Hi,
Sorry for not getting pack to this thread before. I'm still having this
issue that newly compiled Sage is missing many packages.
Overnight I did `make distclean && make --trace --debug=bvjm` on Sage
7.3.beta7 with #20926 applied (gcc6.1 C++ workarounds). I had downgraded
my Make to version 4.1.
The result is the same: Building the docs crashed due to uninstalled
jmol. Other packages are also missing: palp, sympy,
database_cremona_ellcurve, etc.
The missing packages are listed in the beginning of the build:
Makefile:24: update target 'build/make/Makefile' due to: <long list
of dependencies including palp, sympy, jmol, etc.>
They are also mentioned a few pages below:
...
checking for sqrt in -lm... yes
checking multiprecision library... MPIR
checking BLAS library... atlas
checking package versions...
4ti2-1.6.7
alabaster-0.7.8
... <long list of packages including palp, sympy, jmol, etc.>
However, none of the not-installed packages are mentioned again in the
logs! Those that are installed are of course in the log, a few examples:
...
[arb-2.8.1.p0] Finished installing arb-2.8.1.p0.spkg
Successfully remade target file
'/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/arb-2.8.1.p0'.
File
'/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/atlas-3.10.2.p2'
does not exist.
File
'/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/python2-2.7.10.p2'
does not exist.
File
'/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/readline-6.3.008'
does not exist.
File
'/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/ncurses-5.9.20131221'
does not exist.
Must remake target
'/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/ncurses-5.9.20131221'.
Makefile:2142: target
'/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/ncurses-5.9.20131221'
does not exist
sage-logger -p 'sage-spkg ncurses-5.9.20131221'
'/home/jsrn/mat/sage_coding_project/logs/pkgs/ncurses-5.9.20131221.log'
...
[ipython_genutils-0.1.0] Finished installing ipython_genutils-0.1.0.spkg
Successfully remade target file
'/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/ipython_genutils-0.1.0'.
File
'/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/decorator-4.0.6'
does not exist.
Must remake target
'/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/decorator-4.0.6'.
Makefile:1436: update target
'/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/decorator-4.0.6'
due to:
/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/setuptools-21.0.0
sage-logger -p 'sage-spkg decorator-4.0.6'
'/home/jsrn/mat/sage_coding_project/logs/pkgs/decorator-4.0.6.log'
[decorator-4.0.6] Found local metadata for decorator-4.0.6
...
[sphinx-1.4.1.p1] Finished installing sphinx-1.4.1.p1.spkg
Successfully remade target file
'/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/sphinx-1.4.1.p1'.
File
'/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/sagenb-0.13'
does not exist.
File
'/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/flask-0.10.1'
does not exist.
File
'/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/werkzeug-0.11.9'
does not exist.
Must remake target
'/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/werkzeug-0.11.9'.
Makefile:2804: update target
'/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/werkzeug-0.11.9'
due to:
/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/python2-2.7.10.p2
sage-logger -p 'sage-spkg werkzeug-0.11.9'
'/home/jsrn/mat/sage_coding_project/logs/pkgs/werkzeug-0.11.9.log'
...
Makefile:2828: target
'/home/jsrn/mat/sage_coding_project/local/var/lib/sage/installed/zlib-1.2.8.p0'
does not exist
sage-logger -p 'sage-spkg zlib-1.2.8.p0'
'/home/jsrn/mat/sage_coding_project/logs/pkgs/zlib-1.2.8.p0.log'
It looks to me like some explicit dependencies to the not-installed
packages, as has been discussed with Jmol recently, must have been
removed or altered, and that's why Make is not picking up those targets.
Any thoughts?
Best,
Johan
leif writes:
> Johan S. H. Rosenkilde wrote:
>>> Except for the Sage library (and probably docbuilding, not sure), yes.
>>> If you explicitly use 'make -j1', then also the Sage library will be
>>> built sequentially, still using Python's multi-processing though, as
>>> does docbuilding.
>>
>> I've done `make distclean && make -j1`. Let's see how that one goes...
>
> If that still omitted standard packages, I'd suggest to experiment with
> GNU make's debug options (you can also add '-n' aka '--dry-run').
>
> '-d' (='--debug=a') is far too verbose, but e.g. '--debug=bvjm',
> probably also with '--trace' may give you a clue what's happening (or
> why 'make' /doesn't/ build some targets).
>
>
> -leif
>
>
>>> Forgot to ask:
>>>
>>> How does at all local/var/lib/sage/installed/ look like?
>>
>> See below. It doesn't contain the packages I know are missing. I don't
>> know if other packages are also missing.
>>
>> alabaster-0.7.8
>> arb-2.8.1.p0
>> atlas-3.10.2.p2
>> babel-2.3.4
>> backports_abc-0.4
>> backports_shutil_get_terminal_size-1.0.0.p0
>> backports_ssl_match_hostname-3.5.0.1
>> boost_cropped-1.58.0
>> brial-0.8.4.3
>> bzip2-1.0.6-20150304
>> cephes-2.8.p1
>> certifi-2016.2.28
>> cliquer-1.21.p3
>> conway_polynomials-0.4.p0
>> cycler-0.10.0
>> cysignals-1.1.1
>> cython-0.24.p0
>> dateutil-2.2
>> decorator-4.0.6
>> docutils-0.12
>> ecl-16.1.2.p0
>> eclib-20150827
>> ecm-6.4.4
>> fflas_ffpack-1.6.0.p2
>> flask-0.10.1
>> flask_autoindex-0.6
>> flask_babel-0.9
>> flask_oldsessions-0.10
>> flask_openid-1.2.5
>> flask_silk-0.2
>> flint-2.5.2.p0
>> freetype-2.6.3
>> future-0.15.2
>> gap-4.8.3
>> gc-7.2f.p0
>> gf2x-1.1.p1
>> givaro-3.7.1
>> glpk-4.55.p1
>> gsl-2.1
>> iconv-1.14
>> imagesize-0.7.1
>> iml-1.0.4p1.p1
>> ipykernel-4.3.1
>> ipython-4.2.0
>> ipython_genutils-0.1.0
>> itsdangerous-0.24
>> jinja2-2.8
>> jupyter_client-4.2.2
>> jupyter_core-4.1.0
>> lcalc-1.23.p14
>> libfplll-20160331
>> libgap-4.8.3
>> libgd-2.1.1.1.p0
>> libpng-1.2.51.p0
>> linbox-1.3.2.p1
>> lrcalc-1.2.p0
>> m4ri-20140914
>> m4rie-20150908
>> markupsafe-0.23
>> mathjax-2.5
>> matplotlib-1.5.1
>> maxima-5.35.1.p2
>> mpc-1.0.3.p0
>> mpfi-1.5.1
>> mpfr-3.1.4
>> mpir-2.7.2
>> mpmath-0.19
>> ncurses-5.9.20131221
>> networkx-1.11
>> ntl-9.8.1.p0
>> numpy-1.11.0.p0
>> pari-2.8-2771-gb70b447.p0
>> pari_galdata-20080411
>> pari_seadata_small-20090618
>> patch-2.7.5
>> pathlib2-2.1.0
>> pathpy-7.1
>> pexpect-4.0.1.p1
>> pickleshare-0.7.2
>> pillow-3.2.0
>> pip-8.1.2
>> pkgconf-0.9.7
>> pkgconfig-1.1.0
>> planarity-2.2.0
>> ppl-1.1
>> ptyprocess-0.5.1
>> pygments-2.1.3
>> pynac-0.6.7
>> pyparsing-2.1.4
>> python2-2.7.10.p2
>> python_openid-2.2.5
>> pytz-2016.4
>> pyzmq-15.2.0
>> ratpoints-2.1.3.p3
>> readline-6.3.008
>> rw-0.7
>> sagenb-0.13
>> scipy-0.17.1
>> setuptools-21.0.0
>> setuptools_scm-1.11.0
>> simplegeneric-0.8.1
>> singledispatch-3.4.0.3
>> singular-3.1.7p1.p1
>> six-1.10.0
>> snowballstemmer-1.2.1
>> speaklater-1.3
>> sphinx-1.4.1.p1
>> sqlite-autoconf-3130000
>> symmetrica-2.0.p9
>> tachyon-0.98.9.p5
>> tornado-4.3
>> traitlets-4.2.1
>> twisted-16.2.0
>> werkzeug-0.11.9
>> zeromq-4.0.5
>> zlib-1.2.8.p0
>> zn_poly-0.9.p11
>> zope_interface-4.1.3
>>
>>
>> Best,
>> Johan
>>
>>
>> leif writes:
>>
>>> Johan S. H. Rosenkilde wrote:
>>>>> $ make --version
>>>> GNU Make 4.2.1
>>>> Built for x86_64-pc-linux-gnu
>>>>
>>>>> Did you build in parallel, and if so, does probably building
>>>>> sequentially fix the problem (such that the missing packages then get
>>>>> built)?
>>>>
>>>> I just did "make"; the default is still sequential build, right? I have
>>>> no suspect environment variables.
>>>
>>> Except for the Sage library (and probably docbuilding, not sure), yes.
>>> If you explicitly use 'make -j1', then also the Sage library will be
>>> built sequentially, still using Python's multi-processing though, as
>>> does docbuilding.
>>>
>>>
>>> Forgot to ask:
>>>
>>> How does at all local/var/lib/sage/installed/ look like?
>>>
>>>
>>> -leif
>>
>>
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