OpenSSL migration #13958

dpryan79 · 2019-03-07T23:19:04Z

@bioconda/all Thanks to conda-forge largely finishing their migration to OpenSSL 1.1.1, we've now upgraded the bioconda-wide pinnings to match.

Why was this done?

There has been a recent spate of people running into cryptic error messages due to using conda install and it upgrading OpenSSL on them. Recently a new minor release of OpenSSL (1.1.1) was made available in the conda-forge and defaults channels and this version is not compatible with our previous project-wide pinnings (to 1.0.2). Since OpenSSL is typically among the packages in conda config --show aggressive_update_packages and therefore automatically updated upon using conda install, this version change resulted in tools such as samtools no longer having a compatible OpenSSL if they were installed into an environment already before conda install was used to install a package not itself pinned to a compatible OpenSSL version.

What do we need to do now?

We (the core team) have already taken care of updating the most commonly used packages that make use of OpenSSL (samtools, htslib, pysam, etc.), but if you have other packages you're using that you'd like to ensure are compatible with our updated pinnings then use bioconda-utils update-pinning as layed out in the documentation. If you have not already updated your applicable recipes for the recent compiler change change to GCC7 and clang, then not that that will be done at the same time (for more on that, see #13578 ).

We hope this will alleviate the pain many have experienced when faced with cryptic libcrypto-related errors upon using conda install.

As always, please feel free to open an issue and/or ping @bioconda/core if you run into problems.

The text was updated successfully, but these errors were encountered:

jbelyeu · 2019-03-09T00:43:06Z

I'm still having a related issue. Installing with conda works fine, but the samtools package is still pointing to libcrypto.so.1.0.0. Similar to PacificBiosciences/pbbioconda#85

Example:
`
$ samtools

samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

$ openssl version

OpenSSL 1.1.1b 26 Feb 2019

$ conda --version

conda 4.6.7
`

dpryan79 · 2019-03-09T00:47:48Z

What does conda list | grep samtools show?

jbelyeu · 2019-03-09T02:10:04Z

conda list | grep samtools
samtools                  1.9                  hb029021_5    bioconda

dpryan79 · 2019-03-09T08:32:23Z

You'll need to conda install samtools, there are more recent builds against the updated OpenSSL.

jbelyeu · 2019-03-09T20:36:22Z

Ok, great, working now.

ghost · 2019-03-11T13:17:11Z

Hi Devon,

Despite trying to follow your advice mine is still not working.

I get the following error message:

(base) ralphs-imac:~ ralphstadhouders$ samtools
dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib
Referenced from: /Users/ralphstadhouders/bioinformatics/anaconda2/bin/samtools
Reason: image not found
Abort trap: 6

This is what conda list | grep samtools shows:

(base) ralphs-imac:~ ralphstadhouders$ conda list | grep samtools
samtools 1.9 hb029021_5 bioconda

Running conda install samtools just ends in telling me that everything is up to date.

Thanks in advance,
Ralph

bgruening · 2019-03-11T13:20:26Z

@RStadhouders the version you need to install is samtools-1.9-h7c4ea83_11 to the 11 build number. Also try to not install into your root/base environment, always use conda create -n samtools samtools for example.

Hope that helps!

ghost · 2019-03-11T13:56:22Z

Thanks Björn! It’s strange (although I have the feeling I’m forgetting something silly): if I run conda install samtools=1.9=h7c4ea83_11 f I get an error that it can’t find the package. If I do conda search for it I do see it in the bioconda channel (which already exists in my channels list, as conda config —add channels bioconda tells me it’s already there - see below). What am I missing here? I’m using MacOSX btw. PackagesNotFoundError: The following packages are not available from current channels: - samtools==1.9=h7c4ea83_11 -> curl[version='>=7.64.0,<8.0a0'] Current channels: - https://conda.anaconda.org/bioconda/osx-64 - https://conda.anaconda.org/bioconda/noarch - https://conda.anaconda.org/r/osx-64 - https://conda.anaconda.org/r/noarch - https://repo.anaconda.com/pkgs/main/osx-64 - https://repo.anaconda.com/pkgs/main/noarch - https://repo.anaconda.com/pkgs/free/osx-64 - https://repo.anaconda.com/pkgs/free/noarch - https://repo.anaconda.com/pkgs/r/osx-64 - https://repo.anaconda.com/pkgs/r/noarch To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. (base) ralphs-imac:~ ralphstadhouders$ conda search samtools=1.9=h7c4ea83_11 Loading channels: done # Name Version Build Channel samtools 1.9 h7c4ea83_11 bioconda (base) ralphs-imac:~ ralphstadhouders$ conda config --append channels bioconda Warning: 'bioconda' already in 'channels' list, moving to the bottom Op ma 11 mrt. 2019 om 14:20 schreef Björn Grüning <notifications@github.com

…

: @RStadhouders <https://github.com/RStadhouders> the version you need to install is samtools-1.9-h7c4ea83_11 to the 11 build number. Also try to not install into your root/base environment, always use conda create -n samtools samtools for example. Hope that helps! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#13958 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMn1ODicRBUFMx5Js1fNLyq61J6dWqviks5vVlgrgaJpZM4bkUQA> .

dpryan79 · 2019-03-11T14:02:35Z

conda install samtools=1.9 by itself should suffice, you can't give conda install the full hash and build number as far as I know.

ghost · 2019-03-11T14:24:30Z

Thanks, although there are a lot of samtools=1.9 builds around: samtools 1.9 h28b8610_6 bioconda samtools 1.9 h28b8610_7 bioconda samtools 1.9 h46bd0b3_0 bioconda samtools 1.9 h7c4ea83_10 bioconda samtools 1.9 h7c4ea83_11 bioconda samtools 1.9 h8ee4bcc_1 bioconda samtools 1.9 hb029021_2 bioconda samtools 1.9 hb029021_3 bioconda samtools 1.9 hb029021_4 bioconda samtools 1.9 hb029021_5 bioconda samtools 1.9 hb029021_8 bioconda samtools 1.9 he6825b8_9 bioconda And simply trying to install with =1.9 simply results in this: conda install samtools=1.9 Collecting package metadata: done Solving environment: done # All requested packages already installed. Op ma 11 mrt. 2019 om 15:02 schreef Devon Ryan <notifications@github.com>:

…

conda install samtools=1.9 by itself should suffice, you can't give conda install the full hash and build number as far as I know. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#13958 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMn1OOZhuHdH87KUb_f5ocu0hqIFg9Pbks5vVmIRgaJpZM4bkUQA> .

dpryan79 · 2019-03-11T14:27:05Z

Then use `conda update samtools` -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany <devon.ryan@dzne.de>

…

On Mon, Mar 11, 2019 at 3:24 PM Ralph Stadhouders ***@***.***> wrote: Thanks, although there are a lot of samtools=1.9 builds around: samtools 1.9 h28b8610_6 bioconda samtools 1.9 h28b8610_7 bioconda samtools 1.9 h46bd0b3_0 bioconda samtools 1.9 h7c4ea83_10 bioconda samtools 1.9 h7c4ea83_11 bioconda samtools 1.9 h8ee4bcc_1 bioconda samtools 1.9 hb029021_2 bioconda samtools 1.9 hb029021_3 bioconda samtools 1.9 hb029021_4 bioconda samtools 1.9 hb029021_5 bioconda samtools 1.9 hb029021_8 bioconda samtools 1.9 he6825b8_9 bioconda And simply trying to install with =1.9 simply results in this: conda install samtools=1.9 Collecting package metadata: done Solving environment: done # All requested packages already installed. Op ma 11 mrt. 2019 om 15:02 schreef Devon Ryan ***@***.***>: > conda install samtools=1.9 by itself should suffice, you can't give conda > install the full hash and build number as far as I know. > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > < #13958 (comment) >, > or mute the thread > < https://github.com/notifications/unsubscribe-auth/AMn1OOZhuHdH87KUb_f5ocu0hqIFg9Pbks5vVmIRgaJpZM4bkUQA > > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#13958 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGGkGPkmDv2uklDugW6ENxhpqMyeuiDAks5vVmcsgaJpZM4bkUQA> .

ghost · 2019-03-11T14:33:01Z

Same results unfortunately… Version installed/updated is still: samtools 1.9 hb029021_5 bioconda Perhaps removing samtools and a clean install will force conda to use the latest build? Op ma 11 mrt. 2019 om 15:27 schreef Devon Ryan <notifications@github.com>:

…

Then use `conda update samtools` -- Devon Ryan, Ph.D. Email: ***@***.*** Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany ***@***.***> On Mon, Mar 11, 2019 at 3:24 PM Ralph Stadhouders < ***@***.***> wrote: > Thanks, although there are a lot of samtools=1.9 builds around: > > samtools 1.9 h28b8610_6 bioconda > > samtools 1.9 h28b8610_7 bioconda > > samtools 1.9 h46bd0b3_0 bioconda > > samtools 1.9 h7c4ea83_10 bioconda > > samtools 1.9 h7c4ea83_11 bioconda > > samtools 1.9 h8ee4bcc_1 bioconda > > samtools 1.9 hb029021_2 bioconda > > samtools 1.9 hb029021_3 bioconda > > samtools 1.9 hb029021_4 bioconda > > samtools 1.9 hb029021_5 bioconda > > samtools 1.9 hb029021_8 bioconda > > samtools 1.9 he6825b8_9 bioconda > > > And simply trying to install with =1.9 simply results in this: > > > conda install samtools=1.9 > > Collecting package metadata: done > > Solving environment: done > > > # All requested packages already installed. > > Op ma 11 mrt. 2019 om 15:02 schreef Devon Ryan ***@***.*** >: > > > conda install samtools=1.9 by itself should suffice, you can't give conda > > install the full hash and build number as far as I know. > > > > — > > You are receiving this because you were mentioned. > > Reply to this email directly, view it on GitHub > > < > #13958 (comment) > >, > > or mute the thread > > < > https://github.com/notifications/unsubscribe-auth/AMn1OOZhuHdH87KUb_f5ocu0hqIFg9Pbks5vVmIRgaJpZM4bkUQA > > > > . > > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > < #13958 (comment) >, > or mute the thread > < https://github.com/notifications/unsubscribe-auth/AGGkGPkmDv2uklDugW6ENxhpqMyeuiDAks5vVmcsgaJpZM4bkUQA > > . > — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#13958 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMn1OKpo1KFpd6T6ZsVslN0ZfqAxUTvlks5vVmfRgaJpZM4bkUQA> .

dpryan79 · 2019-03-11T14:35:13Z

Yes, give that a whirl.

mikecormier · 2019-03-11T15:30:28Z

Hey @dpryan79, I am having the same problem. That is, I can only install/update samtools to build 5, and am unable to access build 11. However, this seems to be isolated to an anaconda distribution. It seems that there is no problem when using a miniconda distribution. I am not sure why there would be a difference. Any suggestions?

dpryan79 · 2019-03-11T15:34:45Z

What version of conda do you have and what else is in the environment?

mikecormier · 2019-03-11T15:42:40Z

Conda version: conda 4.6.8
This installation of anaconda is new and the environment should be clean

PertuyF · 2019-03-11T19:18:36Z

You should be able to provide part of the build number with conda install samtools=1.9=*_11.

Otherwise, conda install samtools=1.9 --force-reinstall will try to install samtools even if it is already in your environment.

unode · 2019-03-17T01:20:01Z

How should package versions that are no longer in the git repository be handled?
For instance blast==2.6.0 is pinned by rgi==4.4.2 and exists in anaconda but is no longer in git-master nor does it pin openSSL. Due to this it breaks if openssl 1.1 is installed in the conda environment.

dpryan79 · 2019-03-17T07:32:29Z

@unode The general strategy is to ignore them unless absolutely needed. These packages will still install and work fine in new environments, they just won't be able to be mixed with newer versions of other programs.

dpryan79 · 2019-03-19T19:58:09Z

This should be done now, closing.

YantingHuang · 2021-08-04T21:20:13Z

this would work:
conda install -c bioconda samtools=1.9

dpryan79 added the announcement label Mar 7, 2019

pb-cdunn mentioned this issue Mar 8, 2019

Problem with samtools using conda : libcrypto.so.1.0.0 PacificBiosciences/pbbioconda#85

Closed

eclarke mentioned this issue Mar 12, 2019

Added extensions cause samtools error sunbeam-labs/sunbeam#192

Closed

PertuyF mentioned this issue Mar 13, 2019

Undocumented Nanopolish dependency on libcrypto.so #14015

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t-neumann mentioned this issue Mar 18, 2019

Query about running the slamdunk all t-neumann/slamdunk#48

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dpryan79 closed this as completed Mar 19, 2019

PertuyF mentioned this issue Mar 23, 2019

recipe successfully merged, but conda install from bioconda fails #14162

Closed

eclarke mentioned this issue Mar 29, 2019

samtools cannot find libcrypto.so.1.0.0 sunbeam-labs/sunbeam#181

Closed

ressy mentioned this issue Mar 29, 2019

samtools 1.9 dependency pulls in wrong version of openssl #12100

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lumpy.check pointing to incorrect location. brentp/smoove#13

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meren mentioned this issue Aug 6, 2020

[BUG] Samtools shared library libcrypto.so.1.0.0 not found merenlab/anvio#1479

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Check whether riboviz can be set up with Ubuntu LTS 20.04 & update install documentation riboviz/riboviz#271

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AlessioMilanese mentioned this issue Mar 9, 2021

Update to 2.6.0 #27244

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5 tasks

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OpenSSL migration #13958

OpenSSL migration #13958

dpryan79 commented Mar 7, 2019

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YantingHuang commented Aug 4, 2021

OpenSSL migration #13958

OpenSSL migration #13958

Comments

dpryan79 commented Mar 7, 2019

Why was this done?

What do we need to do now?

jbelyeu commented Mar 9, 2019

dpryan79 commented Mar 9, 2019

jbelyeu commented Mar 9, 2019

dpryan79 commented Mar 9, 2019

jbelyeu commented Mar 9, 2019

ghost commented Mar 11, 2019

bgruening commented Mar 11, 2019

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