When running buildout with the Plone-4.3.14-version-configs, the errors below are thrown.
Getting distribution for 'feedparser==5.0.1'.
error: Not a recognized archive type: /tmp/tmpuOPdYIget_dist/feedparser-5.0.1.tar.bz2
An error occurred when trying to install /tmp/tmpuOPdYIget_dist/feedparser-5.0.1.tar.bz2. Look above this message for any errors that were output by easy_install.
While:
Installing instance.
Getting distribution for 'feedparser==5.0.1'.
An internal error occurred due to a bug in either zc.buildout or in a
recipe being used:
Traceback (most recent call last):
File "/home/ida/.virtenv/lib/python2.7/site-packages/zc/buildout/buildout.py", line 2127, in main
getattr(buildout, command)(args)
File "/home/ida/.virtenv/lib/python2.7/site-packages/zc/buildout/buildout.py", line 797, in install
installed_files = self[part]._call(recipe.install)
File "/home/ida/.virtenv/lib/python2.7/site-packages/zc/buildout/buildout.py", line 1557, in _call
return f()
File "/home/ida/.buildout/eggs/plone.recipe.zope2instance-4.2.22-py2.7.egg/plone/recipe/zope2instance/__init__.py", line 114, in install
installed.extend(self.install_scripts())
File "/home/ida/.buildout/eggs/plone.recipe.zope2instance-4.2.22-py2.7.egg/plone/recipe/zope2instance/__init__.py", line 618, in install_scripts
requirements, ws = self.egg.working_set(['plone.recipe.zope2instance'])
File "/home/ida/.buildout/eggs/zc.recipe.egg-1.3.2-py2.7.egg/zc/recipe/egg/egg.py", line 101, in working_set
**kw)
File "/home/ida/.virtenv/lib/python2.7/site-packages/zc/buildout/easy_install.py", line 924, in install
return installer.install(specs, working_set)
File "/home/ida/.virtenv/lib/python2.7/site-packages/zc/buildout/easy_install.py", line 726, in install
for dist in self._get_dist(req, ws):
File "/home/ida/.virtenv/lib/python2.7/site-packages/zc/buildout/easy_install.py", line 570, in _get_dist
dists = [_move_to_eggs_dir_and_compile(dist, self._dest)]
File "/home/ida/.virtenv/lib/python2.7/site-packages/zc/buildout/easy_install.py", line 1704, in _move_to_eggs_dir_and_compile
[tmp_loc] = glob.glob(os.path.join(tmp_dest, '*'))
ValueError: need more than 0 values to unpack
Took a moment to figure out why, because the explanation does not lie in the last error-message, but the preceding one:
Not a recognized archive type, which hints that easy_install cannot handle bunzip-files.
It means that the required sys-package bzip-devel was not present when installing Python.
So one must either install that package and install Python again, or in this case also commenting out the pin for feedparser lets the build run without errors.
Afterwards noticed that feedparser is not in the eggs-cache-dir, as it used to be in another build with same versions-configs. At a glance cannot tell the difference why, but the errors are resolved.
Related
I have downloaded QIIME2 2022.2Version from conda environment using the commands given in the qiime docs.
I have downloaded the data from NCBI SRA and imported in QIIME2 with the help of following commands
Use the manifest file to import the sequences into QIIME 2:
qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path SRA/fastq/manifest/manifest.tsv \
--output-path demux.qza \
--input-format PairedEndFastqManifestPhred33V2
I visualized the demux.qza file using-
qiime demux summarize --i-data demux.qza --o-visualization demux.qzv
The sequences are already demultiplexed and no apadpters were present but when i tried to create ASVs using DADA2 . I got the following error
-qiime dada2 denoise-paired \
--i-demultiplexed-seqs demux.qza
--p-trim-left-f 0
--p-trim-left-r 0
--p-trunc-len-f 220
--p-trunc-len-r 190
--p-n-threads 0
--output-dir work/DADA2_denoising_output
--verbose
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Command: run_dada_paired.R /tmp/tmpennq2f9g/forward /tmp/tmpennq2f9g/reverse /tmp/tmpennq2f9g/output.tsv.biom /tmp/tmpennq2f9g/track.tsv /tmp/tmpennq2f9g/filt_f /tmp/tmpennq2f9g/filt_r 220 190 0 0 2.0 2.0 2 12 independent consensus 1.0 0 1000000
R version 4.1.2 (2021-11-01)
Loading required package: Rcpp
DADA2: 1.22.0 / Rcpp: 1.0.8 / RcppParallel: 5.1.5
Filtering Error in x$yield(...) :
_DNAencode(): invalid DNAString input character: '' (byte value 4)
Execution halted
Traceback (most recent call last):
File "/home/pragya/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 279, in denoise_paired
run_commands([cmd])
File "/home/pragya/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/pragya/anaconda3/envs/qiime2-2022.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmpennq2f9g/forward', '/tmp/tmpennq2f9g/reverse', '/tmp/tmpennq2f9g/output.tsv.biom', '/tmp/tmpennq2f9g/track.tsv', '/tmp/tmpennq2f9g/filt_f', '/tmp/tmpennq2f9g/filt_r', '220', '190', '0', '0', '2.0', '2.0', '2', '12', 'independent', 'consensus', '1.0', '0', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/pragya/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py", line 339, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/home/pragya/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/pragya/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in callable_executor
output_views = self._callable(**view_args)
File "/home/pragya/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 292, in denoise_paired
raise Exception("An error was encountered while running DADA2"
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
See above for debug info.
I have looked for all the possible options but nothing worked .Can somebody help me with this.
Thanks in advanceenter image description here
I am trying to build XTK following this link on Linux running on Oracle VirtualBox to get non-minified xtk.js. I am getting following error when I tried to generate the xtk-deps.js on running deps.py file:
Generating dependency file for XTK...
Traceback (most recent call last):
File "/root/Downloads/X-master/lib/google-closure-library/closure/bin/build/depswriter.py", line 212, in <module>
main()
File "/root/Downloads/X-master/lib/google-closure-library/closure/bin/build/depswriter.py", line 196, in main
path_to_source[depspath] = source.Source(source.GetFileContents(srcpath))
File "/root/Downloads/X-master/lib/google-closure-library/closure/bin/build/source.py", line 126, in GetFileContents
return fileobj.read()
File "/usr/lib/python2.7/codecs.py", line 668, in read
return self.reader.read(size)
File "/usr/lib/python2.7/codecs.py", line 474, in read
newchars, decodedbytes = self.decode(data, self.errors)
File "/usr/lib/python2.7/encodings/utf_8_sig.py", line 104, in decode
return codecs.utf_8_decode(input, errors)
UnicodeDecodeError: 'utf8' codec can't decode byte 0x9a in position 4584: invalid start byte
Could not generate dependency file.
Could anybody please explain why this error is coming.
There's probably some non-uft8 characters in your code (most likely in X.js).
Take my experience for example, in the X.js of XTK, I found there's a non-English word (maybe a German or French name) in line #210. What I did is to delete the character and run build.py again. The encode error didn't appear again.
What worked for me is that I used an earlier commit of google closure library for building XTK and it worked perfectly.
I had to search XTK's commit history extensively to know which version of closure library they were using to build it.
PS: Earlier I posted similar solution here. But the post was deleted by moderator so sharing it here again.
We recently got a new Linux machine that got re-imaged from our older machine where our current plone installation resides. I am trying to run buildout on the new machine but I am getting this AssertionError on our plonetheme src product.
Installing 'buildout.dumppickedversions', 'buildout.sanitycheck'.
We have the distribution that satisfies 'buildout.dumppickedversions==0.5'.
Picked: buildout.sanitycheck = 1.0b1
Develop: '/var/db/zope/plone43/zeocluster/src/products.okctypes'
in: '/var/db/zope/plone43/zeocluster/src/products.okctypes'
/tmp/tmpVPeu_l -q develop -mxN -d /var/db/zope/plone43/zeocluster/develop-eggs/tmp4eer1vbuild
Develop: '/var/db/zope/plone43/zeocluster/src/plonetheme.ourtheme'
in: '/var/db/zope/plone43/zeocluster/src/plonetheme.ourtheme'
/tmp/tmppWGq8Z -q develop -mxN -d /var/db/zope/plone43/zeocluster/develop-eggs/tmpUl2ukSbuild
No local packages or download links found for PasteScript
Traceback (most recent call last):
File "/tmp/tmppWGq8Z", line 11, in <module>
execfile('/var/db/zope/plone43/zeocluster/src/plonetheme.ourtheme/setup.py')
File "/var/db/zope/plone43/zeocluster/src/plonetheme.ourtheme/setup.py", line 37, in <module>
paster_plugins=["ZopeSkel"],
File "/var/db/zope/plone43/Python-2.7/lib/python2.7/distutils/core.py", line 112, in setup
_setup_distribution = dist = klass(attrs)
File "/var/db/zope/plone43/buildout-cache/eggs/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 221, in __init__
self.fetch_build_eggs(attrs.pop('setup_requires'))
File "/var/db/zope/plone43/buildout-cache/eggs/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 245, in fetch_build_eggs
parse_requirements(requires), installer=self.fetch_build_egg
File "/var/db/zope/plone43/buildout-cache/eggs/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 580, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/var/db/zope/plone43/buildout-cache/eggs/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 825, in best_match
return self.obtain(req, installer) # try and download/install
File "/var/db/zope/plone43/buildout-cache/eggs/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 837, in obtain
return installer(requirement)
File "/var/db/zope/plone43/buildout-cache/eggs/distribute-0.6.28-py2.7.egg/setuptools/dist.py", line 294, in fetch_build_egg
return cmd.easy_install(req)
File "/var/db/zope/plone43/buildout-cache/eggs/distribute-0.6.28-py2.7.egg/setuptools/command/easy_install.py", line 592, in easy_install
raise DistutilsError(msg)
distutils.errors.DistutilsError: Could not find suitable distribution for Requirement.parse('PasteScript')
While:
Installing.
Processing develop directory '/var/db/zope/plone43/zeocluster/src/plonetheme.ourtheme'.
An internal error occurred due to a bug in either zc.buildout or in a
recipe being used:
Traceback (most recent call last):
File "/var/db/zope/plone43/buildout-cache/eggs/zc.buildout-1.7.1-py2.7.egg/zc/buildout/buildout.py", line 1866, in main
getattr(buildout, command)(args)
File "/var/db/zope/plone43/buildout-cache/eggs/zc.buildout-1.7.1-py2.7.egg/zc/buildout/buildout.py", line 487, in install
installed_develop_eggs = self._develop()
File "/var/db/zope/plone43/buildout-cache/eggs/zc.buildout-1.7.1-py2.7.egg/zc/buildout/buildout.py", line 727, in _develop
zc.buildout.easy_install.develop(setup, dest)
File "/var/db/zope/plone43/buildout-cache/eggs/zc.buildout-1.7.1-py2.7.egg/zc/buildout/easy_install.py", line 1184, in develop
*args) == 0
AssertionError
*************** PICKED VERSIONS ****************
[versions]
*************** /PICKED VERSIONS ***************
Our Product's init.py script contains the following:
# See http://peak.telecommunity.com/DevCenter/setuptools#namespace-packages
try:
__import__('pkg_resources').declare_namespace(__name__)
except ImportError:
from pkgutil import extend_path
__path__ = extend_path(__path__, __name__)
I've seen a similar error reported here but the answer provided does not apply to our case. We have other products in src but this is the only one causing problems.
Can someone please help us with this error?
Check the setup.py file in your theme package. You'll likely find:
# The next two lines may be deleted after you no longer need
# addcontent support from paster and before you distribute
# your package.
setup_requires=["PasteScript"],
paster_plugins = ["ZopeSkel"],
Remove those lines. They are included in the generated template for your package so that you may use Zopeskel local commands to add new functionality. You don't need it after development, and it's often a source of problems later.
The alternative solution, as mentioned in the comments, is to make sure you have the right egg in your local buildout cache. But why have old development packages sitting around on a live site?
According to the directions of Openstack Official Heat/Plugins wiki https://wiki.openstack.org/wiki/Heat/Plugins, we only need "To install a plugin, copy the Python modules to one of the configured plugin directories. Note that heat-engine must be restarted after this in order to load the new plugins.". But I hit the following error messages after I restart heat-engine..
[root#cs14 heat]# heat-engine
2015-05-04 06:02:09.774 20839 WARNING heat.common.config [-] HT-A65A0DF The "instance_user" option in heat.conf is deprecated and will be removed in the Juno release.
[05/04/2015 06:02:10 EDT]heatCRITICAL : ImportError: No module named my_heat_plugin.client
Traceback (most recent call last):
File "/usr/bin/heat-engine", line 67, in <module>
srv = engine.EngineService(cfg.CONF.host, rpc_api.ENGINE_TOPIC)
File "/usr/lib/python2.6/site-packages/heat/engine/service.py", line 288, in __init__
resources.initialise()
File "/usr/lib/python2.6/site-packages/heat/engine/resources/__init__.py", line 44, in initialise
_load_global_environment(global_env)
File "/usr/lib/python2.6/site-packages/heat/engine/resources/__init__.py", line 49, in _load_global_environment
_load_global_resources(env)
File "/usr/lib/python2.6/site-packages/heat/engine/resources/__init__.py", line 54, in _load_global_resources
manager = plugin_manager.PluginManager(__name__)
File "/usr/lib/python2.6/site-packages/heat/engine/plugin_manager.py", line 58, in __init__
self.modules = list(modules())
File "/usr/lib/python2.6/site-packages/heat/common/plugin_loader.py", line 91, in load_modules
module = _import_module(importer, module_name, package)
File "/usr/lib/python2.6/site-packages/heat/common/plugin_loader.py", line 72, in _import_module
module = loader.load_module(module_name)
File "/usr/lib64/python2.6/pkgutil.py", line 238, in load_module
mod = imp.load_module(fullname, self.file, self.filename, self.etc)
File "/usr/lib/heat/abc_heat_plugin/resources/abc/abc_server.py", line 24, in <module>
from abc_heat_plugin.client import constants as const
ImportError: No module named abc_heat_plugin.client
To solve this problem, I've figured out two ways which are workable.
Method 1. copy abc_heat_plugin to /usr/lib/python2.6/site-packages and restart heat-engine
Method 2. use .pth file.
1) Create a file /usr/lib/python2.6/site-packages/.pth with the following three lines (no need to do this if it exists)
/usr/lib/heat
/usr/lib/heat/abc_heat_plugin
/usr/lib/heat/abc_heat_plugin/client
2) copy plugin "my_heat_plugin" to /usr/lib/heat
3) restart heat service
BUT both ways have to do more than the official guide, so I wonder whether I missed anything important. Any suggestions? Thanks.
(BTW, my_heat_plugin is working well.)
I think the basic idea is that you drop the resource in /usr/lib/heat, but any modules or packages that are used by the resource must be installed the usual way. You sort of did that manually by moving the files to site-packages.
Take a look at any of the plugins in heat/contrib for example. There are a few that have dependencies such as clients to other OpenStack services, and in all cases the assumption is made that those clients were installed separately.
So if you can, just create a setup.py for your client package, and install that separately from the heat plugin.
I'm new to plone and im trying to get the send as PDF add on to work. I have added:
pisa
pyPdf
html5lib
reportlab
to the buildout file and have configured the collective.sendaspdf send as PDF add-on. Whenever I try click on the send as PDF option, it does nothing. Help will be appreciated.
The traceback in the error log has the following information:
Exception Value
'ascii' codec can't decode byte 0xe2 in position 8192: ordinal not in range(128)
Traceback (innermost last):
Module ZPublisher.Publish, line 126, in publish
Module ZPublisher.mapply, line 77, in mapply
Module ZPublisher.Publish, line 46, in call_object
Module jquery.pyproxy.plone, line 66, in _jquery
Module collective.sendaspdf.browser.ajax, line 56, in show_send_form
Module collective.sendaspdf.browser.ajax, line 44, in _show_send_form
Module collective.sendaspdf.browser.base, line 237, in make_pdf
Module collective.sendaspdf.browser.base, line 223, in generate_pdf_file
Module collective.sendaspdf.transforms.pisa, line 16, in html_to_pdf
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 8192: ordinal not in range(128)
When I try to install wkhtmltopdf through build out by using bin/buildout after modifying the buildout.cfg file, I get the following error:
While:
Installing.
Error: Missing option: buildout:parts
****** PICKED VERSIONS *******
[versions]
****** /PICKED VERSIONS ******
I have done everything it says in this link: https://github.com/vincent-psarga/collective.sendaspdf
I have made the following changes in my buildout file(buildout.cfg):
parts =
instance
zopepy
zopeskel
unifiedinstaller
repozo
backup
chown
wkhtmltopdf
wkhtmltopdf_executable
environment-vars =
zope_i18n_compile_mo_files true
PYTHON_EGG_CACHE ${buildout:directory}/var/.python-eggs
WKHTMLTOPDF_PATH ${buildout:directory}/wkhtmltopdf
[wkhtmltopdf]
recipe = hexagonit.recipe.download
url = http://wkhtmltopdf.googlecode.com/files/wkhtmltopdf-0.9.9-static-amd64.tar.bz2
[wkhtmltopdf_executable]
recipe = collective.recipe.cmd
on_install = true
on_update = true
cmds =
cd ${buildout:directory}/parts/wkhtmltopdf
mv wkhtmltopdf-amd64 wkhtmltopdf
chmod +x wkhtmltopdf
Can you please tell me what I did wrong?. Help will be deeply appreciated. Thank you
I'm the main developer of Send as PDF. One simple question: do you really need to use Pisa/report lab ?
I've added it at the beginning of the tool development but the support for this PDF generator will be dropped soon (wkhtmltopdf works like a charm and it's a bit hard to maintain both supports).
If you look at the product's README, there is explanations for installing WKHtmlToPDF: https://github.com/vincent-psarga/collective.sendaspdf
I strongly suggest you to use this tool, there's more options for it than what you would have with Pisa.
If you really need Pisa/reportlab, I'll take a look at the issue anyway ;)
Cheers,
Vincent
Looking over the source code I think you have hit a bug here.
The code expects the HTML being input to be a unicode string, but this is not the case for you, and re-encoding it to ASCII fails.
You'll need to file a bug report with your traceback in the collective.sendaspdf issue tracker on GitHub.