Errors during transaction when installing QIIME2-2019.10

Technical Support
4

Hi @yanxianl,

Try

conda remove --name qiime2-2019.10 --all

to remove the environment and then re-install.

Best,
Justine

1 Like
5

Hi Justine, I tried your suggested command and it returned an error:

Remove all packages in environment /home/nutrition_group/miniconda3/envs/qiime2-2019.10:
PackagesNotFoundError: The following packages are missing from the target environment: -

The QIIME2 installation guides didn't help either:

If you receive errors during the installation process, such as gfortran errors, please ensure you are following the installation instructions that are compatible with your platform. Other errors are often resolved by running conda env remove -n qiime2-2019.10 to remove the failed environments, then running conda clean -y --all to clean the local conda installation, and finally re-running the installation instructions above.

6

Sorry for my stupid question - did you restart your computer after miniconda/anaconda installation and before trying to install Qiime2?

7

Just tried restarting the PC before and after installing the miniconda, and tried to install qiime2-2019.10 again. Still, no luck though. Thanks!

9

Hey @yanxianl,

Based on the first error message, it looks like something went wrong with the TLS handshake, sometimes that's because a server is misconfigured, your OS isn't up to date, or there's a firewall preventing access.

The three URLS being downloaded seem to be coming from different hosts (mostly)

So my guess is it's a firewall situation. Are you able to click and download those links manually, and do you see anything like a redirect when you do so?

That test doesn't help us install anything, but it'll help us figure out the network situation.

11

Hello,

I am trying to natively install qiime2-2019.7 on my Mac OS High Sierra. I ran the command below:

conda env create -n qiime2-2019.7 --file qiime2-2019.7-py36-osx-conda.yml

The error message I keep getting is as follows

conda env create -n qiime2-2019.7 --file qiime2-2019.7-py36-osx-conda.yml
Collecting package metadata (repodata.json): done
Solving environment: done
Preparing transaction: done
Verifying transaction: done
Executing transaction: / b'Enabling notebook extension jupyter-js-widgets/extension...\n - Validating: \x1b[32mOK\x1b[0m\n'
done
ERROR conda.core.link:_execute(700): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.1-r351_0'.
Rolling back transaction: done
class: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.1-r351_0
location of failed script: /Users/ylor/miniconda3/envs/qiime2-2019.7/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==

==> script output <==
stdout: ERROR: post-link.sh was unable to download any of the following URLs with the md5sum 2fd536521151e2ff37217b5cfee8cec4:
https://bioconductor.org/packages/3.9/data/annotation/src/contrib/GenomeInfoDbData_1.2.1.tar.gz
https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.1.tar.gz
https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.1_src_all.tar.gz

stderr: % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
curl: (60) SSL certificate problem: unable to get local issuer certificate
More details here: curl - SSL CA Certificates

curl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
curl: (60) SSL certificate problem: unable to get local issuer certificate
More details here: curl - SSL CA Certificates

curl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
curl: (60) SSL certificate problem: unable to get local issuer certificate
More details here: curl - SSL CA Certificates

curl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.

return code: 1

kwargs:
{}

Traceback (most recent call last):
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1074, in call
return func(*args, **kwargs)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda_env/cli/main.py", line 78, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda_env/cli/main_create.py", line 102, in execute
result[installer_type] = installer.install(prefix, pkg_specs, args, env)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda_env/installers/conda.py", line 32, in install
unlink_link_transaction.execute()
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/core/link.py", line 249, in execute
self._execute(tuple(concat(interleave(itervalues(self.prefix_action_groups)))))
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/core/link.py", line 716, in _execute
rollback_excs,
conda.CondaMultiErrorclass: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.1-r351_0
location of failed script: /Users/ylor/miniconda3/envs/qiime2-2019.7/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==

==> script output <==
stdout: ERROR: post-link.sh was unable to download any of the following URLs with the md5sum 2fd536521151e2ff37217b5cfee8cec4:
https://bioconductor.org/packages/3.9/data/annotation/src/contrib/GenomeInfoDbData_1.2.1.tar.gz
https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.1.tar.gz
https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.1_src_all.tar.gz

stderr: % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
curl: (60) SSL certificate problem: unable to get local issuer certificate
More details here: curl - SSL CA Certificates

curl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
curl: (60) SSL certificate problem: unable to get local issuer certificate
More details here: curl - SSL CA Certificates

curl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
curl: (60) SSL certificate problem: unable to get local issuer certificate
More details here: curl - SSL CA Certificates

curl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.

return code: 1

kwargs:
{}

: <exception str() failed>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Users/ylor/miniconda3/bin/conda-env", line 7, in
sys.exit(main())
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda_env/cli/main.py", line 89, in main
return conda_exception_handler(do_call, args, parser)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1366, in conda_exception_handler
return_value = exception_handler(func, *args, **kwargs)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1077, in call
return self.handle_exception(exc_val, exc_tb)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1108, in handle_exception
return self.handle_application_exception(exc_val, exc_tb)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1124, in handle_application_exception
self._print_conda_exception(exc_val, exc_tb)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1128, in _print_conda_exception
print_conda_exception(exc_val, exc_tb)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1051, in print_conda_exception
stderrlog.error("\n%r\n", exc_val)
File "/Users/ylor/miniconda3/lib/python3.7/logging/init.py", line 1407, in error
self._log(ERROR, msg, args, **kwargs)
File "/Users/ylor/miniconda3/lib/python3.7/logging/init.py", line 1514, in _log
self.handle(record)
File "/Users/ylor/miniconda3/lib/python3.7/logging/init.py", line 1523, in handle
if (not self.disabled) and self.filter(record):
File "/Users/ylor/miniconda3/lib/python3.7/logging/init.py", line 751, in filter
result = f.filter(record)
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/gateways/logging.py", line 60, in filter
record.msg = record.msg % new_args
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/init.py", line 123, in repr
errs.append(e.repr())
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/init.py", line 62, in repr
return '%s: %s' % (self.class.name, text_type(self))
File "/Users/ylor/miniconda3/lib/python3.7/site-packages/conda/init.py", line 81, in str
return text_type(self.message % self._kwargs)
ValueError: unsupported format character 'T' (0x54) at index 684

I have tried deleting and installing miniconda multiple times as well as deleting and downloading the qiime2-2019.7-py36-osx-conda.yml file multiple times to no avail. I have also tried downloading the file not being downloaded and unpacking that by hand, but that does not work either.

Any suggestions would be greatly appreciated!

Thank you.

12

Hey @ylor,

I believe @yanxianl is having an identical issue right now, so I’m going to merge this thread into that one (noting that your QIIME 2 version is 2019.7 instead of .10)

13

So we have two examples of this error now. It appears that @ylor is able to download those files manually, which suggests it may not be strictly a network problem.

Summarizing some observations:

@ylor is on OS X High Sierra
@yanxianl appears to be on Linux of some variety

The error isn't the post-link like I thought at first, it's the source that it can't find.

Slightly different TLS errors:

Both are from curl, which might be stale (I don't know if conda uses curl or libcurl directly).

14

Hi Evan, I’m using ubuntu 14.04. I was able to download the first and third package manually by clicking on the links in the terminal. The link of the second package, however, returned a 404 Not Found error.

Based on your suggestion that this could be a firewall problem, I turned off the firewall by running sudo ufw disable and tried installing qiime2-2019.10 again but I got the same error message.

15

Hi all,

I missed yanxianl's post when I was searching the forum. Thank you for pointing it out, Evan.

I did get an error with the wget command to manually download the .yml file. I was able to download the .yml file by using the --no-check-certificate suggestion and by downloading the .yml file directly by clicking the link provided in the qiime2 docs for if an error is encountered with wget. See below for my wget error.

wget https://data.qiime2.org/distro/core/qiime2-2019.10-py36-osx-conda.yml

--2019-11-14 10:36:02-- https://data.qiime2.org/distro/core/qiime2-2019.10-py36-osx-conda.yml

Resolving data.qiime2.org... 52.35.38.247

Connecting to data.qiime2.org|52.35.38.247|:443... connected.

ERROR: cannot verify data.qiime2.org's certificate, issued by '[email protected],CN=A10_RES2_SSLi_Cert,OU=ESN,O=Department of the Interior,L=Reston,ST=VA,C=US':

Unable to locally verify the issuer's authority.

To connect to data.qiime2.org insecurely, use `--no-check-certificate'.

How would I resolve this source issue? When I look in my ./miniconda3/pkgs/, the bioconductor-genomeinfodbdata-1.2.0-r351_0.tar.bz2 file does exist and is unpacked already, so how can it not find the source?

Thanks.

16

Hello,

I totally got the same problem with yanxianl. Mine is also Ubuntu 14.04.
Is there any chance to this 2019.10 release can cause the trouble in Ubuntu 14.04?

Preparing transaction: done
Verifying transaction: done
Executing transaction: - Enabling notebook extension jupyter-js-widgets/extension...
- Validating: OK

done
ERROR conda.core.link:_execute(700): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.1-r351_0'.
Rolling back transaction: done
Traceback (most recent call last):
File "/miniconda2/bin/conda-env", line 7, in
sys.exit(main())
File "/miniconda2/lib/python2.7/site-packages/conda_env/cli/main.py", line 89, in main
return conda_exception_handler(do_call, args, parser)
File "/miniconda2/lib/python2.7/site-packages/conda/exceptions.py", line 1366, in conda_exception_handler
return_value = exception_handler(func, *args, **kwargs)
File "/miniconda2/lib/python2.7/site-packages/conda/exceptions.py", line 1077, in call
return self.handle_exception(exc_val, exc_tb)
File "/miniconda2/lib/python2.7/site-packages/conda/exceptions.py", line 1108, in handle_exception
return self.handle_application_exception(exc_val, exc_tb)
File "/miniconda2/lib/python2.7/site-packages/conda/exceptions.py", line 1124, in handle_application_exception
self._print_conda_exception(exc_val, exc_tb)
File "/miniconda2/lib/python2.7/site-packages/conda/exceptions.py", line 1128, in _print_conda_exception
print_conda_exception(exc_val, exc_tb)
File "/miniconda2/lib/python2.7/site-packages/conda/exceptions.py", line 1051, in print_conda_exception
stderrlog.error("\n%r\n", exc_val)
File "/miniconda2/lib/python2.7/logging/init.py", line 1200, in error
self._log(ERROR, msg, args, **kwargs)
File "/miniconda2/lib/python2.7/logging/init.py", line 1293, in _log
self.handle(record)
File "/miniconda2/lib/python2.7/logging/init.py", line 1302, in handle
if (not self.disabled) and self.filter(record):
File "/miniconda2/lib/python2.7/logging/init.py", line 617, in filter
if not f.filter(record):
File "/miniconda2/lib/python2.7/site-packages/conda/gateways/logging.py", line 60, in filter
record.msg = record.msg % new_args
File "/miniconda2/lib/python2.7/site-packages/conda/init.py", line 142, in repr
return '%s: %s' % (self.class.name, self.unicode())
File "/miniconda2/lib/python2.7/site-packages/conda/init.py", line 137, in unicode
errs.append(e.repr())
File "/miniconda2/lib/python2.7/site-packages/conda/init.py", line 75, in repr
return '%s: %s' % (self.class.name, self.unicode())
File "/miniconda2/lib/python2.7/site-packages/conda/init.py", line 71, in unicode
res = '%s' % (new_message % new_kwargs)
ValueError: unsupported format character 'T' (0x54) at index 674

17

Thanks for the additional details everyone!

Right now I am thinking this is a client-side issue with certificates. Since @yanxianl and @junkim83 are on Ubuntu 14.04 this isn’t very surprising. Cryptography on the web doesn’t move as fast as some things, but it does tend to improve year over year, so a five year old distribution of Ubuntu is probably missing some things that allow it to complete the TLS handshake. Is updating to Ubuntu 18.04 an option? That is the currently support LTS release.

I suspect @ylor’s situation is somewhat similar in that, while their OS X should be plenty up to date, likely the version of curl being used is stale and/or not looking in the right place in OS X. @ylor, what does:

which curl

tell you?

1 Like
18

Hi Evan,

I was wondering about whether it had something to do with the curl version I was currently using also...

which curl gives me /usr/bin/curl

If you're interested in the specific curl version:
curl -V

curl 7.54.0 (x86_64-apple-darwin17.0) libcurl/7.54.0 LibreSSL/2.0.20 zlib/1.2.11 nghttp2/1.24.0

Protocols: dict file ftp ftps gopher http https imap imaps ldap ldaps pop3 pop3s rtsp smb smbs smtp smtps telnet tftp

Features: AsynchDNS IPv6 Largefile GSS-API Kerberos SPNEGO NTLM NTLM_WB SSL libz HTTP2 UnixSockets HTTPS-proxy

19

Hi Evan, upgrading the Ubuntu to 18.04 is not an option at the moment. We’ll have to do that months later. Do you think using an older version of miniconda allows for installation of previous qiime2 version, say qiime2-2019.7?

20

A quick update: I was able to install and run qiime2-2019.4. Installing newer versions, qiime2-2019.7 and qiime2-2019.10 threw the same error that I posted. For now, I’ll stick with qiime2-2019.4 and update the ubuntu to 18.04 later.

2 Likes
21

Update: On Ubuntu 18.04 LTS, I got same error which is I got on Ubuntu 14.04 LTS. Now, I solved. In my case, it was firewall. Not on my system, it was on my institute’s policy. I contacted to IT guys and asked them to check the firewall during my installation and they found so many addresses (even qiime2.org) are blocked by their new firewalls (actually they said it is https something, I did not understand exactly but it was sort of firewalls). Anyway, IT guy released those address which cause the bad or failed handshaking and Now I installed Qiime2-2019.10 successfully both on Ubuntu 18.04 LTS and 14.04 LTS.

@yanxianl, if you are also in sort of institute, university or company, you can try contact IT guy on your workplace. maybe it will help.

2 Likes
22

Hi @junkim83, thanks for sharing your solution! Now I suspect that I may have the exact same problem as we just recently changed the network connection of our linux machine. I'll get in touch with the IT department at our University and see what happens.

1 Like
23

Hi all,

I believe it is a network firewall issue for me as well. My IT guys said that the issue could be because of the new SSL decryptions recently implemented which is blocking some previously working access. I was able to natively install qiime2-2019.7 while off my work network just fine.

2 Likes