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.
Related
For setting up AWS MWAA with snowflake, as per the AWS documentation here, I created a requirements.txt file with following content:
--constraint "https://raw.githubusercontent.com/apache/airflow/constraints-2.2.2/constraints-3.7.txt"
apache-airflow[snowflake]
This worked successfully. Next I wanted to add dbt to my eco-system and updated my constraint file to:
--constraint "https://raw.githubusercontent.com/apache/airflow/constraints-2.2.2/constraints-3.7.txt"
apache-airflow[snowflake]
dbt-core==1.1.1
dbt-snowflake==1.1.0
Now this is where things start breaking. I get the following error when I build this-
ERROR: Cannot install snowflake-connector-python[secure-local-storage]==2.7.0 because these package versions have conflicting dependencies.
The conflict is caused by:
snowflake-connector-python[secure-local-storage] 2.7.0 depends on keyring!=16.1.0 and <22.0.0; extra == "secure-local-storage"
The user requested (constraint) keyring==23.2.1
This seems really weird since both versions: snowflake-connector-python 2.7.0 and keyring==23.2.1 are enforced in the airflow constraint file itself: https://raw.githubusercontent.com/apache/airflow/constraints-2.2.2/constraints-3.7.txt
It is highly unlikely that airflow constraint file is incorrect. Am I missing something here?
Yes, I guess there are some inconsistencies and version conflicts. What I ended up doing is copying all libraries from constraints.txt to requirements.txt, removing unused libraries and run ./mwaa-local-env test-requirements to check for inconsistencies.
Then I manually changed versions of all version conflicts.
Details
I am getting a build failure of my read-the-docs that I don't understand. The assertion of "verbatim" in line 2151 of nbsphinx.py is causing the build failure. So the build fails when I try to include the Jupyter Notebook tutorials I created. I compared current versions of the tutorials to previous versions which had not caused the build to fail, and I can't find a difference that could account for the current failure.
Read the Docs project URL: lofti_gaia
Build URL: https://github.com/logan-pearce/lofti_gaia
Read the Docs username: logan-pearce
Expected Result
A passing build including *.ipynb files
Actual Result
Build failed at line 2151 of nbsphinx.py due to assertion of 'Verbatim' failing.
Terminal output:
Running Sphinx v4.1.2
loading translations [en]... done
making output directory... done
WARNING: html_static_path entry '_static' does not exist
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [latex]: all documents
updating environment: 0 added, 0 changed, 0 removed
looking for now-outdated files... none found
processing lofti_gaia.tex... index installation tutorials/QuickStart tutorials/Tutorial api lofti loftitools
resolving references...
done
writing... failed
Exception occurred:
File "/home/docs/checkouts/readthedocs.org/user_builds/lofti-gaia/conda/latest/lib/python3.7/site-packages/nbsphinx.py", line 2151, in depart_codearea_latex
assert 'Verbatim' in lines[0]
AssertionError
The full traceback has been saved in /tmp/sphinx-err-x1h83s3m.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!
According to the github issue 584 for nbsphinx (https://github.com/spatialaudio/nbsphinx/issues/584), this is due to a compatibility issue with sphinx 4.1.0. It can be gotten around by requiring sphinx version 4.0.2.
So in my requirements.txt file, I included sphinx==4.0.2, after which the build passes. So now my requirements.txt file looks like:
numpy
matplotlib
astropy>=4.0.1.post1
astroquery>=0.4
sphinx==4.0.2
ipython==7.19.0
nbsphinx>=0.8.6
and the build passes.
I have encountered the same issue. I did not solve it with .ipynb format, but converting the jupyter notebook to .rst format works.
May it helps
Reaching out to the wider group as I am totally stumped trying to install Intel MPSS 4.x for my Xeon Phi 7220P.
I followed the precise steps in this link: Intel MPSS Linux User Guide Rev 4.4.1, and did it 3 times to make sure I wasn't missing any steps or making mistakes, but keep getting the following error readout:
modprobe: WARNING: Module mic_x200_dma not found.
modprobe: WARNING: Module scif_bus not found.
modprobe: WARNING: Module vop_bus not found.
modprobe: WARNING: Module cosm_bus not found.
modprobe: WARNING: Module scif not found.
modprobe: WARNING: Module vop not found.
modprobe: WARNING: Module mic_cosm not found.
modprobe: WARNING: Module mic_x200 not found.
As a result of this, I cant do the basic MPSS commands such as micctrl -s etc nor use the Xeon Phi whatsoever.
I am running Centos 7 (862 kernel), and know its not listed in the Intel pdf, but did not think this should be causing an issue as it seems that the above kernel modules are simply not being installed seemingly from Intel MPSS - but not sure if this diagnosis is correct.
Would appreciate your help - many thanks in advance!
It is complaining about that because at one point your kernel got updated from 3.10.0-514.el7 to a later version, (it happens automatically when you do a yum update, annoying I know)
Check your kernel version by running
uname -r
When you installed/compiled all the modules they were placed into /lib/modules/3.10.0-514.el7.x86_64 which is where the source code you have exported to.
You have 2 options:
Recompile the source code to work for your current kernel version (which is a pain and has it's own problems)
Revert your host kernel back to 3.10.0-514.el7 via grub config (example here) and everything will work nicely
I too struggled with this very much in the beginning and I had to read pretty much every line of source code and spend countless hours debugging until I found out. At this point there is nothing I do not know about the Xeon Phi x100/x200.
The documentation is not bad, but it didn't cover this bare essential, which is frustrating.
I am following these instructions(https://www.digitalocean.com/community/tutorials/how-to-install-and-use-graphite-on-an-ubuntu-14-04-server)
to install statsd and graphite, but am running into below stated problem. Seems like this is not a graphite issue but python issue. Does anybody know how to resolve this?
~/build > sudo service carbon-cache start
* Starting Graphite backend daemon carbon-cache
Traceback (most recent call last):
File "/usr/bin/carbon-cache", line 32, in <module>
run_twistd_plugin(__file__)
File "/usr/lib/python2.7/dist-packages/carbon/util.py", line 90, in run_twistd_plugin
config.parseOptions(twistd_options)
File "/usr/local/lib/python2.7/dist-packages/twisted/application/app.py", line 604, in parseOptions
usage.Options.parseOptions(self, options)
File "/usr/local/lib/python2.7/dist-packages/twisted/python/usage.py", line 269, in parseOptions
raise UsageError("Unknown command: %s" % sub)
twisted.python.usage.UsageError: Unknown command: carbon-cache
I was following the same instructions and encountered the same problem.
Moving or removing the /usr/local/lib/python2.7/dist-packages/twisted directory also resolved the issue for me.
You can use for example the following command to change the name of the problematic directory:
mv /usr/local/lib/python2.7/dist-packages/twisted /usr/local/lib/python2.7/dist-packages/twisted2
Then use sudo service carbon-cache start again
Background
I had the same issue on my Ubuntu 14.04 machine. Some investigation indicates that there are two virtually identical areas for twisted plugins on my machine.
/usr/local/lib/python2.7/dist-packages/twisted
and
/usr/lib/python2.7/dist-packages/twisted
I am not sure where these two areas originate from. Perhaps one comes with the distro and the other is created through a manual pip install twisted that I may have done at one time. I suspect that the /usr/local/lib/python2.7/dist-packages/ area gets populated with content when I install packages using pip. So this problem my eventually be attributed to users (e.g. me) installing twisted via pip and via the apt package system.
In any case, a diff through these areas showed that the carbon related files were installed into the /usr/lib/python2.7/dist-packages/ area. dpkg -L graphite-carbon also indicates that the package files go into the /usr/lib/python2.7/dist-packages/ area.
However, when the carbon start script is run is appears that /usr/local/lib/python2.7/dist-packages/twisted/plugins area is used leading to the plugin not being found.
I assume that this issue is related to the modules search path. As can be seen below the /usr/local/lib/python2.7/dist-packages/ comes before the /usr/lib/python2.7/dist-packages/ in my default path.
$ python
Python 2.7.6 (default, Mar 22 2014, 22:59:56)
[GCC 4.8.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> sys.path
['',
'/usr/lib/python2.7',
'/usr/lib/python2.7/plat-x86_64-linux-gnu',
'/usr/lib/python2.7/lib-tk',
'/usr/lib/python2.7/lib-old',
'/usr/lib/python2.7/lib-dynload',
'/usr/local/lib/python2.7/dist-packages',
'/usr/lib/python2.7/dist-packages',
'/usr/lib/python2.7/dist-packages/PILcompat',
'/usr/lib/python2.7/dist-packages/gtk-2.0',
'/usr/lib/pymodules/python2.7',
'/usr/lib/python2.7/dist-packages/ubuntu-sso-client']
>>>
for some reason twisted was messing up something with graphite.
read on the internet that manually removng twisted solves the problem.
Tried it and it works now
just did
sudo rm -rf /usr/local/lib/python2.7/dist-packages/twiste*
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!