" -f
"C:/Users/~1/DOCUME~1/R/R-33~1.1/share/make/winshlib.mk"
SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)'
SHLIB="ipoptr.dll" ' had status 127 ERROR: compilation failed for
package 'ipoptr'
* removing 'C:/Users/Documents/R/R-3.3.1/library/ipoptr' Warning in install.packages : running command
'"C:/Users/~1/DOCUME~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l
"C:\Users\Documents\R\R-3.3.1\library"
"C:/cygwin64/home/Ipopt-3.12.6/Ipopt/contrib/RInterface"' had status 1
Warning in install.packages : installation of package
‘C:/cygwin64/home/Ipopt-3.12.6/Ipopt/contrib/RInterface’ had non-zero
exit status
Does anyone know what I could do to resolve this?
EDIT: After installing RTools and adding it to my PATH I get ipoptr.cpp:22:34: fatal error: IpIpoptApplication.hpp: No such file or directory
#include "IpIpoptApplication.hpp", i.e. it seems that ipoptr.cpp cannot find IpIpoptApplication.hpp (which is in a subdirectory of the build folder) and later on in the error still the same Warning: running command 'make -f "Makevars.win" -f ' had status 2.... Copying this file over to the location of ipoptr.cpp moves the error one file further to another similar file that it cannot find. I suspect it cannot find these files because of something being wrong with my makevars.win file (I suspect that that's the file that should point to the currently missing files). Does anyone have an idea what this could be?
EDIT 2: Might it have to do with the comment here indicating that in some cases LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$IPOPTDIR/build/lib should be set? How do I do this? Should this be done in R or cygwin?
I am using Anaconda to manage my R-installation. It works great for packages available in the R-channels provided by Anaconda, but I am having troubles installing packages not contained in the Anaconda repos.
I have tried a few different approaches, all listed below together with their error output.
1. install.packages('rafalib')
Suggested to work here conda - How to install R packages that are not available in "R-essentials"?. My .libPaths() points to '/home/user/anaconda2/lib/R/library'.
Out:
--- Please select a CRAN mirror for use in this session ---
Error in download.file(url, destfile = f, quiet = TRUE) :
unsupported URL scheme
Error: .onLoad failed in loadNamespace() for 'tcltk', details:
call: fun(libname, pkgname)
error: Can't find a usable init.tcl in the following directories:
/opt/anaconda1anaconda2anaconda3/lib/tcl8.5 ./lib/tcl8.5 ./lib/tcl8.5 ./library ./library ./tcl8.5.18/library ./tcl8.5.18/library
This probably means that Tcl wasn't installed properly.
I installed tcl from the conda channel r-old, but install.packages() still threw the same error message.
2. options(menu.graphics=FALSE) and then install.packages('rafalib')
I got a list of mirrors and chose one.
Out:
Selection: 15
trying URL 'http://cran.utstat.utoronto.ca/src/contrib/rafalib_1.0.0.tar.gz'
Content type 'application/x-gzip' length 11798 bytes (11 KB)
==================================================
downloaded 11 KB
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
The downloaded source packages are in
‘/tmp/Rtmphwpta0/downloaded_packages’
Warning message:
In install.packages("rafalib") :
installation of package ‘rafalib’ had non-zero exit status
Both 2 and 3 are from Disable/suppress tcltk popup for CRAN mirror selection in R
3. Setting the mirror in ~/.Rprofile
Before trying install.packages(), I added the following to my ~/.Rprofile.
## Default repo
local({r <- getOption("repos");
r["CRAN"] <- "http://cran.us.r-project.org";
options(repos=r)})
Out:
trying URL 'http://cran.us.r-project.org/src/contrib/rafalib_1.0.0.tar.gz'
Content type 'application/x-gzip' length 11798 bytes (11 KB)
==================================================
downloaded 11 KB
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
The downloaded source packages are in
‘/tmp/RtmppIz9rT/downloaded_packages’
Warning message:
In install.packages("rafalib") :
installation of package ‘rafalib’ had non-zero exit status
4. Setting the download method to 'curl' or 'wget'.
While keeping the new ~/.Rprofile configuration. I guess this wasn't necessary since the package seems to be downloading fine now, but I tested it just in case.
Out:
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘rafalib’ failed
Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
download had nonzero exit status
5. Manual download of rafalib
install.packages('../Downloads/rafalib_1.0.0.tar.gz', repos=NULL, type='source')
Out:
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
Warning message:
In install.packages("../Downloads/rafalib_1.0.0.tar.gz", repos = NULL, :
installation of package ‘../Downloads/rafalib_1.0.0.tar.gz’ had non-zero exit status
6. Building a conda package from rafalib
I opened a separate issue for this Errors building R-packages for conda. In short, it complains about missing dependencies that I already have installed. Update I got a round the dependency problem and I am now stuck at the same rl_signal_event_hook-error as for my other approaches.
7. sudo ln /usr/lib/libncursesw.so.6 /usr/lib/libncursesw.so.5
As per https://github.com/conda/conda/issues/1679, but it didn't fix the issue for me.
So it seems like I can now download the package fine, but installing it fails. I have seen the error message sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook previously when using R with irkernel in the Jupyter Notebook, but it has never obstructed my work. I have never seen anything relating to that error message when running python through anaconda.
I'm out of ideas. Does anyone know how I can install R-packages not provided by anaconda, such as rafalib or swirl?
I am on Linux (Antergos, an Arch derivative) with kernel 4.4.5-1-ARCH.
UPDATE 2016/04/15
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.
Detailed post on managing packages that are and are not in Anaconda R: http://ihrke.github.io/conda.html
Essentially is using commands:
conda skeleton cran <package_name>
conda build <package_name>
If the package has dependencies that are also not in Anaconda:
conda skeleton cran <dependency1>
conda skeleton cran <dependency2>
conda build <package_name>
Essentially I would agree with this post in saying that I don't understand how install.packages() works with Anaconda. What I seem to see is that Anaconda creates a R environment where all the packages installed from install.packages() are kept.
Whenever I am working in Jupyter with R, I use this environment and am able to access all the packages that I have installed with install.packages()
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.