Update Jmol release to use new security certificate

gutow commented 9 years ago

A mistake at the certificate authority used by Jmol has revoked the old security certificate for Jmol. This means that the java versions older than 14.4.0_2015.10.14 will not work in any browsers. Since we default to the javascript version, this is not a disaster but may cause problems for those using complicated 3D.

Also, a tiny PHP script was for some reason deleted - let's not do it.

New package: https://www.dropbox.com/s/rkrvybyyh5zuv5z/jmol-14.6.1_2016.07.11.tar.bz2

CC: @kcrisman @williamstein

Component: packages: standard

Keywords: Jmol, java

Author: Andrey Novoseltsev

Branch/Commit: b6db4a7

Reviewer: Matthias Koeppe

Issue created by migration from https://trac.sagemath.org/ticket/19430

novoselt commented 8 years ago

Branch: u/novoselt/upgrade_jmol

novoselt commented 8 years ago

New commits:

`e79d16d`	`MathJax patches were no relative to the root of the upstream sources, like patches for other spkgs.`
`73d01bd`	`Reworked jmol installation to be somewhat more consistent.`
`7bb48f7`	`ntl patches were not quite conformant either, due to the layout of the ntl upstream tarball`
`ca88d3c`	`Reformat ATLAS patches to conform with other spkgs (the root of the ATLAS source tarball is src/, not src/ATLAS)`
`b48b391`	`Clean up patching of rubiks`
`66ceeb2`	`Rewrite Singular ptches to comply to the new standard format`
`c6f2f64`	`Make tachyon conform to the standard patch format.`
`8bce0b3`	`Merge remote-tracking branch 'trac/u/embray/patch-normalization-2' into upgrade_jmol`
`d1a1bba`	`Upgrade jmol to 14.6.1`

novoselt commented 8 years ago

Changed dependencies from notebook to #20933

novoselt commented 8 years ago

Changed author from gutow to Andrey Novoseltsev

novoselt commented 8 years ago

Commit: d1a1bba

novoselt commented 8 years ago

Description changed:

--- 
+++ 
@@ -1,3 +1,6 @@
 A mistake at the certificate authority used by Jmol has revoked the old security certificate for Jmol.  This means that the java versions older than 14.4.0_2015.10.14 will not work in any browsers.  Since we default to the javascript version, this is not a disaster but may cause problems for those using complicated 3D.

-New Jmol/JSmol will need testing.  Hopefully, this will just require packaging the new Jmol/JSmol.
+Also, a tiny PHP script was for some reason deleted - let's not do it.
+
+New package:
+https://cloud.sagemath.com/projects/e2420ae7-534b-4b83-962d-3e4511cfe836/files/jmol-14.6.1_2016.07.11.tar.bz2

novoselt commented 8 years ago

comment:4

And in case SMC is not quite working, an alternative link https://www.dropbox.com/s/rkrvybyyh5zuv5z/jmol-14.6.1_2016.07.11.tar.bz2?dl=0

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 8 years ago

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

b6db4a7 Upgrade jmol to 14.6.1

7ed8c4ca-6d56-4ae9-953a-41e42b4ed313 commented 8 years ago

Changed commit from d1a1bba to b6db4a7

novoselt commented 8 years ago

comment:6

Since it does not have to depend on #20933 and that one needs to be updated, I've rebased.

novoselt commented 8 years ago

Changed dependencies from #20933 to none

mkoeppe commented 8 years ago

comment:7

The updated package seems to work for me; but #20978 still doesn't work with the new version.

mkoeppe commented 8 years ago

Reviewer: Matthias Koeppe

novoselt commented 8 years ago

comment:9

Thank you for reviewing!

I've seen #20978, but I don't really care about Java version for a few years - even when it works it is annoying to keep pressing confirmations and then of course there is no way to save it on campus computers. My main motivation for this upgrade having the PHP script included.

vbraun commented 8 years ago

comment:10

I can't download it: Error opening 'jmol-14.6.1_2016.07.11.tar.bz2' -- "Traceback (most recent call last):\n File \"/usr/local/bin/smc-compute\", line 9, in \n load_entry_point('smc-pyutil==1.1', 'console_scripts', 'smc-compute')()\n File \"/usr/local/lib/python2.7/dist-packages/smc_pyutil/smc_compute.py\", line 1016, in main\n args.func(args)\n File \"/usr/local/lib/python2.7/dist-packages/smc_pyutil/smc_compute.py\", line 886, in g\n result = getattr(Project(project_id=project_id, dev=args.dev, projects=args.projects, single=args.single), function)(**kwds)\n File \"/usr/local/lib/python2.7/dist-packages/smc_pyutil/smc_compute.py\", line 681, in read_file\n raise RuntimeError(\"path (=%s) must be at most %s bytes, but it is %s bytes\"%(path, maxsize, size))\nRuntimeError: path (=jmol-14.6.1_2016.07.11.tar.bz2) must be at most 20000000 bytes, but it is 38106981 bytes\n"

novoselt commented 8 years ago

comment:11

How about this one? https://www.dropbox.com/s/rkrvybyyh5zuv5z/jmol-14.6.1_2016.07.11.tar.bz2?dl=0

mkoeppe commented 8 years ago

comment:12

the one from dropbox is what I reviewed. The other gave me a checksum error

novoselt commented 8 years ago

Description changed:

--- 
+++ 
@@ -3,4 +3,4 @@
 Also, a tiny PHP script was for some reason deleted - let's not do it.

 New package:
-https://cloud.sagemath.com/projects/e2420ae7-534b-4b83-962d-3e4511cfe836/files/jmol-14.6.1_2016.07.11.tar.bz2
+https://www.dropbox.com/s/rkrvybyyh5zuv5z/jmol-14.6.1_2016.07.11.tar.bz2?dl=0

novoselt commented 8 years ago

comment:14

I'll take the liberty of setting back to positive review since there is a confirmation that this link worked. I am already using this package in SageMathCell, so would be nice to have it in 7.3.

novoselt commented 8 years ago

comment:15

Apparently SageMathCloud link managed to propagate to the servers and it is now possible to "download" this new jmol with the following message in the package log

Found local metadata for jmol-14.6.1_2016.07.11.p0
Invalid checksum for cached file /home/sc_serv/sage/upstream/jmol-14.6.1_2016.07.11.tar.bz2, deleting
Attempting to download package jmol-14.6.1_2016.07.11.tar.bz2 from mirrors
http://mirrors.mit.edu/sage/spkg/upstream/jmol/jmol-14.6.1_2016.07.11.tar.bz2
[......................................................................]
Traceback (most recent call last):
  File "/home/sc_serv/sage/build/bin/sage-download-file", line 28, in <module>
    run_safe()
  File "/home/sc_serv/sage/build/bin/../sage_bootstrap/download/cmdline.py", line 115, in run_safe
    run()
  File "/home/sc_serv/sage/build/bin/../sage_bootstrap/download/cmdline.py", line 97, in run
    app.download_tarball(args.url_or_tarball, args.destination)
  File "/home/sc_serv/sage/build/bin/../sage_bootstrap/download/app.py", line 43, in download_tarball
    tarball.download()
  File "/home/sc_serv/sage/build/bin/../sage_bootstrap/tarball.py", line 163, in download
    raise ChecksumError('checksum does not match')
sage_bootstrap.tarball.ChecksumError: checksum does not match

and no clue what is wrong on the console:

make[2]: Leaving directory '/home/sc_serv/sage/build/make'
Makefile:839: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/home/sc_serv/sage/build/make'

real    0m7.713s
user    0m7.200s
sys     0m1.264s
***************************************************************
Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make all'):

The build directory may contain configuration files and other potentially
helpful information. WARNING: if you now run 'make' again, the build
directory will, by default, be deleted. Set the environment variable
SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.

Makefile:16: recipe for target 'all' failed
make: *** [all] Error 1

Is it possible to report for which package make returned an error?

novoselt commented 8 years ago

Description changed:

--- 
+++ 
@@ -3,4 +3,4 @@
 Also, a tiny PHP script was for some reason deleted - let's not do it.

 New package:
-https://www.dropbox.com/s/rkrvybyyh5zuv5z/jmol-14.6.1_2016.07.11.tar.bz2?dl=0
+https://www.dropbox.com/s/rkrvybyyh5zuv5z/jmol-14.6.1_2016.07.11.tar.bz2

vbraun commented 8 years ago

Changed branch from u/novoselt/upgrade_jmol to b6db4a7

sagemath / sage

Update Jmol release to use new security certificate #19430