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rocker-org / rocker

R configurations for Docker
https://rocker-project.org
GNU General Public License v2.0
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Singularity support broken #403

Closed louisaslett closed 4 years ago

louisaslett commented 4 years ago

The Singularity support discussed in #277 and documented at https://www.rocker-project.org/use/singularity/ seems to no longer work with the latest image, because the pam-helper seems to have been dropped.

I get the following:

$ PASSWORD=mypass singularity exec rstudio.simg \
>     rserver --www-port 8080 --auth-none=0 --auth-pam-helper-path=pam-helper
INFO:    Convert SIF file to sandbox...
12 May 2020 16:55:23 [rserver] ERROR PAM helper binary does not exist at /usr/lib/rstudio-server/bin/pam-helper; LOGGED FROM: bool rstudio::server::pam_auth::pamLogin(const string&, const string&) /var/lib/jenkins/workspace/IDE/open-source-pipeline/v1.2-patch/src/cpp/server/ServerPAMAuth.cpp:445

The error line appears once I type in a username and password to log in.

This did not happen with an image I pulled just 4 days ago.

eddelbuettel commented 4 years ago

Thanks -- that had already been reported a few days ago @cboettig just addressed and closed it but possibly over in ../rocker-ver.

sahilseth commented 4 years ago

Sorry, could you expand which image to use? I see this issue with the latest image:

singularity pull --name rstudio.simg docker://rocker/rstudio:latest
cboettig commented 4 years ago

I see:

singularity pull --name rstudio.simg docker://rocker/rstudio:latest  && PASSWORD=mypass singularity exec rstudio.simg rserver --www-port 8080 --auth-none=0 --auth-pam-helper-path=pam-helper
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Copying blob d51af753c3d3 skipped: already exists
Copying blob fc878cd0a91c skipped: already exists
Copying blob 6154df8ff988 skipped: already exists
Copying blob fee5db0ff82f skipped: already exists
Copying blob 6197d0183c3e done
Copying blob cc38af15fb27 done
Copying blob bfe86122602d done
Copying blob d43205b1ea96 done
Copying config c5922368e6 done
Writing manifest to image destination
Storing signatures
2020/05/17 17:15:02  info unpack layer: sha256:d51af753c3d3a984351448ec0f85ddafc580680fd6dfce9f4b09fdb367ee1e3e
2020/05/17 17:15:03  info unpack layer: sha256:fc878cd0a91c7bece56f668b2c79a19d94dd5471dae41fe5a7e14b4ae65251f6
2020/05/17 17:15:03  info unpack layer: sha256:6154df8ff9882934dc5bf265b8b85a3aeadba06387447ffa440f7af7f32b0e1d
2020/05/17 17:15:03  info unpack layer: sha256:fee5db0ff82f7aa5ace63497df4802bbadf8f2779ed3e1858605b791dc449425
2020/05/17 17:15:03  info unpack layer: sha256:6197d0183c3ee34e5fc122979227ba450ebf345cc0e0d646a70c8bd66051b34c
2020/05/17 17:15:03  info unpack layer: sha256:cc38af15fb2762456ff0d538eb4a2a562db8e7a1951aa60f916a670c01ae0cc0
2020/05/17 17:15:08  info unpack layer: sha256:bfe86122602d202b32d94cd0e722fe9861d05c566b008cc4fe2e74b599e0792e
2020/05/17 17:15:21  info unpack layer: sha256:d43205b1ea960b16ca541d157fc764a888043331da27e379351c502d7c2dd6e8
INFO:    Creating SIF file...
INFO:    Build complete: rstudio.simg

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