"/usr/bin/ld: cannot find -lpolyml"
I received this error when compiling a source sml file with polyc on Debian 10.
polyc requires the deb package 'libpolyml-dev', even though it is not installed by default when installing the deb package 'polyml'.
So, 'apt install libpolyml-dev' resolved the issue.
Related
I'm trying to build snappy, but I end up getting the error
error while loading shared libraries: libatomic.so.1: cannot open shared object file: No such file or directory
When I go look in /lib/gcc/x86_64-redhat-linux/8/ I do find a file libatomic.so
Which has the contents
INPUT ( /usr/lib64/libatomic.so.1.2.0 )
then if I go looking in /usr/lb64/ only these files exist
libatomic_ops_gpl.so.1
libatomic_ops_gpl.so.1.1.2
libatomic_ops.so.1
libatomic_ops.so.1.1.1
I try doing yum install libatomic_ops.x86_64, it says nothing to do. That is the only package that comes up when doing yum search libatomic.
I'm confused with how to solve this issue. Thanks!
For what it matters, this is a redhat 8.6 machine.
This was solved by running dnf install gcc, this updated gcc and allowed for yum install libatomic to work
I'm trying to install the package "Tax4Fun" but keep failing.
I've tried 2 different ways:
install.packages("devtools")
devtools::install_url("http://tax4fun.gobics.de/Tax4Fun/Tax4Fun_0.3.1.tar.gz")
library(Tax4Fun)
The error that I get is:
ERROR: dependency 'biom' is not available for package 'Tax4Fun'
I've also tried installing biom directly
BiocManager::install("biom")
which does not work either
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installing package(s) 'biom'
Installation path not writeable, unable to update packages: boot, foreign, KernSmooth,
mgcv, nlme, survival
Warning message:
package ‘biom’ is not available (for R version 3.6.1)
The other way I've tried to install Tax4Fun directly is
BiocManager::install("Tax4Fun")
I get the following error code:
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installing package(s) 'Tax4Fun'
Installation path not writeable, unable to update packages: boot, foreign, KernSmooth,
mgcv, nlme, survival
Warning message:
package ‘Tax4Fun’ is not available (for R version 3.6.1)
Please help :)
You need to install it by downloading the packages from source (http://tax4fun.gobics.de). Then it depends whether you are running on Linux/Mac or Windows.
From the command line, you navigate to the folder containing the .tar.gz downloaded package. Then you should install it using:
R CMD INSTALL Tax4Fun_0.3.1.tar.gz
But dependancies are not installed by default. So you need to install dependancies manually, Qiimer and Biom, which are both deprecated on Cran. You install them using the same command, after you have downloaded the packages from the Cran archives.
Before that, you need to also install their dependancies in R:
install.packages("pheatmap")
install.packages("RJSONIO")
Then you should be able to proceed as mentioned above: install Qiimer and Biom from the command line first. Then Tax4Fun from the command line too.
If you are running on Windows you should have quite the same issues, but the installation of the different packages and dependancies is different. You can have a look at the readme at http://tax4fun.gobics.de
I have been trying to install obspy and have been running into a lot of problems. I want to install obspy which has a dependency on pyproj. But apparently obspy only works with pyproj 1.9.5.1, which I tried installing using pip (pip3 install pyproj==1.9.5.1), but only got the errors like-
_proj.c:7488:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
Digging deeper I found that it might be a Cython problem, and installing pyproj directly from github might help, because it would apparently make Cython recompile all the necessary files. Something along the lines of -
pip3 install git+https://github.com/jswhit/pyproj.git
However this one gives the error -
ERROR: Minimum supported proj version is 6.2.0, installed version is 5.2.0.
I di try installing a higher version of libproj-dev (sudo apt install libproj-dev=6.2.0) however it shows that there is no candidate for 6.2.0. I tried downloading the deb file and installing from that using -
sudo apt-get install ~/Downloads/libproj-dev_6.2.0-1_amd64.deb
which just leads to the error -
The following packages have unmet dependencies:
libproj-dev : Depends: libproj15 (= 6.2.0-1) but it is not installable
E: Unable to correct problems, you have held broken packages.
But I think this is not the right way to install for me anyway, since I need a specific version. Hence I tried installing directly from the tarball of the release -
pip3 install https://github.com/pyproj4/pyproj/archive/v1.9.5.1rel.tar.gz
Which leads to the first error I had, evidently due to Cython.
With errors on everything I tried to do to fix this, I am not sure what even is relevant to my problem now.
Any help is appreciated, and if this site is not the correct place for this question, please help me migrate it to its proper destination.
I am on Ubuntu 18.10.
The problem is, that Cython-generated c-files don't work for Python-3.7 if generated with Cython versions up to 0.27.3 (at least): The setup.py of pyproj (at least in the version 1.9.5.1) doesn't regenerate the_proj.c, which is generated with Cython 0.23.2 and thus the installation cannot succeed.
You have the following options:
stay on Python3.6 where everything works out of the box.
regenerate _proj.c with a current Cython-version.
For the second option:
download and unzip your prefered version from https://github.com/pyproj4/pyproj/releases/tag/v1.9.5.1rel and switch to the created folder pyproj-1.9.5.1rel.
check, that the cython-version is >=0.27.3. via cython --version.
regenerate the _proj.c file via cython -3 _proj.pyx (_proj.pyx looks like Python3-code, but also language_level=2 (i.e. cython -2 _proj.pyx) will probably work.
install running pip install .
pyproj 1.9.5.1 was release at Jan 7, 2016. At that time, the latest version Python was 3.5. In my tests. pyproj 1.9.5.1 failed to be installed on Python 3.7.4, but succeeded on Python 3.5.7.
You need to create a environment with Python 3.5 by pyenv or conda.
References
pyproj 1.9.5.1 release
Python release history
I am trying to install Agave under Fedora, but I got this error:
configure: error: gnome-doc-utils >= 0.3.2 not found
I tried to compile and install the gnome-doc-utils from this page, but i still got this error,and when i try the
yum list installed gnome-doc-utils*
command, I can't find the package. Do I have to register the package after installing? I don't think I have a error for the make install, because I don't see any the text error in the process, or I could be wrong.
In general, package managers (tools like yum) don't know that something has been installed on your machine unless it was installed as a package. If an agave package for Fedora exists, I would suggest using that instead of compiling from source.
I have installed the latest Haskell Platform for MAC OSX and I get the error "Setup: failed to parse output of 'ghc-pkg dump'" when I do anything with Cabal.
So I looked at my versions:
ralphtq$ ghc-pkg list Cabal
/Library/Frameworks/GHC.framework/Versions/612/usr/lib/ghc-6.12.1/package.conf.d
Cabal-1.8.0.2
ralphtq-mac-mini:cabal-install-0.6.4 ralphtq$ cabal --version
cabal-install version 0.6.2
using version 1.6.0.3 of the Cabal library
This is telling me that even though I have Cabal 1.8 the cabal-instal is at version 0.6.2. I have tried to correct that using darcs to get the latest version of cabal-install, but I cannot get passed the error:
ralphtq$ sh bootstrap.sh
Checking installed packages for ghc-6.12.1...
parsec is already installed and the version is ok.
network is already installed and the version is ok.
Cabal is already installed and the version is ok.
mtl is already installed and the version is ok.
HTTP is already installed and the version is ok.
zlib is already installed and the version is ok.
cleaning...
Linking Setup ...
Configuring cabal-install-0.9.1...
Setup: At least the following dependencies are missing:
Cabal ==1.9.*
It is expecting Cabal to be >= 1.9.
I tried to install a previous version of Cabal but got the following error:
...
...
[50 of 51] Compiling Distribution.Simple ( Distribution/Simple.hs, Distribution/Simple.o )
[51 of 51] Compiling Main ( Setup.hs, Setup.o )
Linking Setup ...
Configuring Cabal-1.6.0.2...
Setup: failed to parse output of 'ghc-pkg dump'
I am back to the same problem.
I have also tried a complete re-install of the platform.
What are my next options? Help appreciated, thx.
Either you have installed an old version of the Haskell Platform, or you have a mixed up environment where you have installed over the top of an existing, older install, and so now have a mixture of ghc-pkg versions from 6.10.x and 6.12.x
Try removing those ghc-pkg and cabal binaries, and then installing the Platform. That way you won't have those old executables lying around.