I ran into an odd issue that I cannot fix in any way and I was hoping someone here may have a better understanding of whats wrong;
I am unable to use RWebLogo package - even run the simplest examples due to the same missing Ghostscript error.
e.g. running:
library(RWebLogo)
aln <- c('CCAACCCAA', 'CCAACCCTA', 'AAAGCCTGA', 'TGAACCGGA')
weblogo(seqs=aln, file.out='mylogo.pdf')
Throws this error:
Traceback (most recent call last):
File "/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RWebLogo/extdata/weblogo-3.3/weblogo", line 71, in <module>
weblogolib._cli.main()
File "/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RWebLogo/extdata/weblogo-3.3/weblogolib/_cli.py", line 82, in main
formatter(data, format, opts.fout)
File "/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RWebLogo/extdata/weblogo-3.3/weblogolib/__init__.py", line 757, in pdf_formatter
gs = GhostscriptAPI()
File "/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RWebLogo/extdata/weblogo-3.3/weblogolib/__init__.py", line 196, in __init__
raise EnvironmentError("Could not find Ghostscript on path."
EnvironmentError: Could not find Ghostscript on path. There should be either a gs executable or a gswin32c.exe on your system's path
I have installed ghostscript ver 9.15 with configure/make/install in the terminal and then added the PATH to bash profile and executed it. When I run gs in the terminal it works, confirming it is set to the system path, yet the same error still occurs. Even after rebooting.
I tried adding the gs to the environment in R directly:
Sys.setenv(R_GSCMD = "/Applications/ghostscript-9.15/bin/gs")
which also hasn't helped... Gives exactly the same error. When I search the R environment it shows that gs is there.
Important version information:
MAC: OS Yosemite 10.10.1;
R version 3.1.1 (2014-07-10);
Platform: x86_64-apple-darwin10.8.0 (64-bit);
RWebLogo_1.0.3
Do you know of any issue that may have cause this problem? I'm new to programming, so I am worried I may be missing something basic. I would be grateful for any advice. Thank you!
I have gotten in touch with Omar, the author of RWebLogo, and he has been really helpful in pinpointing my problems and resolving the issue.
First, he advised to run the RWebLogo on a test sequence on the terminal:
/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RWebLogo/extdata/weblogo-3.3/weblogo -f test_seqs.txt -o ~/Desktop/out.pdf -F pdf
Change the base directory (everything before extdata/weblogo …) of the script above to be whatever the command below gives you in R:
system.file(package = 'RWebLogo')
I ran it and got a new error: the lack of numpy. I actually had the numpy installed but without full user privileges. After reinstalling numpy, the RWebLogo was successfully running from the terminal.
Still, the RStudio was throwing a GhostScript error. Omar suggested that there is a problem with an older version of RStudio running on Yosemite (I currently have 10.10.1), and sent me a link to an updated RStudio version where the problem was fixed.
http://www.r-bloggers.com/r-and-rstudio-incompatibility-with-yosemite-mac-os-x-10-10/
I got the updated RStudio and everything works great there right now. Hope this helps someone with a similar issue!
Related
I successfully use mypyc in my project and it has performed well until just a couple days ago. I now get the following error:
File "mypyc/__main__.py", line 18, in <module>
KeyError: '__file__'
Line 18 above, i.e., the line that is failing, is just
base_path = os.path.join(os.path.dirname(__file__), '..')
which I wouldn't expect to fail. I am in my venv virtualenv when I execute mypyc using the same command as has always worked before.
I thought perhaps a regression was introduced in mypyc so I used git to go back in time to see if that line had changed in any recent version of mypy, but it hadn't.
I also tried downgrading mypy to an older version that worked before but that version also failed with the same error. To be sure it wasn't being experienced by others I also checked the issues at the mypy repo on github and did a search for __file__ to see if that part of the error message showed up and it didn't. Perhaps it is some weird issue with my environment?
I experience the issue with venv virtualenvs created with Python 3.10, 3.10.1 but also 3.9.9 too. It worked fine on Python 3.10 before. Any ideas on what to investigate next?
I am trying to install openstack Wallaby on Ubuntu 20.04. I already installed Keystone and Glance and they work as expected. But after I installed Placement and tried to verify it using 'placement-status upgrade check' I constantly get the same error.
Error:
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/oslo_upgradecheck/upgradecheck.py", line 196, in run
return conf.command.action_fn()
File "/usr/lib/python3/dist-packages/oslo_upgradecheck/upgradecheck.py", line 104, in check
result = func_name(self, **kwargs)
File "/usr/lib/python3/dist-packages/oslo_upgradecheck/common_checks.py", line 41, in check_policy_json
policy_path = conf.find_file(conf.oslo_policy.policy_file)
File "/usr/lib/python3/dist-packages/oslo_config/cfg.py", line 2543, in find_file
raise NotInitializedError()
oslo_config.cfg.NotInitializedError: call expression on parser has not been invoked
Is this normal at this stage or am I doing something wrong here?
I already checked the database connections (user and password work and database is made). And I also checked the username, password and url options in keystone_authtoken in placement.conf but I can't find what's wrong.
I also encountered this problem with Wallaby on Ubuntu 20.04. I solved it with installing Placement from PyPI instead of Ubuntu package manager so far. You should consider how implement starting Placement automatically if you install Placement from this instruction.
Install and configure Placement from PyPI
https://docs.openstack.org/placement/wallaby/install/from-pypi.html
I had the same problem so changed to Victoria, same issue. Digging about in the docs though I found the issue. The command that populate the database looks similar for Keystone, Glance and Placement but for placement the command should be 'su -s /bin/sh -c "placement-manage db sync" placement'. Notice that for placement it is 'db sync' not 'db_sync' as it is for the others. I created scripts, well actuall am using ansible and just cut and pasted between them and my guess is you have done the same. Basically as it does not run the database is empty hence the error.
Guy
I've downloaded miktex, tinytex and ghostscript and tried changing the path since the problem seems to be in the path. So far nothing has helped me and I would appreciate some help:
This is my error message:
Error: LaTeX failed to compile Uebungsblatt1_MAT183.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Uebungsblatt1_MAT183.log for more info.
In addition: Warning message:
In has_crop_tools() :
Tool(s) not installed or not in PATH: ghostcript
-> As a result, figure cropping will be disabled.
Execution halted
Any help or try to troubleshoot would be appreciated. Thank you
I have figured this out for myself by now: what I did was that I first uninstalled MikTex and tinytex because they apparently were clashing somehow. Then I reinstalled tinytex - this time typing it directly into the console instead of using the installing tool from R - so I typed everything at a time and executed it. It had me restart R and updated some files then too. Since then it has worked flawlessly. Also, I did the same on my other computer (MacBook) where it didn't work so chances are pretty good that that might solve that same problem for someone else out there. Thanks to everybody who tried helping and improved the question or sent responses.
Which code you tried to compile?
Sometimes this error rise when a letter is missed in the \begin function. If you tried to compile an array, do not forget to use the same letters as rows you need.
Example:
$$|x|=\left\{\begin{array}{ll} -x & \text{si }x\le 0\\ x & \text{si }x\ge 0 \end{array}\right.$$
I am trying to run a Julia program using Gurobi solver on Windows.
I have already set up my GUROBI_HOME in windows as C:\gurobi701\win64.
Here is the error message in Atom:
error msg
I have done the following in Julia interactive shell:
Pkg.add("Gurobi")
also
Pkg.update()
Also, I checked whether or not my gurobi license file is not properly set up by running their example:
> gurobi_cl C:\gurobi701\win64\examples\data\coins.lp
The output seems fine: output for gurobi command line
What is the possible error here?
Thanks a lot for help!!!
Today's (1 Mar 2016) OpenSSL release has caused the following error when running Plone/Zope
.buildout/eggs/ZODB3-3.10.5-py2.7-linux-x86_64.egg/persistent/cPersistence.so: undefined symbol: SSLv2_method
It's hard to see what's going on since it's a binary file. I also tried updating to ZODB3 3.11.0 which yields the following traceback
.buildout/eggs/ZConfig-2.9.0-py2.7.egg/ZConfig/loader.py", line 217, in schemaComponentSource
package=package)
ZConfig.SchemaResourceError: could not load package ZServer:
.buildout/eggs/zope.security-3.7.4-py2.7-linux-x86_64.egg/zope/security/_proxy.so: undefined symbol: SSLv2_method
Package name: 'ZServer'
File name: 'component.xml'
Package path: None
Is there any workaround for this other than reverting OpenSSL?
zope security is a compiled egg, like all the ones ending with -py2.7-linux-x86_64.egg.
As the traceback says, it cannot find anymore a symbol.
Probably you have to recompile it with the new openssl-dev.
I would try (on a development server first):
backup your compiled egg (mkdir eggs-backup && mv `eggs/zope.security-3.7.4-py2.7-linux-x86_64.egg eggs-backup/)
rerun buildout
This will recompile your missing egg.
Hopefully it works and hopefully it is the only one linked to that library.
Anyway, dependending on the way you patched openssl you may have a lot of other issues (I am thinking about Python, urllib*, curl, wget, ...)
OpenSSL 1.0.2g by default doesn't build with SSLv2 (because of the recent DROWN attack). You may need to manually build it without OPENSSL_NO_SSL2 flag.
(but in fact you shouldn't do this if you're doing some server-related stuff, there is a serious security reason because of which it was disabled, see https://drownattack.com)
I was able to resolve this by upgrading python to 2.7.10+, and then upgrading Pillow and lxml.