optional packages and binder

[Enrique Artal]

I want to make available some of my notebooks in binder. I found very useful sage-binder-env but I ran into problems in a case where I needed an optional package, namely gap_packages. As stated I installed make package using the Dockerfile but the installation stops with an error in make all-toolchain. I guess I need to install more packages but I do not know which ones. Best regards, Enrique.

[Vincent Delecroix]

Dear Enrique,

It would be helpful to have the complete error message and the log
of the failed build. And if you know how to do that, you can open
a trac ticket.

Also, it would be nice to have docker images for Sage with most (if
not all) optional packages installed.

Vincent

[Enrique Artal]

Cher Vincent,

I hope to add now enough additional info. I am using mybinder.org (I did not find another address); my Dockerfile is adapted from a file in sage-binder-env: 

FROM sagemath/sagemath:8.8
	USER root
	RUN apt-get -qq update \
	&& apt-get -qq install -y --no-install-recommends gcc build-essential make \
	&& apt-get -qq clean
	USER sage
	RUN sage -i gap_packages
	# Make sure the contents of the repository is in ${HOME}
	COPY --chown=sage:sage . ${HOME}

In the original file the version was 8.6; 8.9 did not work. The whole log is:

Waiting for build to start...

Picked Git content provider.

Cloning into '/tmp/repo2dockerarcwd43e'...

HEAD is now at a95a550 Update Dockerfile

Using DockerBuildPack builder

Step 1/6 : FROM sagemath/sagemath:8.8

 ---> 8826a965812be...

Step 2/6 : USER root

 ---> Running in 5de1f0b3cfbb

Removing intermediate container 5de1f0b3cfbb

 ---> c39c95bbdcff

Step 3/6 : RUN apt-get -qq update  && apt-get -qq install -y --no-install-recommends gcc build-essential make  && apt-get -qq clean

 ---> Running in fe5e1e365ff8

debconf: delaying package configuration, since apt-utils is not installed

Selecting previously unselected package libgdbm3:amd64.

(Reading database ... 7609 files and directories currently installed.)

Preparing to unpack .../libgdbm3_1.8.3-13.1_amd64.deb ...

Unpacking libgdbm3:amd64 (1.8.3-13.1) ...

Selecting previously unselected package perl-modules-5.22.

Preparing to unpack .../perl-modules-5.22_5.22.1-9ubuntu0.6_all.deb ...

Unpacking perl-modules-5.22 (5.22.1-9ubuntu0.6) ...

Preparing to unpack .../libbz2-1.0_1.0.6-8ubuntu0.2_amd64.deb ...

Unpacking libbz2-1.0:amd64 (1.0.6-8ubuntu0.2) over (1.0.6-8) ...

Processing triggers for libc-bin (2.23-0ubuntu11) ...

Setting up libbz2-1.0:amd64 (1.0.6-8ubuntu0.2) ...

Processing triggers for libc-bin (2.23-0ubuntu11) ...

Selecting previously unselected package libperl5.22:amd64.

(Reading database ... 8846 files and directories currently installed.)

Preparing to unpack .../libperl5.22_5.22.1-9ubuntu0.6_amd64.deb ...

Unpacking libperl5.22:amd64 (5.22.1-9ubuntu0.6) ...

Selecting previously unselected package perl.

Preparing to unpack .../perl_5.22.1-9ubuntu0.6_amd64.deb ...

Unpacking perl (5.22.1-9ubuntu0.6) ...

Selecting previously unselected package bzip2.

Preparing to unpack .../bzip2_1.0.6-8ubuntu0.2_amd64.deb ...

Unpacking bzip2 (1.0.6-8ubuntu0.2) ...

Selecting previously unselected package make.

Preparing to unpack .../archives/make_4.1-6_amd64.deb ...

Unpacking make (4.1-6) ...

Selecting previously unselected package libdpkg-perl.

Preparing to unpack .../libdpkg-perl_1.18.4ubuntu1.6_all.deb ...

Unpacking libdpkg-perl (1.18.4ubuntu1.6) ...

Selecting previously unselected package xz-utils.

Preparing to unpack .../xz-utils_5.1.1alpha+20120614-2ubuntu2_amd64.deb ...

Unpacking xz-utils (5.1.1alpha+20120614-2ubuntu2) ...

Selecting previously unselected package patch.

Preparing to unpack .../patch_2.7.5-1ubuntu0.16.04.2_amd64.deb ...

Unpacking patch (2.7.5-1ubuntu0.16.04.2) ...

Selecting previously unselected package dpkg-dev.

Preparing to unpack .../dpkg-dev_1.18.4ubuntu1.6_all.deb ...

Unpacking dpkg-dev (1.18.4ubuntu1.6) ...

Selecting previously unselected package build-essential.

Preparing to unpack .../build-essential_12.1ubuntu2_amd64.deb ...

Unpacking build-essential (12.1ubuntu2) ...

Setting up libgdbm3:amd64 (1.8.3-13.1) ...

Setting up perl-modules-5.22 (5.22.1-9ubuntu0.6) ...

Setting up libperl5.22:amd64 (5.22.1-9ubuntu0.6) ...

Setting up perl (5.22.1-9ubuntu0.6) ...

update-alternatives: using /usr/bin/prename to provide /usr/bin/rename (rename) in auto mode

Setting up bzip2 (1.0.6-8ubuntu0.2) ...

Setting up make (4.1-6) ...

Setting up libdpkg-perl (1.18.4ubuntu1.6) ...

Setting up xz-utils (5.1.1alpha+20120614-2ubuntu2) ...

update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode

Setting up patch (2.7.5-1ubuntu0.16.04.2) ...

Setting up dpkg-dev (1.18.4ubuntu1.6) ...

Setting up build-essential (12.1ubuntu2) ...

Processing triggers for libc-bin (2.23-0ubuntu11) ...

Removing intermediate container fe5e1e365ff8

 ---> fa9dc2999b1d

Step 4/6 : USER sage

 ---> Running in d86e77e74948

Removing intermediate container d86e77e74948

 ---> 6535d64a4eae

Step 5/6 : RUN sage -i gap_packages

 ---> Running in e012d50d35ae

make: *** No rule to make target 'all-toolchain'.  Stop.

Removing intermediate container e012d50d35ae

The command '/bin/sh -c sage -i gap_packages' returned a non-zero code: 2

I think the non-zero code is variable. Thanks, Enrique.

[Vincent Delecroix]

Estimado Enrique,

If you want to compile anything, you should be using development
docker image, that is

sagemath/sagemath-dev

(you can tag if 8.8 if you wish). Be careful that the image is
twice bigger. See the documentation at

https://hub.docker.com/u/sagemath/sagemath

Vincent

[Enrique Artal]

Thanks for the type. It built the image (including gap_packages) but when pushing it to binder it failed because a wrong checksum of "usr/lib64/perl5/vendor_perl/Unicode/Collate/Locale/kok.pl"

[Alexander Konovalov]

This is an example by Nicolas M. Thiéry which worked earlier this week: https://github.com/OpenDreamKit/demo-semigroup-representation-theory/blob/master/Dockerfile 

Hope it may help. Is your setup somewhere on GitHub?

Best wishes

Alex

[Enrique Artal]

Yes:

https://github.com/enriqueartal/GuervilleViuZariskiPairs

Thanks for the link, I am going to try. Best wishes, Enrique.

[Enrique Artal]

Thanks for the help to Alexander and Vincent. It works now (branch sage); I have no excuses to avoid to add more comments to the notebook. Best, Enrique.