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[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
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MacOS build fails due to failure to install SeqAn #247

Closed paoloczi closed 3 years ago

paoloczi commented 3 years ago

MacOS builds on GitHub Actions are failing due to a problem installing the SeqAn2 library.

The following command in shasta/scripts/InstallPrerequisites-macOS.sh is used to install the SeqAn2 library:

brew install brewsci/bio/seqan@2

That command currently fails with the following messages:

==> Installing seqan@2 from brewsci/bio
==> Downloading https://archive.org/download/brewsci/bottles-bio/seqan%402-2.4.0.catalina.bottle.tar.gz
curl: (22) The requested URL returned error: 403 
Error: Failed to download resource "seqan@2"
Download failed: https://archive.org/download/brewsci/bottles-bio/seqan%402-2.4.0.catalina.bottle.tar.gz

Manual download of that file via wget also fails similarly:

wget https://archive.org/download/brewsci/bottles-bio/seqan%402-2.4.0.catalina.bottle.tar.gz
--2021-04-07 09:57:49--  https://archive.org/download/brewsci/bottles-bio/seqan%402-2.4.0.catalina.bottle.tar.gz
Resolving archive.org (archive.org)... 207.241.224.2
Connecting to archive.org (archive.org)|207.241.224.2|:443... connected.
HTTP request sent, awaiting response... 403 Forbidden
2021-04-07 09:57:50 ERROR 403: Forbidden.

It could be that this is an intermittent failure of the brewsci server. However, it is possible that this is not the correct way to install SeqAn2 on macOS. In this case, we need to fix the installation command.

I will have to disable macOS builds on GitHub Actions until this is fixed. If we don't have a fix by the time we create the next release, we will have to exclude macOS from the release.

paoloczi commented 3 years ago

Today (4/13/2021) I noticed that the above wget no longer fails. Therefore I tried re-enabling the macOS 10.15 build. However installation of SeqAn2 still fails. The error is different now:

==> Installing seqan@2 from brewsci/bio
==> Downloading https://ghcr.io/v2/brewsci/bio/seqan%402-2.4.0.catalina.bottle.tar.gz
curl: (22) The requested URL returned error: 404 
Error: Failed to download resource "seqan@2"
Download failed: https://ghcr.io/v2/brewsci/bio/seqan%402-2.4.0.catalina.bottle.tar.gz

A manual wget gets the same error.

ASLeonard commented 3 years ago

I run shasta on a linux cluster, but I have a macOS laptop, so I had been keeping up with this out of curiosity. My mac is version 10.15.7 (19H524)

Previously both the brew and wget attempts failed with the same errors you had, but as of just now the brew approach works.

brew install brewsci/bio/seqan@2

==> Installing seqan@2 from brewsci/bio
==> Downloading https://ghcr.io/v2/brewsci/bio/seqan/2/manifests/2.4.0
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/brewsci/bio/seqan/2/blobs/sha256:1fe83b7b478611b6fc28fe4eb7bc34e8d7846c6bc8dda57ae37d3e4e40d9e821
==> Downloading from https://pkg-containers-az.githubusercontent.com/ghcr1/blobs/sha256:1fe83b7b478611b6fc28fe4eb7bc34e8d7846c6bc8dda57ae37d3e4e40d9e821?se=2021-04-14T13%3A00%3A00Z&sig=eugiAhp1baiwqKcp3zS%2FWPETp3FLgz9aAAo0%2FLVB%2Bb4%3D&sp=r&spr=https&sr=b&sv=2019-12-12
######################################################################## 100.0%
==> Pouring seqan@2--2.4.0.catalina.bottle.tar.gz
🍺  /usr/local/Cellar/seqan@2/2.4.0: 1,888 files, 35.1MB

The wget download also works fine now.

paoloczi commented 3 years ago

Thank you for the tip @ASLeonard! Based on this, I will try and re-enable the macOS 10.15 build one more time.

paoloczi commented 3 years ago

Yes, the macOS 10.15 build is back to life. I will leave this issue open for a bit in case the problem shows up again, as it has been intermittent.

Thank you for your help @ASLeonard!

paoloczi commented 3 years ago

The macOS build is failing again with the same error. I will leave it on for now so we can see if it comes back to life.

ASLeonard commented 3 years ago

It seems to be working again (hopefully for more than a day this time).

paoloczi commented 3 years ago

Yes. The last failure was 8 days ago. If it makes it two weeks I will close this issue, and I can always reopen it if the problem reappears.

paoloczi commented 3 years ago

These intermittent server failures have disappeared, at least for now, so I will close this issue.