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.
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've recently replaced Win10 by Linux Debian 11.2 on my PC (hence I'm a newbee in Linux). Now, not all programs are available as deb-Files.
I tried to compile source code - here a synthesizer ams-2.2.0 - from a tar.gz files (after unzipping into a separate folder) with steps (as written in the INSTALL.TXT to this source, and obviously usual)
./configure
make
make install
I get a bunch of error messages for missing files, when running ./congigure most resolved by installation of missing packages, but at last it fails with error message:
checking for QTCore Qt5Gui Qt5Widgets >= 5.0... no
configure: error: cannot find Qt5 library >= 5.0
(hope to get all written correctly, because I can't copy from the terminal ... Ctrl-Shift-C doesn't seem to work)
I checked the installation in synaptics and found that Qt-Version is 5.12. So what's wrong here?
I'm afraid to have this error message everytime I try to compile different source codes.
You need to install libqtcore and libqtwidgets with development headers, they are in qtbase5-dev package.
sudo apt install build-essential qtbase5-dev qtchooser
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 tried to use gotk3 for creating desktop application. I follow the instruction in gotk3 wiki and this installing-on-linux wiki to install it. But then I get this error while executing go get -v:
gcc errors for preamble:
In file included from ../../gotk3/gotk3/gdk/gdk_since_3_22.go:23:0:
./gdk_since_3_22.go.h:22:8: error: unknown type name 'GdkMonitor'
static GdkMonitor *
^
I've tried to delete the gotk3 directory, and then trying to go get -v again, but still, it didn't work.
I also checked the GTK version that installed in my Ubuntu 16.04 using apt-cache policy libgtk2.0-0 libgtk-3-0 | grep Installed. And it shows this:
Installed: 2.24.30-1ubuntu1.16.04.2
Installed: 3.18.9-1ubuntu3.3
What did I do wrong? Thanks
GdkMonitor was introduced in GTK+ 3.22. Your version is 3.18.
go get -tags gtk_3_18 github.com/gotk3/gotk3/gtk at the very beginning of building (see here NOTE section) should fix things