bugGNU Astronomy Utilities - Bugs: bug #57891, make fails after successfully...

 
 

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bug #57891: make fails after successfully bootstrapping and configuring

Submitter:  Kartik Ohri <lucifer13>
Submitted:  Tue 25 Feb 2020 02:13:53 PM UTC
   
 
Category:  Installation Severity:  3 - Normal
Item Group:  Crash Status:  Fixed
Privacy:  Public Assigned to:  makhlaghi
Open/Closed:  Closed

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Sun 21 Feb 2021 01:55:40 AM UTC, comment #11: 

This issue should be fixed by the recent series of commits related to the installation: Commit 4687c256e, Commit e723937db9 and Commit ffe22747f6. They fixed similar issues on another system with similar errors.

So I am closing this bug. But if you do get the chance to do a clean bootstrap and build and you confront this error again, please re-open this bug.

Mohammad Akhlaghi <makhlaghi>
Group administrator
Wed 26 Feb 2020 11:41:26 PM UTC, comment #10: 

Kartik, in the suggested value to LIBS, you shouldn't add `-lgit2' (from the warning in the end of the configure script, we know that that you don't have libgit2, so don't add it).

Mohammad Akhlaghi <makhlaghi>
Group administrator
Wed 26 Feb 2020 11:39:23 PM UTC, comment #9: 

I tried bootstrapping Gnuastro from source and couldn't reproduce the error unfortunately (it was built successfully)!

Sachim, the fact that it built successfully before, but is suddenly failing for you is very strange!!! Did you update your version of Gnulib (by running `git pull')? Or maybe did you update your operating system?

Kartik, Can you please try the tarball is well? In the instructions, I had first asked to install from the tarball (which has been tested more), then go onto the version controlled source. We should see if this is a problem that has been recently added since the previous release on systems like yours, or if it always existed. The warning at the end of the configure script is about an un-related optional dependency (libgit2).

For both: probably there is some good information to help find the solution in the output of the configure step also. Can you please run `git clean -fxd' (to delete all non-version controlled files), and re-do the bootstrap? Afterwards when you run `./configure && make -j8', send me the full output. You can run it like this so it also cleans the terminal


reset && ./configure && make -j8


Since adding the `LIBS' variable to the `./configure' script fixed the problem with GSL, it will probably also solve the problem with WCSLIB and other libraries is well. So after sending the output of the command above, if you configure Gnuastro like below it should work:


./configure LIBS="-lgit2 -ltiff -llzma -ljpeg -lwcs -lcfitsio -lcurl -lz -lgsl -lgslcblas -lm -lc"


For some reason, on your systems, these linking flags aren't being passed onto the programs!!!

Mohammad Akhlaghi <makhlaghi>
Group administrator
Wed 26 Feb 2020 08:55:43 PM UTC, comment #8: 

I didn't try to build from tarball.
I tried your command. Here is the new log. Also, there is a warning from configure at the top as well. I don't remember if it was there previously as well.

(file #48504)

Kartik Ohri <lucifer13>
Wed 26 Feb 2020 05:31:56 PM UTC, comment #7: 

Now it's showing the error in a different file

libtool: link: gcc -Wall -O3 -pthread -o .libs/astcrop main.o ui.o crop.o wcsmode.o onecrop.o  -L../../lib ../../bootstrapped/lib/.libs/libgnu.a /dev/shm/gnuastro-0.11.24-5600/lib/.libs/libgnuastro.so -lpthread -pthread
/usr/bin/ld: ui.o: undefined reference to symbol 'wcshdo'
/usr/local/lib/libwcs.so.7: error adding symbols: DSO missing from command line

I've installed the gsl library from the source. It worked well before the last commit but suddenly showed this error. To fix it even installed the library from my package manager. Also ./configure LIBS="-lgsl -lgslcblas -lm" showed the same result. I also reverted back to my last commit but it's still there.

Sachin Kumar Singh <sks_15>
Wed 26 Feb 2020 12:17:03 AM UTC, comment #6: 

Just as a small test, can you try running the configure script, while settings LIBS like below, then configure it:


./configure LIBS="-lgsl -lgslcblas -lm"
make


If this works, then the problem is probably that the linking command isn't being passed. If it still doesn't work, there is probably a problem with the installed GSL library. By the way, how did you install GSL?

Mohammad Akhlaghi <makhlaghi>
Group administrator
Tue 25 Feb 2020 10:42:08 PM UTC, comment #5: 

On a side-note, does it install successfully when you build from the tarball?

Mohammad Akhlaghi <makhlaghi>
Group administrator
Tue 25 Feb 2020 10:37:43 PM UTC, comment #4: 

I am on Ubuntu 19.10.

Here is the info you asked for:

dependency_libs=' -R/usr/local/lib  -ltiff -llzma -ljpeg -L/usr/local/lib -lwcs -lcfitsio /usr/lib/x86_64-linux-gnu/libcurl.la -lz /usr/local/lib/libgsl.la /usr/local/lib/libgslcblas.la -lm -lc -lpthread'

CONFIG_LDADD = -ltiff -llzma -ljpeg -L/usr/local/lib -lwcs -R/usr/local/lib -lcfitsio -lcurl -lz -L/usr/local/lib -lgsl -L/usr/local/lib -lgslcblas -lm -R/usr/local/lib -lm

Kartik Ohri <lucifer13>
Tue 25 Feb 2020 10:11:28 PM UTC, comment #3: 

This is good, thanks ;-)! This is the main error line:


/usr/bin/ld: /usr/local/lib/libgsl.so.25: error adding symbols: DSO missing from command line


The GSL library can't be linked with in building the Convolve program. For some reason, the exact libraries that it links with isn't printed on your system. What is your OS by the way?

For example on my computer, the command to link the Convolve program looks like this:


libtool: link: gcc -Wall -O3 -pthread -o .libs/astconvolve main.o ui.o convolve.o  -L../../lib ../../bootstrapped/lib/.libs/libgnu.a /dev/shm/source-0.11.26-288d/lib/.libs/libgnuastro.so -L/usr/local/lib -lgit2 -ltiff -llzma -ljpeg -lwcs -lcfitsio -lcurl -lz /usr/local/lib/libgsl.so /usr/local/lib/libgslcblas.so -lm -lc -pthread -Wl,-rpath -Wl,/usr/local/lib


But on your system, it looks like this


libtool: link: gcc -Wall -O3 -pthread -o .libs/astconvolve main.o ui.o convolve.o  -L../../lib ../../bootstrapped/lib/.libs/libgnu.a /home/amcap1712/gnuastro/lib/.libs/libgnuastro.so -lpthread -pthread


However, it has successfully found the need for linking with GSL from the first line quoted above. Probably the problem is in the ordering on your system.

This should be visible in the `libgnuastro.la' file. You can find it in the `lib/' directory. Can you send value of the `dependency_lib' variable in that file?

You should also see the list of libraries in the top-level `Makefile'. Can you post the value of `CONFIG_LDADD' in there?

Mohammad Akhlaghi <makhlaghi>
Group administrator
Tue 25 Feb 2020 09:26:29 PM UTC, comment #2: 

I had uploaded the wrong log file previously. I have fixed that now and uploaded the correct logs.

Kartik Ohri <lucifer13>
Tue 25 Feb 2020 09:03:12 PM UTC, comment #1: 

Thanks for reporting this. In the attached `log.txt' file, I only see three lines about `Postman-1573300134947'. Can you please send the full output on the terminal? From the moment you run `make' until it crashes.

Mohammad Akhlaghi <makhlaghi>
Group administrator
Tue 25 Feb 2020 02:13:53 PM UTC, original submission:  

I am trying to build gnuastro from version controlled source. I have successfully run bootstrapped and run ./configure but running make fails with the following output.



Kartik Ohri <lucifer13>

 

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Attached Files
file #48504:  log.txt added by lucifer13 (144KiB - text/plain)
file #48499:  log.txt added by lucifer13 (93KiB - text/plain)
file #48497:  log.txt added by lucifer13 (226B - text/plain)

 

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  • -email is unavailable- added by sks_15 (Posted a comment)
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    Follow 7 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2021-02-21 makhlaghi StatusNone Fixed
        Assigned toNone makhlaghi
        Open/ClosedOpen Closed
    2020-02-26 lucifer13 Attached File- Added log.txt, #48504
    2020-02-25 lucifer13 Attached File- Added log.txt, #48499
    2020-02-25 lucifer13 Carbon-Copy- Added makhlaghi
    2020-02-25 lucifer13 Attached File- Added log.txt, #48497

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