#5964: Some R doctests related to documentation fail when perl-modules not
installed at compile-time
------------------------+---------------------------------------------------
Reporter: tornaria | Owner: was
Type: defect | Status: new
Priority: major | Milestone:
Component: interfaces | Keywords:
------------------------+---------------------------------------------------
The doctest failures:
{{{
sage -t "devel/sage/sage/interfaces/r.py"
**********************************************************************
File "/usr/src/sage-3.4.1/devel/sage/sage/interfaces/r.py", line 665:
sage: r.help('print.anova')
Expected:
anova package:stats R Documentation
...
'coefficients', 'effects', 'fitted.values', 'residuals',
'summary', 'drop1', 'add1'.
Got:
No documentation for 'print.anova' in specified packages and
libraries:
you could try 'help.search("print.anova")'
**********************************************************************
File "/usr/src/sage-3.4.1/devel/sage/sage/interfaces/r.py", line 1707:
sage: print length._sage_doc_()
Expected:
length package:base R Documentation
...
<BLANKLINE>
Got:
No documentation for 'length' in specified packages and libraries:
you could try 'help.search("length")'
**********************************************************************
File "/usr/src/sage-3.4.1/devel/sage/sage/interfaces/r.py", line 1780:
sage: print length._sage_doc_()
Expected:
length package:base R Documentation
...
<BLANKLINE>
Got:
No documentation for 'length' in specified packages and libraries:
you could try 'help.search("length")'
**********************************************************************
3 items had failures:
1 of 3 in __main__.example_23
1 of 5 in __main__.example_68
1 of 4 in __main__.example_73
***Test Failed*** 3 failures.
For whitespace errors, see the file /usr/src/sage-3.4.1/tmp/.doctest_r.py
[5.1 s]
}}}
----
Looking at the {{{install.log}}} shows two types of "failure":
- missing {{{makeinfo}}}:
{{{
you should 'make docs' now ...
make[3]: Entering directory
`/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/doc'
make[4]: Entering directory
`/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/doc/manual'
'makeinfo' v4.7 or later needed to make HTML docs but missing on your
system.
file R-FAQ.html will be missing
creating doc/manual/version.texi
'makeinfo' v4.7 or later needed to make HTML docs but missing on your
system.
file R-data.html will be missing
'makeinfo' v4.7 or later needed to make HTML docs but missing on your
system.
file R-exts.html will be missing
'makeinfo' v4.7 or later needed to make HTML docs but missing on your
system.
file R-intro.html will be missing
'makeinfo' v4.7 or later needed to make HTML docs but missing on your
system.
file R-ints.html will be missing
'makeinfo' v4.7 or later needed to make HTML docs but missing on your
system.
file R-lang.html will be missing
make[5]: Entering directory
`/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/doc/html'
make[5]: Leaving directory
`/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/doc/html'
make[4]: Leaving directory
`/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/doc/manual'
make[3]: Leaving directory
`/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/doc'
}}}
- missing perl module {{{File/Basename.pm}}}:
{{{
make[3]: Entering directory
`/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/src/library'
building all R object docs (text, HTML, LaTeX, examples)
make[4]: Entering directory
`/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/src/library'
Can't locate File/Basename.pm in @INC (@INC contains:
/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/share/perl /etc/perl
/usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
/usr/local/lib/site_perl .) at ../../share/perl/build-help.pl line 18.
BEGIN failed--compilation aborted at ../../share/perl/build-help.pl line
18.
Can't locate File/Basename.pm in @INC (@INC contains:
/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/share/perl /etc/perl
/usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
/usr/local/lib/site_perl .) at ../../share/perl/build-help.pl line 18.
BEGIN failed--compilation aborted at ../../share/perl/build-help.pl line
18.
Can't locate File/Basename.pm in @INC (@INC contains:
/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/share/perl /etc/perl
/usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
/usr/local/lib/site_perl .) at ../../share/perl/build-help.pl line 18.
BEGIN failed--compilation aborted at ../../share/perl/build-help.pl line
18.
Can't locate File/Basename.pm in @INC (@INC contains:
/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/share/perl /etc/perl
/usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
/usr/local/lib/site_perl .) at ../../share/perl/build-help.pl line 18.
BEGIN failed--compilation aborted at ../../share/perl/build-help.pl line
18.
Can't locate File/Basename.pm in @INC (@INC contains:
/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/share/perl /etc/perl
/usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
/usr/local/lib/site_perl .) at ../../share/perl/build-help.pl line 18.
BEGIN failed--compilation aborted at ../../share/perl/build-help.pl line
18.
Can't locate File/Basename.pm in @INC (@INC contains:
/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/share/perl /etc/perl
/usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
/usr/local/lib/site_perl .) at ../../share/perl/build-help.pl line 18.
BEGIN failed--compilation aborted at ../../share/perl/build-help.pl line
18.
Can't locate File/Basename.pm in @INC (@INC contains:
/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/share/perl /etc/perl
/usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
/usr/local/lib/site_perl .) at ../../share/perl/build-help.pl line 18.
BEGIN failed--compilation aborted at ../../share/perl/build-help.pl line
18.
Can't locate File/Basename.pm in @INC (@INC contains:
/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/share/perl /etc/perl
/usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
/usr/local/lib/site_perl .) at ../../share/perl/build-help.pl line 18.
BEGIN failed--compilation aborted at ../../share/perl/build-help.pl line
18.
Can't locate File/Basename.pm in @INC (@INC contains:
/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/share/perl /etc/perl
/usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
/usr/local/lib/site_perl .) at ../../share/perl/build-help.pl line 18.
BEGIN failed--compilation aborted at ../../share/perl/build-help.pl line
18.
Can't locate File/Basename.pm in @INC (@INC contains:
/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/share/perl /etc/perl
/usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
/usr/local/lib/site_perl .) at ../../share/perl/build-help.pl line 18.
BEGIN failed--compilation aborted at ../../share/perl/build-help.pl line
18.
Can't locate File/Basename.pm in @INC (@INC contains:
/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/share/perl /etc/perl
/usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
/usr/local/lib/site_perl .) at ../../share/perl/build-help.pl line 18.
BEGIN failed--compilation aborted at ../../share/perl/build-help.pl line
18.
Can't locate File/Basename.pm in @INC (@INC contains:
/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/share/perl /etc/perl
/usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
/usr/local/lib/site_perl .) at ../../share/perl/build-help.pl line 18.
BEGIN failed--compilation aborted at ../../share/perl/build-help.pl line
18.
make[4]: *** [help-indices] Error 2
make[4]: Leaving directory
`/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/src/library'
make[3]: *** [docs] Error 2
make[3]: Leaving directory
`/usr/src/sage-3.4.1/spkg/build/r-2.6.1.p22/src/src/library'
make[2]: [docs] Error 2 (ignored)
}}}
----
This is on a "barebones" debian lenny, which only has {{{perl-base}}}, but
no {{{perl-modules}}} installed, thus {{{File/Basename.pm}}} is indeed
missing.
Reinstalling r-2.6.1.p22.spkg ''after'' {{{apt-get install perl-modules}}}
fixes the issue: the {{{install.log}}} still complains about missing
{{{makeinfo}}}, but that seems irrelevant, and the doctest in
{{{devel/sage/sage/interfaces/r.py}}} pass.
I believe the prereq test actually checks if perl is installed, but that
seems to not be enough. Adding a check for a few required perl modules may
be in order... (cf #5517, whose dependency on {{{File/Copy.pm}}} was
actually eliminated, but the point stands).
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/5964>
Sage <http://sagemath.org/>
Sage - Open Source Mathematical Software: Building the Car Instead of
Reinventing the Wheel
--~--~---------~--~----~------------~-------~--~----~
You received this message because you are subscribed to the Google Groups
"sage-trac" group.
To post to this group, send email to [email protected]
To unsubscribe from this group, send email to
[email protected]
For more options, visit this group at
http://groups.google.com/group/sage-trac?hl=en
-~----------~----~----~----~------~----~------~--~---
