Opened 8 years ago
Closed 6 years ago
#11678 closed defect (worksforme)
sage-4.7 gives error on relocating the root directory
Reported by: | ppurka | Owned by: | tdb |
---|---|---|---|
Priority: | minor | Milestone: | sage-duplicate/invalid/wontfix |
Component: | relocation | Keywords: | flask notebook easy-install.pth easy_install |
Cc: | leif, rkirov | Merged in: | |
Authors: | Reviewers: | Punarbasu Purkayastha | |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description
I installed sage-4.7 in a directory as ~/tmp/Downloadz/sage/sage-4.7 and I could run sage by doing cd ~/tmp/Downloadz/sage/sage-4.7; ./sage -n
A day ago, I decided to move the directory into a more permanent location (from ~/tmp :)) and moved the whole folder by mv ~/tmp/Downloadz/sage/sage-4.7 ~/Installations/.. Now, on trying to run sage, I get the following errors:
First, for the notebook:
~/Installations/sage-4.7> ./sage -n ---------------------------------------------------------------------- | Sage Version 4.7, Release Date: 2011-05-23 | | Type notebook() for the GUI, and license() for information. | ---------------------------------------------------------------------- Please wait while the Sage Notebook server starts... Traceback (most recent call last): File "/home/ppurka/Installations/sage-4.7/local/bin/sage-notebook", line 9, in <module> from sage.server.notebook.all import notebook File "/home/ppurka/Installations/sage-4.7/local/lib/python2.6/site-packages/sage/server/notebook/all.py", line 22, in <module> from sagenb.notebook.all import * ImportError: No module named sagenb.notebook.all
For sage itself:
...allations/sage-4.7 [130] > ./sage ---------------------------------------------------------------------- | Sage Version 4.7, Release Date: 2011-05-23 | | Type notebook() for the GUI, and license() for information. | ---------------------------------------------------------------------- --------------------------------------------------------------------------- ImportError Traceback (most recent call last) /home/ppurka/Installations/sage-4.7/local/bin/<string> in <module>() /home/ppurka/Installations/sage-4.7/local/lib/python2.6/site-packages/sage/misc/preparser_ipython.py in <module>() 6 ########################################################################### 7 ----> 8 import sage.misc.interpreter 9 10 import preparser /home/ppurka/Installations/sage-4.7/local/lib/python2.6/site-packages/sage/misc/interpreter.py in <module>() 100 101 import os --> 102 import log 103 import re 104 /home/ppurka/Installations/sage-4.7/local/lib/python2.6/site-packages/sage/misc/log.py in <module>() 63 64 import interpreter ---> 65 import latex 66 import misc 67 /home/ppurka/Installations/sage-4.7/local/lib/python2.6/site-packages/sage/misc/latex.py in <module>() 39 import subprocess 40 ---> 41 from misc import tmp_dir, graphics_filename 42 import sage_eval 43 from sage.misc.misc import SAGE_DOC /home/ppurka/Installations/sage-4.7/local/lib/python2.6/site-packages/sage/misc/misc.py in <module>() 2104 return "0"*(size-len(str(s))) + str(s) 2105 -> 2106 import sage.server.support 2107 2108 def embedded(): /home/ppurka/Installations/sage-4.7/local/lib/python2.6/site-packages/sage/server/support.py in <module>() 17 import sage.misc.pager 18 ---> 19 import sage.misc.sagedoc as sagedoc 20 import sage.misc.sageinspect as sageinspect 21 /home/ppurka/Installations/sage-4.7/local/lib/python2.6/site-packages/sage/misc/sagedoc.py in <module>() 26 from sage.misc.viewer import browser 27 from sage.misc.misc import SAGE_DOC, tmp_dir ---> 28 from sagenb.misc.sphinxify import sphinxify 29 import sage.version 30 ImportError: No module named sagenb.misc.sphinxify WARNING: Failure executing code: 'import sage.misc.preparser_ipython; sage.misc.preparser_ipython.magma_colon_equals=True' --------------------------------------------------------------------------- ImportError Traceback (most recent call last) /home/ppurka/Installations/sage-4.7/local/lib/python2.6/site-packages/IPython/ipmaker.pyc in force_import(modname) 64 reload(sys.modules[modname]) 65 else: ---> 66 __import__(modname) 67 68 /home/ppurka/Installations/sage-4.7/local/bin/ipy_profile_sage.py in <module>() 1 import os 2 if 'SAGE_CLEAN' not in os.environ: ----> 3 import sage.misc.misc 4 from sage.misc.interpreter import preparser, _ip 5 preparser(True) /home/ppurka/Installations/sage-4.7/local/lib/python2.6/site-packages/sage/misc/misc.py in <module>() 2104 return "0"*(size-len(str(s))) + str(s) 2105 -> 2106 import sage.server.support 2107 2108 def embedded(): /home/ppurka/Installations/sage-4.7/local/lib/python2.6/site-packages/sage/server/support.py in <module>() 17 import sage.misc.pager 18 ---> 19 import sage.misc.sagedoc as sagedoc 20 import sage.misc.sageinspect as sageinspect 21 /home/ppurka/Installations/sage-4.7/local/lib/python2.6/site-packages/sage/misc/sagedoc.py in <module>() 26 from sage.misc.viewer import browser 27 from sage.misc.misc import SAGE_DOC, tmp_dir ---> 28 from sagenb.misc.sphinxify import sphinxify 29 import sage.version 30 ImportError: No module named sagenb.misc.sphinxify Error importing ipy_profile_sage - perhaps you should run %upgrade? WARNING: Loading of ipy_profile_sage failed. <ERROR: name 'sage_prompt' is not defined>
grep-ing the sources leads to tons of files which have the earlier path hardcoded into the source files. Just a sample:
~/Installations/sage-4.7> grep -r Downloadz * <showing only some output here> Binary file devel/sage/sage/__init__.pyc matches Binary file devel/sage/sage/misc/package.pyc matches Binary file devel/sage/sage/misc/lazy_import_cache.pyc matches Binary file devel/sage/sage/misc/__init__.pyc matches Binary file local/lib/python2.6/site-packages/speaklater-1.2-py2.6.egg/speaklater.pyc matches
All the errors were fixed as soon as I made a symbolic link as follows:
ln -s ~/Installations/sage-4.7 ~/tmp/Downloadz/sage/.
Since the file ~/Installations/sage-4.7/README.txt claims that sage should be relocatable, I believe this is a relocation bug in sage.
If it matters, my system is a Gentoo Linux amd64 system. I do have a sage-4.7 installation in / installed via the sage-on-gentoo overlay. This installation (the one in ~/Installations) was compiled "manually" by downloading the sage tarball from the website. It was originally compiled inside the ~/tmp/Downloadz/sage directory.
Change History (22)
comment:1 Changed 8 years ago by
- Cc leif added
comment:2 follow-up: ↓ 4 Changed 8 years ago by
comment:3 Changed 8 years ago by
P.S.: If it's just the .pyc
files, you may cure your installation by simply removing them; they'll get recompiled the next time Python executes their respective .py
files.
(I of course don't consider this a solution to the general problem, but it also would be helpful to know whether there are further files which still contain the old location and hinder Sage from starting up without the symbolic link from its original location. AFAIK there'll always remain some "harmless" RPATH
s in shared libraries pointing to the old location.)
comment:4 in reply to: ↑ 2 Changed 8 years ago by
Replying to leif:
Did you notice a message
The Sage install tree may have moved (from ... to ...) Changing various hardcoded paths (please wait at most a few minutes)... Do not interrupt this.when you first started
./sage
in the new directory (~/Installations/sage-4.7/
)?
I'm not sure if (or rather doubt that) Sage will fully work in the presence of another system-wide Sage installation, i.e., if another (different)
sage
is in yourPATH
.The latter might be the problem.
Sorry, I don't clearly remember what was the output at the very first run of sage.
Deleting the .pyc files doesn't work. I get the same error as I got earlier. If I have the symlink, then it does work fine, irrespective of the system wide sage installation. I know that it uses the sage (at least the notebook) from the directory ~/Installations, since I am running the rkirov-flask notebook in that directory. But you are right, there might be other things which are getting mixed up. I will simply try recompiling the local sage installation again.
comment:5 follow-ups: ↓ 6 ↓ 10 Changed 8 years ago by
In the file SAGE_ROOT/local/lib/python/site-packages/easy-install.pth
, there should be a line containing "sagenb". Is the path there relative (../../../../devel/sagenb
) or absolute? If it's absolute, what happens if you replace it with the relative path I gave?
comment:6 in reply to: ↑ 5 Changed 8 years ago by
Replying to jhpalmieri:
In the file
SAGE_ROOT/local/lib/python/site-packages/easy-install.pth
, there should be a line containing "sagenb". Is the path there relative (../../../../devel/sagenb
) or absolute? If it's absolute, what happens if you replace it with the relative path I gave?
I know I once fixed this (especially if SAGE_PATH
was set), but I don't recall if that sagenb spkg ever finally got merged.
comment:7 follow-up: ↓ 9 Changed 8 years ago by
Leif: I think the issue is the flask notebook. With the "classic" notebook, I don't seem to have this problem, and the spkg-install file tries to make the path relative, but when I tried the installation instructions for the flask notebook, I got an absolute path for the notebook (referring to "rkirov-flask" instead of "sagenb"), and it renders my Sage installation non-relocateable.
comment:8 Changed 8 years ago by
Replying to ppurka:
Replying to leif:
Did you notice a message
The Sage install tree may have moved (from ... to ...) Changing various hardcoded paths (please wait at most a few minutes)... Do not interrupt this.
when you first started
./sage
in the new directory (~/Installations/sage-4.7/
)?
I'm not sure if (or rather doubt that) Sage will fully work in the presence of another system-wide Sage installation, i.e., if another (different)
sage
is in yourPATH
.The latter might be the problem.
Sorry, I don't clearly remember what was the output at the very first run of sage.
Well, you can retry by simply renaming the $SAGE_ROOT
directory. ;-)
If I have the symlink, then it does work fine, irrespective of the system wide sage installation. I know that it uses the sage (at least the notebook) from the directory ~/Installations, since I am running the rkirov-flask notebook in that directory. But you are right, there might be other things which are getting mixed up. I will simply try recompiling the local sage installation again.
You could just rename your system-wide sage
command, in /usr/bin/
or /usr/local/bin/
I guess. (command -v sage
should show which one is used when you're outside the separate Sage installation.)
comment:9 in reply to: ↑ 7 Changed 8 years ago by
Replying to jhpalmieri:
Leif: I think the issue is the flask notebook. With the "classic" notebook, I don't seem to have this problem, and the spkg-install file tries to make the path relative, but when I tried the installation instructions for the flask notebook, I got an absolute path for the notebook (referring to "rkirov-flask" instead of "sagenb"), and it renders my Sage installation non-relocateable.
Ah, so it's an upstream problem... :D
comment:10 in reply to: ↑ 5 Changed 8 years ago by
Replying to jhpalmieri:
In the file
SAGE_ROOT/local/lib/python/site-packages/easy-install.pth
, there should be a line containing "sagenb". Is the path there relative (../../../../devel/sagenb
) or absolute? If it's absolute, what happens if you replace it with the relative path I gave?
Excellent! This fixes the relocation problem. Indeed rkirov-flask was written as a full path instead of the relative one. So, this is not a bug in sage relocation per se.
comment:11 follow-up: ↓ 12 Changed 8 years ago by
Can someone report this upstream, to Rado?
comment:12 in reply to: ↑ 11 Changed 8 years ago by
Replying to leif:
Can someone report this upstream, to Rado?
I will see him tomorrow, so I will tell him :)
comment:13 follow-up: ↓ 14 Changed 8 years ago by
I don't understand python's setuptools, but I haven't hardcoded the path anywhere. My guess is that doing "python setup.py develop" does that. Once flask becomes a proper spkg this should go away (hopefully).
comment:14 in reply to: ↑ 13 Changed 8 years ago by
- Keywords flask notebook easy-install.pth easy_install added
Replying to rkirov:
I don't understand python's setuptools, but I haven't hardcoded the path anywhere. My guess is that doing "python setup.py develop" does that. Once flask becomes a proper spkg this should go away (hopefully).
In SageNB, we use
python setup.py develop --egg-path ../../../../devel/sagenb
but that apparently doesn't always work, so I hacked SageNB's spkg-dist
which creates its spkg-install
:
... cd "$SAGE_ROOT/local/lib/python/site-packages" ... if ! grep sagenb easy-install.pth >/dev/null; then # Ugly work-around, we haven't found the real cause yet (see #10176): echo "No sagenb path found in 'easy-install.pth'"'!' echo "Adding relative sagenb path to 'easy-install.pth'..." sed -e '$ i \../../../../devel/sagenb' easy-install.pth > easy-install.pth.$$ if [ $? -ne 0 ]; then echo >&2 "Error adding relative sagenb path to 'easy-install.pth'." exit 1 fi else echo "Making sagenb path in 'easy-install.pth' relative..." sed 's/^.*sagenb.*$/..\/..\/..\/..\/devel\/sagenb/' easy-install.pth > easy-install.pth.$$ if [ $? -ne 0 ]; then echo >&2 "Error patching 'easy-install.pth' to have relative path to SageNB." exit 1 fi fi ... # The following fails only on wrong file permissions etc.: mv -f easy-install.pth.$$ easy-install.pth if [ $? -ne 0 ]; then echo >&2 "Error overwriting original 'easy-install.pth'." exit 1 fi ...
(IIRC the trouble with a completely missing sagenb
path was caused by having SAGE_PATH
set to ".
", but I'm not sure.)
comment:15 follow-up: ↓ 16 Changed 8 years ago by
There is actually absolutely no difference between rkirov-flask/spkg-dist and sagenb-main/spkg-dist. So, this problem will probably "magically go away" once rkirov-flask is actually packaged.
comment:16 in reply to: ↑ 15 Changed 8 years ago by
Replying to ppurka:
There is actually absolutely no difference between rkirov-flask/spkg-dist and sagenb-main/spkg-dist. So, this problem will probably "magically go away" once rkirov-flask is actually packaged.
Yeah, but Rado could add a script (or just a note on that) to the project page.
For the record:
The --egg-path ...
was actually introduced at #10097, and only affects the sagenb.egg-link
file, therefore Mitesh added replacing the absolute path in easy-install.pth
by a relative one.
#10176 and #10192 (the latter patching sage-spkg
, and still needing review) dealt with a completely missing sagenb
entry in easy-install.pth
, due to SAGE_PATH="."
(and removed ln -snf
, see below).
Note that the -n
option of ln -snf
isn't defined by POSIX, and -- worse -- shows different behaviour on GNU/Linux and Solaris, so we must not use it. I'd also change the rkirov-flask
installation instructions, though currently explicitly for Linux, accordingly.
comment:17 Changed 8 years ago by
- Cc rkirov added
comment:18 Changed 7 years ago by
This is still a problem with sage-4.7.2 + jasongrout-flask.
comment:19 Changed 6 years ago by
- Milestone changed from sage-5.6 to sage-duplicate/invalid/wontfix
- Reviewers set to Punarbasu Purkayastha
- Status changed from new to needs_review
comment:20 Changed 6 years ago by
- Status changed from needs_review to positive_review
comment:21 Changed 6 years ago by
sagenb has long ago been merged. And this ticket is pointless now.
comment:22 Changed 6 years ago by
- Resolution set to worksforme
- Status changed from positive_review to closed
Did you notice a message
when you first started
./sage
in the new directory (~/Installations/sage-4.7/
)?I'm not sure if (or rather doubt that) Sage will fully work in the presence of another system-wide Sage installation, i.e., if another (different)
sage
is in yourPATH
.The latter might be the problem.