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From: Mohammad Akhlaghi
Date: Fri, 27 Nov 2020 23:35:12 +0000
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.4.3

Thanks a lot for the check Bruno,

Did you see the message I sent a few hours ago (forwarded message below)? I was able to track down the Gnulib commit causing this issue.

To answer your questions: there isn't any 'stdio.h' in either of '/dev/shm/gnuastro-0.13.58-dad9/lib' or '/src/dir/gnuastro/lib'.

Thanks for reporting the problems with bootstrapping:

About LaTeX dependency in the boostrapping phase: its because some of the figures of the Gnuastro manual (like those in [1] or [2]) are created by LaTeX at this phase.

In the version controlled source of Gnuastro, we only keep the hand-written LaTeX source of these figures. But these figures are necessary for a normal build of the tarball (since they are mentioned in the Texinfo source). If we building them during the building of the documentation, then users will be forced to have LaTeX and its necessary packages to build Gnuastro. But if we do it during bootstrapping, only the developers need to have it.

Generally, all the bootstrapping dependencies of Gnuastro are documented in [3], which includes the list of necessary LaTeX packages. Gnuastro's mandatory dependencies are also listed in [4]. But to simplify the installation of the dependencies, we have added the commands to install them with some common package managers in [5]

Thanks a lot,

[1] https://www.gnu.org/software/gnuastro/manual/html_node/Circles-and-the-complex-plane.html [2] https://www.gnu.org/software/gnuastro/manual/html_node/Sampling-theorem.html [3] https://www.gnu.org/software/gnuastro/manual/html_node/Bootstrapping-dependencies.html [4] https://www.gnu.org/software/gnuastro/manual/html_node/Mandatory-dependencies.html [5] https://www.gnu.org/software/gnuastro/manual/html_node/Dependencies-from-package-managers.html

-------- Forwarded Message --------
Date: Fri, 27 Nov 2020 14:07:44 +0000
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
To: Paul Eggert <eggert@cs.ucla.edu>
CC: Gnulib bugs <bug-gnulib@gnu.org>

I found the Gnulib commit causing the problem:


Gnuastro (on Commit c70f16c8f13c) builds with no warnings when bootstrapped with the previous Gnulib commit (cb432e7d6144). But on this Gnulib commit (387d654cabd) I get these warnings.

Since nothing has changed in Gnuastro, I guess the problem lies in this commit of Gnulib. Please let me know if I need to check anything else.

Thanks again for all the great work on Gnulib,

On 11/27/20 8:55 PM, Bruno Haible wrote:
Mohammad Akhlaghi wrote:
But I got many warnings related to '_GL_ATTRIBUTE_SPEC_PRINTF_SYSTEM' in
'error.h' and 'argp.h'. You can see some of them in the P.S, and the
full build log (with the warnings in the middle of the build commands)
is available in this compressed text file:


 From this log it is clear that gnulib generated an stdio.h file
in /dev/shm/gnuastro-0.13.58-dad9/bootstrapped/lib/

Later on, the command that produces the warnings is, in directory
/dev/shm/gnuastro-0.13.58-dad9/lib :

libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/src/dir/gnuastro/lib -I.. 
-I/src/dir/gnuastro/bootstrapped/lib -DSYSCONFIG_DIR=\"/usr/local/etc\" 
-I/home/myuser/.local/include -Wall -g -O0 -pthread -MT arithmetic-bitlsh.lo -MD -MP -MF 
.deps/arithmetic-bitlsh.Tpo -c /src/dir/gnuastro/lib/arithmetic-bitlsh.c -o 

It looks like some other stdio.h file has taken precedence. Do you have
such a file in some of the directories mentioned as -I options, such as
/src/dir/gnuastro/lib ?

This would explain it.


PS: I tried to check out gnuastro and build it, but failed:

1) During './bootstrap --gnulib-srcdir=$GNULIB_SRCDIR' already it builds
some documentation. (Shouldn't this be part of 'make pdf'?) It fails:

   ! LaTeX Error: File `biblatex.sty' not found.

   Type X to quit or <RETURN> to proceed,
   or enter new name. (Default extension: sty)

   Enter file name:

2) During '../configure CPPFLAGS=-Wall':
checking Ghostscript version... 9.26

Missing MANDATORY dependencies (necessary to continue):
  - GNU Scientific Library (GSL): https://www.gnu.org/software/gsl
  - CFITSIO: https://heasarc.gsfc.nasa.gov/fitsio
  - WCSLIB: http://www.atnf.csiro.au/people/mcalabre/WCS

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