Opened 2 years ago
Closed 21 months ago
#13292 closed defect (fixed)
Bad symlink SAGE_DATA/graphs/graphs.db in binary distributions
Reported by: | steven | Owned by: | tbd |
---|---|---|---|
Priority: | major | Milestone: | sage-5.4 |
Component: | distribution | Keywords: | broken symlink, graphs database, binary distributions bdist |
Cc: | jdemeyer, schilly | Merged in: | |
Authors: | Jeroen Demeyer | Reviewers: | Leif Leonhardy |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description
I downloaded the file sage-5.1-linux-64bit-ubuntu_12.04_lts-x86_64-Linux.tar.lzma from the official website. Sage was unable to use the graphs database.
An example of failure is (taken from the documentation):
Q = GraphQuery(display_cols=['graph6','num_vertices','degree_sequence'],num_edges=['<=',5],min_degree=1)
The file SAGE_DATA/graphs/graphs.db is a broken symlink to /tmp/graphs.db.cm5Li3EYGT. Replacing it with a link to graphs.db.orig fixed the problem.
From sage root directory:
$ cd data/graphs $ rm graphs.db $ ln -s graphs.db.orig graphs.db $ ls -l total 2452 lrwxrwxrwx 1 steven steven 14 Jul 26 14:35 graphs.db -> graphs.db.orig -rw-r--r-- 1 steven steven 1258496 May 20 2007 graphs.db.orig -rw-r--r-- 1 steven steven 1247018 Apr 4 21:56 isgci_sage.xml
Change History (12)
comment:1 follow-up: ↓ 2 Changed 2 years ago by leif
- Component changed from databases to distribution
- Keywords binary distributions bdist added
- Owner changed from was to tbd
comment:2 in reply to: ↑ 1 Changed 2 years ago by leif
Replying to leif:
I can confirm that random symbolic links are at least in all current binary dists for Linux...
On the other hand, I cannot reproduce this error (with Sage 5.2.rc0). I.e., sage -bdist works for me w.r.t. this.
comment:3 Changed 2 years ago by leif
sage-bdist looks sane as well, so that's probably a problem with the buildbot setup or other scripts not part of the Sage distribution itself.
comment:4 Changed 2 years ago by leif
- Cc jdemeyer schilly added
- Priority changed from major to blocker
- Summary changed from Bad symlink SAGE_DATA/graphs/graphs.db to Bad symlink SAGE_DATA/graphs/graphs.db in binary distributions
Unfortunately this is still true for the new 5.2 binaries, at least all the Linux ones.
comment:5 Changed 2 years ago by jdemeyer
It's because of the buildbot setup.
This goes back to the Mitesh Patel days, which is sage-4.6 or something. So I don't understand why nobody ever noticed this before.
comment:6 Changed 2 years ago by leif
FWIW, some of the temporaries are kept as well:
leif@redhawk:~$ ls -l /tmp/graphs.db.* -rw------- 1 buildbot buildbot 1258496 2012-07-27 05:51 /tmp/graphs.db.Uc0awza1Zl -rw------- 1 buildbot buildbot 1258496 2012-07-27 02:01 /tmp/graphs.db.zX74CFVi9b
No idea why they're copied to /tmp at all, since the database is fairly small.
At least the original files are also part of the bdists...
comment:7 follow-up: ↓ 8 Changed 2 years ago by jdemeyer
- Priority changed from blocker to major
I agree it should be fixed, but I don't see why it should be a "blocker".
comment:8 in reply to: ↑ 7 Changed 2 years ago by leif
Replying to jdemeyer:
I agree it should be fixed, but I don't see why it should be a "blocker".
Because otherwise nobody notices this issue... ;-)
comment:9 follow-up: ↓ 10 Changed 2 years ago by jdemeyer
- Status changed from new to needs_review
Fixed this on the buildbot and made one new binary: http://boxen.math.washington.edu/home/buildbot/binaries/sage/5.2.rc1/sage-5.2.rc1-linux-64bit-ubuntu_8.04.4_lts-x86_64-Linux.tar.gz
If this looks good, please set this to positive_review.
comment:10 in reply to: ↑ 9 Changed 2 years ago by leif
Replying to jdemeyer:
Fixed this on the buildbot and made one new binary: http://boxen.math.washington.edu/home/buildbot/binaries/sage/5.2.rc1/sage-5.2.rc1-linux-64bit-ubuntu_8.04.4_lts-x86_64-Linux.tar.gz
If this looks good, please set this to positive_review.
Well, the new bdist tarball looks sane w.r.t. graphs.db (and I haven't found other references to temporary files), but I (so far) haven't tested the bdist itself, and I should probably review the change(s) to some script(s)...
comment:11 Changed 22 months ago by jdemeyer
- Milestone changed from sage-5.4 to sage-5.5
- Reviewers set to Leif Leonhardy
- Status changed from needs_review to positive_review
The buildbot scripts aren't part of Sage, so I don't think these need to be reviewed. Anyway, the problem is fixed.
comment:12 Changed 21 months ago by jdemeyer
- Milestone changed from sage-5.5 to sage-5.4
- Resolution set to fixed
- Status changed from positive_review to closed
I can confirm that random symbolic links are at least in all current binary dists for Linux:
Haven't yet tracked this down.