I downloaded Julia(v0.5.2) from here, then unpacked the downloaded folder. after that i install AtOM and set uber-juno for it.
when i wrote in console 2+2, i got such error:
We tried to launch Julia from:
julia
This path can be changed in the settings.
Details:
/bin/sh: 1: julia: not found
How can i solve this problem?
thank you.
Note that: when i wrote in shell: julia myprogram.jl ,
i got such error:
The program 'julia' is currently not installed.
while i unpacked julia.tgz by tar
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")
Recently we have downgraded R(latest) to 3.3.0 to RHEL.
Which requires to install xlsx and other rJava dependent packages, though I have deep dived into every possible duplicate and tried all options.
Details:
Command Executed
R CMD javareconf
Error:
.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/lib64/R/lib64/R/lib/libR.a(CommandLineArgs.o): could not read symbols: Bad value
collect2: ld returned 1 exit status
make[2]: *** [libjri.so] Error 1
make[2]: Leaving directory /tmp/RtmpH1WhQR/R.INSTALL4a1266bbb309/rJava/jri/src'
`
Net search: I searched and found following link
https://github.com/BVLC/caffe/issues/2171 suggests to use
export CXXFLAGS=-fPIC
but no luck also I do not see CMakeCache.txt in the R folder, still not clear which piece I am missing and any help will be highly appreciated.
NOTE: This might seem to be a duplicate, but seriously I have already tried all the related/relevant posts on stackoverflow.
I resolved this, by manually placing the rJava folder(which I had in a different environment while we used R latest version), while entering into R add this following command before installing rJava dependant libraries:
.libPaths("/usr/lib64/R/library")
Change the path to the path where R is installed.
Hope this helps.
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.
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.
I’m experiencing some troubles when I try to install R dependencies with the command :
install.packages(c(“Rcpp”,”RJSONIO”,”bitops”,”digest”,”functional”,”itertools”,”reshape2″,”string ”,”plyr”,”caTools”),repos=’http://cran.revolutionanalytics.com’)
packages are downloaded but then all I get are the messages
/usr/lib64/R/bin/R: line 8: uname: command not found
/usr/lib64/R/bin/R: line 143: exec: sh: not found
repeated as many times as the number of packages I am trying to install.
I am using R version 3.2.2, rstudio-server 0.99.489 in Hortonworks Sandbox with hadoop 2.3 (Oracle Virtualbox).
Do you have any suggestions?
Thanks for your help.
I know this question was asked 7 months ago. But I just had the same problem stefanod did and I Googled left and right without finding a solution. Then for absolutely no reasonable reason it just worked. Here is what I have tried and what eventually solves my problem:
So I use R 3.2.2, rstudio-server 0.98.994 in Hortonworks Hadoop Sandbox HDP 2.4 in VMWare. I logged in the virtual machine using the Shell Web Client Method. The entire process was done with root privilege. I followed this instruction: https://jsolderitsch.wordpress.com/hortonworks-sandbox-r-and-rstudio-install/ except that I used updated versions of R and RStudio Server. Everything worked fine until I invoked R in the shell and attempted
install.packages('foo.bar', repos='http://cran.revolutionanalytics.com')
Then I had exactly the same error messages as in this Q.
I checked my $PATH and used whereis COMMANDNAME to check if I had the uname command at the right place. Seems I do.
I then quit R. Inside CentOS I used wget to manually download the .tar.gz files of the packages and their dependencies. I then tried to install those packages manually:
[root#sandbox ~]# sudo R CMD INSTALL foo.bar.tar.gz
* installing to library ‘/usr/lib64/R/library’
* installing *source* package ‘foo.bar’ ...
** package ‘foo.bar’ successfully unpacked and MD5 sums checked
** libs
sh: make: command not found
ERROR: compilation failed for package ‘foo.bar’
* removing ‘/usr/lib64/R/library/foo.bar’
sh: rm: command not found
At this time RStudio was already installed. So I logged into RStudio in my browser at port 8787 and tried install.packages in RStudio and every package installed fine.
I guess the take-home message is to install packages inside RStudio instead of inside R in the shell.
BTW I also cannot log in RStudio as root; says invalid username and password.