I am not able to install a BioPerl Module via cpanm. With
sudo cpanm Bio::SeqIO
The output says:
--> Working on Bio::SeqIO
Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz ... OK
Configuring BioPerl-1.006922 ... OK
Building and testing BioPerl-1.006922 ... FAIL
! Installing Bio::SeqIO failed. See /home/administrator/.cpanm/work/1398677477.16274/build.log for details. Retry with --force to force install it.
When adding --force it says:
--> Working on Bio::SeqIO
Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz ... OK
Configuring BioPerl-1.006922 ... OK
Building and testing BioPerl-1.006922 ... FAIL
! Testing BioPerl-1.006922 failed but installing it anyway.
Successfully installed BioPerl-1.006922
1 distribution installed
So I am not sure whether I can use BioPerl now properly? Can I simply ignore that the testing failed?
I have already tried to reinstall CPAN with
o conf init
in the CPAN prompt, but the outcome was the same. I am working with Perl V5.14.2 and cpanm -v brings me:
cpanm (App::cpanminus) 1.6933 on perl 5.014002 built for x86_64-linux-gnu-thread-multi
Work directory is /home/administrator/.cpanm/work/1398677790.16651
You have make /usr/bin/make
You have LWP 6.05
You have /bin/tar: tar (GNU tar) 1.26
I am happy with any help, since I am a totally Linux newbie.
BioPerl uses many modules that you might not have installed. From BioPerl INSTALL file:
Remember that there are over 900 modules in BioPerl and the test
suite is running more than 12000 individual tests, a few failed tests
may not affect your usage of BioPerl
Most of the time you will not need these additional modules depending on what modules within BioPerl you are using. I'm sure that BioPerl has installed correctly on you system. I would work through http://www.bioperl.org/wiki/HOWTO:Beginners to learn BioPerl. If you get errors running these basic codes in the HOWTO, repost another question.
Good luck,
Paul
Related
First of all, sorry for my english and sorry for taking your time, I'm pretty sure the answers are online but it seems like I can't find the right keywords for this issue.
The problem: Python2 is installed but still asked as a dependency for every python2 module I want to install with my package manager.
I built python2 from source on Archlinux in a proot environment
(because I use termux on a non rooted phone and it's probably why yay did not worked as expected to install python2) and I think I did it well because "python2" open the python command line and "python2 -V" return me "Python 2.7.18", i can execute python scripts with it, etc.
I built python by downloading and uncompressing python2 from python.org, then in the uncompressed file ./configure --enable-optimization , make -s and make install.
I'm a noob so i don't know but i probably just need a way to handle python2 with pacman or a way to tell pacman that python2 is indeed installed.
repo.
I know to handle manualy built pkgs with pacman, but not software built from source. So i'v found a PKGBUILD for python2 but (again, probably because of the proot) when i use makepkg here what's happen :
[...
...
...]
==> Extracting sources...
-> Extracting Python-2.7.18.tar.xz with bsdtar
==> Starting prepare()...
bsdtar: Removing leading '/' from member names
patching file Makefile.pre.in
patch: setting attribute security.selinux for security.selinux: Permission denied
==> ERROR: A failure occurred in prepare().
Aborting...
So if anyone know how could i make makepkg works as intended or how could i tell pacman that python2 is already installed, it would totaly make my day.
PS : I know python2 is deprecated and as it's not updated anymore the security is getting worse and worse, but it's not for my main setup so don't worry. I also think i could install modules manually but it is not something i wish to do since i'd like to install the all BlackArch repo.
I did compile Ignite Application successfully.
but The Binary didn't work.
/tmp/tmp.Nw0IPD6ru3/cmake-build-debug-local-container/planet_engine: error while loading shared libraries: libjvm.so: cannot open shared object file: No such file or directory
how can I make to it work?
Also, I compiled C++ Examples successfully. such as ignite-compute-example.
and, I execute that but I got an error message.
An error occurred: JVM library is not found (did you set JAVA_HOME environment variable?)
and I using a nightly release version 2.8.0.20190213 because I couldn't build to version 2.7 in my environment.
I posted environment values down.
IGNITE_HOME=
TERM=xterm-256color
SHELL=/bin/bash
LIBRARY_PATH=/root/jre1.8.0_201/lib/amd64/server:/root/jre1.8.0_201/lib/amd64/
LC_NUMERIC=ko_KR.UTF-8
SSH_TTY=/dev/pts/0
JRE_HOME=/root/jre1.8.0_201
USER=root
LS_COLORS=rs=0:d...
LD_LIBRARY_PATH=/root/jre1.8.0_201/lib/amd64/server:/root/jre1.8.0_201/lib/amd64/
CLASS_PATH=/root/jdk-11.0.2/lib:
LC_TELEPHONE=ko_KR.UTF-8
MAIL=/var/mail/root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/root/jdk-11.0.2/bin
LC_IDENTIFICATION=ko_KR.UTF-8
JAVA_HOME=/root/jdk-11.0.2
LANG=en_US.UTF-8
LC_MEASUREMENT=ko_KR.UTF-8
JDK_HOME=/root/jdk-11.0.2/lib
SHLVL=1
HOME=/root
LOGNAME=root
LESSOPEN=| /usr/bin/lesspipe %s
LESSCLOSE=/usr/bin/lesspipe %s %s
LC_TIME=ko_KR.UTF-8
LC_NAME=ko_KR.UTF-8
_=/usr/bin/env
Thank you for reading. :)
I got it.
I am working on a docker container environment.
and therefore I am using remote build and debug with ssh and gdb.
finally, I found out why it couldn't find libjvm.so and why couldn't read environment values such as JAVA_HOME.
because it is working in gdb for now.
I confirmed that it is working when without gdb.
I will find a solution.
and, if I have been found, I will update the answer.
[Solved]
I share how I make solved that.
I was using an Oracle JDK-11 through source install.
but Ignite C++ client need something different with latest released jdk versions.
Ignite need a directory structure like this
JAVA_HOME/ (as JDK install directory)
- jre/
- lib/
- lib/
...
I solved by apt install openjdk-8-jdk.
openjdk-8-jdk have structure for what Ignite need.
i added JAVA_HOME, IGNITE_HOME, at /etc/environment.
It works finally.
but I got another problem. HAHA
I am so sad.
This also GDB problem..
So, I'm working on a robotframework test project, and the goal is to run several test suites in parallel. For this purpose, pabot was chosen as the solution. I am trying to implement it, but with little success.
My issue is: after installing Pabot (which, I might say, I did by cloning the project and running "setup.py install", instead of using pip, since the corporate proxy I'm behind has proven an obstacle I can't overcome), I created a new directory in the project tree, moved some suites there, and ran:
pabot --processes 2 --outputdir pabot_results Login*.robot
Doing so results in the following error message:
2018-10-10 10:27:30.449000 [PID:9676] [0] EXECUTING Suites.LoginAdmin
2018-10-10 10:27:30.449000 PID:400 EXECUTING Suites.LoginUser
2018-10-10 10:27:30.777000 PID:400 FAILED Suites.LoginUser
2018-10-10 10:27:30.777000 [PID:9676] [0] FAILED Suites.LoginAdmin
WARN: No output files in "pabot_results\pabot_results"
Output:
[ ERROR ] Reading XML source '' failed: invalid mode ('rb') or filename
Try --help for usage information.
Elapsed time: 0 minutes 0.578 seconds
Upon inspecting the stderr file that was generated, I have this message:
Traceback (most recent call last):
File "C:\Python27\Lib\site-packages\robotframework-3.1a2.dev1-py2.7.egg\robot\running\runner.py", line 22, in
from .context import EXECUTION_CONTEXTS
ValueError: Attempted relative import in non-package
Apparently, this has to do with something from the runner.py script, which, if I'm not mistaken, came with the installation of robotframework. Since manually modifying that script does not seem to me the optimal solution, my question is, what am I missing here? Did I forget to do anything while setting this up? Or is this an issue of compatibility between versions?
This project is using Maven as the tool to manage dependencies. The version I am running is 3.5.4. I am using a Windows 10, 64bit system; I have Python 2.7.14, and Robot Framework 3.1a2.dev1. The Pabot version is 0.44. Obviously, I added C:\Python27 and C:\Python27\Scripts to the PATH environment variable.
Edit: I am also using robotframework-maven-plugin version 1.4.0.8, if that happens to be relevant.
Edit 2: added the error messages in text format.
I believe I've come across an issue similar when setting up parallel execution on my machine. Firstly I would confirm that pabot is installed using pip show robotframework-pabot.
Then you should define the directory your results are going to using -d.
I then modified the name of the -o to Output.xml to make it easy to identify.
This is a copy of the code I use. Runs optimally with 8 processes
pabot --processes 8 -d results -o Output.xml Tests
Seems that you stumbled on a bug in the prerelease version of robot framework (3.1a2.dev1).
Please install a release version of robot framework. For example 3.0.4.
Just in case anyone happens to stumble upon this issue in the future:
Since I can't use pip, and I tried a good deal of workarounds that eventually made things more unstable, I ended up saving my project and removing everything Python-related from my system, so as to allow me to install everything from scratch. In a Windows 10, 64bit system, I used:
Python 2.7.14
wxPython 2.8.12.1, win64, unicode, for py27
setuptools 40.2.0 (to allow me to use the easy_install command)
Robot Framework 3.0.4
robotremoteserver 1.1
Selenium2Library 3.0.0
and Pabot version 0.45.
I might add that, when installing the Selenium2Library the way I described above, it eventually tries to download some things from the pip repositories - which, if you have a proxy, will cause you trouble. I solved this problem by browsing https://pypi.org/simple/selenium/, manually downloading the 2.53.6 .tar.gz file, then extracting it and running setup.py install on the command line.
PS: Ideally, though, anyone should be able to use proxy settings from the command line (--proxy http://user:password#server:port) to get pip and then use it; however, for some reason, probably related to network security configurations that I didn't want to lose time with, this didn't work in my case.
include sympy python packages into Chaquopy:
I started with the example python provided by Chaquopy available at github (https://github.com/chaquo/chaquopy) for Android studio 3.0.1.
Than I created 2 wheel files from the sympy source () files, based on python 3.6.3, see the below files that wheel generated:
"mpmath-1.0.0-py3-none-any.whl"
"sympy-1.1.1-py3-none-any.whl"
I tried to install the above files into the build.gradle of the demo example from 1., for testing purposes I tried some of there own wheel files (that process succeeded), but could not install my own wheel files.
I am fairly certain that the local wheel files that I generated are placed in the proper directory, because if I change the directory in the gradle file it complains that it cannot find the file.
I included the wheel files in the build.gradle(Module:app) file as follows:
python {
// Enable and edit the following line if "python" is not on your PATH.
// buildPython "C:/Python27/python.exe"
version "3.6.3"
// Android UI demo
pip {
install "Pygments==2.2.0" // Also used in Java API demo
}
pip {
install "wheels/mpmath-1.0.0-py3-none-any.whl"
// install "wheels/sympy-1.1.1-py3-none-any.whl"
// install "numpy==1.9.2"
// install "numpy==1.14.0"
}
When created the build gradle generates the following error:
sympy-1.1.1-py3-none-any.whl is not a supported wheel on this platform.
Exit status 1
:app:generatePy2DebugPythonRequirements FAILED
FAILURE: Build failed with an exception.
What went wrong:
Execution failed for task ':app:generatePy2DebugPythonRequirements'.
Process 'command 'python'' finished with non-zero exit value 1
Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.
Get more help at https://help.gradle.org
BUILD FAILED in 2s
7 actionable tasks: 1 executed, 6 up-to-date
Does anyone have an idea what could be wrong?
sympy and mpmath have now been added to the Chaquopy wheel repository (https://github.com/chaquo/chaquopy/issues/20), so you don't need to build your own anymore.
Did some further investigation and did see that I somehow compiled for Py2, while my wheel files where version 3 changing this resulted in a correct executable.
It did run into a different issue, while the mpmath module could be imported into the interactive python console (part of the demo app), the sympy module gave an error:
ModuleNotFoundError: no module named 'distutils'
Let me know if anyone ran into a similar problem!
I have Debian Linux(64-bit) in VirtualBox.
Ram: 8Gb (for Debian 4Gb)
CPU: i5-3470
If any other details are needed please tell me.
I have followed instructions written here, and here you can see the console log.
For some reason I am unable to to build phantomjs and I can't understand why its not working... Have searched a lot, but couldn't find any thread which would be about this error.
--- EDIT ---
When I executed this command:
./configure --with-openssl-includes=/usr/include/openssl-1.0/ --with-openssl-libraries=/usr/lib/openssl-1.0/
Output was this:
--with-openssl-includes=/usr/include/openssl-1.0/: invalid command-line switch
--with-openssl-libraries=/usr/lib/openssl-1.0/: invalid command-line switch
The output of the console has changed but I still get errors: https://pastebin.com/wbgi8syg
Looks like you are on stretch (or later) and that you are already aware of the libssl vs libssl1.0 case.
Therefore, if you don't have libssl-dev installed, this line will get you further:
python build.py --qt-config "-I /usr/include/openssl-1.0/ -L /usr/lib/openssl-1.0/"
If you already have it installed and my suggestion doesn't work, you can uninstall libssl-dev for the time to build phantomjs which will likely avoid having to play further with configuration related variables.