experimental package macaulay2-1.1-r7221.p0.spkg fails to install

[sagetrac-mariah]

sage-4.7.1 on the Skynet machine eno (x86_64-Linux-core2-fc) fails to install the experimental package macaulay2-1.1-r7221.p0.spkg.

(Note that installing optional package gdbm-1.8.3.spkg is a prerequiste for installing macaulay2-1.1-r7221.p0.spkg.)

Rather than fix this problem, it may be better to upgrade to
a more recent version of Macaulay2, such as macaulay2-1.4-r12617.

eno% ./sage -i ../optional/bug/macaulay2-1.1-r7221.p0.spkg
Installing ../optional/bug/macaulay2-1.1-r7221.p0.spkg
Calling sage-spkg on ../optional/bug/macaulay2-1.1-r7221.p0.spkg
Warning: Attempted to overwrite SAGE_ROOT environment variable
macaulay2-1.1-r7221.p0
Machine:
Linux eno 2.6.40-4.fc15.x86_64 #1 SMP Fri Jul 29 18:46:53 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux
Deleting directories from past builds of previous/current versions of macaulay2-1.1-r7221.p0
Extracting package /home/mariah/sage/sage-4.7.1-x86_64-Linux-core2-fc-macaulay2/../optional/bug/macaulay2-1.1-r7221.p0.spkg ...
-rw-r----- 1 mariah sage 2652090 Dec 24  2008 /home/mariah/sage/sage-4.7.1-x86_64-Linux-core2-fc-macaulay2/../optional/bug/macaulay2-1.1-r7221.p0.spkg
Finished extraction
****************************************************
Host system
uname -a:
Linux eno 2.6.40-4.fc15.x86_64 #1 SMP Fri Jul 29 18:46:53 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux
****************************************************
****************************************************
CC Version
gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/gcc-4.6.1/x86_64-Linux-core2-fc/libexec/gcc/x86_64-unknown-linux-gnu/4.6.1/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: /usr/local/gcc-4.6.1/src/gcc-4.6.1/configure --enable-languages=c,c++,fortran --with-gnu-as --with-gnu-as=/usr/local/binutils-2.21/x86_64-Linux-core2-fc-gcc-4.5.1-rh/bin/as --with-gnu-ld --with-ld=/usr/local/binutils-2.21/x86_64-Linux-core2-fc-gcc-4.5.1-rh/bin/ld --with-gmp=/usr/local/mpir-2.4.0/x86_64-Linux-core2-fc-gcc-4.6.0-rh --with-mpfr=/usr/local/mpfr-3.0.1/x86_64-Linux-core2-fc-mpir-2.4.0-gcc-4.6.0-rh --with-mpc=/usr/local/mpc-0.9/x86_64-Linux-core2-fc-mpir-2.4.0-mpfr-3.0.1-gcc-4.6.0-rh --prefix=/usr/local/gcc-4.6.1/x86_64-Linux-core2-fc
Thread model: posix
gcc version 4.6.1 (GCC) 
****************************************************
+ autoconf

...stuff deleted...

checking for a BSD-compatible install... /usr/bin/install -c
checking for gawk... gawk
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in `/home/mariah/sage/sage-4.7.1-x86_64-Linux-core2-fc-macaulay2/spkg/build/macaulay2-1.1-r7221.p0/src/BUILD/normal':
configure: error: C compiler cannot create executables
See `config.log' for more details

Depends on #13234

Component: packages: experimental

Keywords: sd32, sd40.5

Author: Andrey Novoseltsev

Reviewer: John Perry

Issue created by migration from https://trac.sagemath.org/ticket/11710

[nexttime]

comment:1

Attaching config.log in this case wouldn't be bad.

But as you mentioned, the package is fairly old anyway, which doesn't necessarily mean a newer version will install seamlessly. Did you already try that?

[sagetrac-mariah]

comment:2

Yes, I tried installing a newer version. It did not go well, and
I have abandoned the effort for now. (Other things are demanding my attention.) Perhaps someone else will have better luck!

[nexttime]

Description changed:

--- 
+++ 
@@ -1,9 +1,9 @@
-sage-4.7.1 on eno (x86_64-Linux-core2-fc) fails to install experimental package macaulay2-1.1-r7221.p0.spkg.  
+sage-4.7.1 on the [Skynet machine eno](http://wiki.sagemath.org/skynet#Eno) (x86_64-Linux-core2-fc) fails to install the [experimental package macaulay2-1.1-r7221.p0.spkg](http://www.sagemath.org//packages/experimental/macaulay2-1.1-r7221.p0.spkg).
 
-(Note that installing optional package gdbm-1.8.3.spkg is a prerequiste for installing macaulay2-1.1-r7221.p0.spkg.)
+(Note that installing [optional package gdbm-1.8.3.spkg](http://www.sagemath.org/packages/optional/gdbm-1.8.3.spkg) is a prerequiste for installing `macaulay2-1.1-r7221.p0.spkg`.)
 
 Rather than fix this problem, it may be better to upgrade to
-a more recent version of macaulay2, such as macaulay2-1.4-r12617.
+a more recent version of [Macaulay2](http://www.math.uiuc.edu/Macaulay2/), such as [macaulay2-1.4-r12617](http://www.math.uiuc.edu/Macaulay2/Downloads/SourceCode/Macaulay2-1.4-r12617-src.tar.bz2).
 
 ```
 eno% ./sage -i ../optional/bug/macaulay2-1.1-r7221.p0.spkg
@@ -45,5 +45,5 @@
 configure: error: in `/home/mariah/sage/sage-4.7.1-x86_64-Linux-core2-fc-macaulay2/spkg/build/macaulay2-1.1-r7221.p0/src/BUILD/normal':
 configure: error: C compiler cannot create executables
 See `config.log' for more details
+```
 
-```

[williamstein]

Changed keywords from none to sd32

[novoselt]

comment:5

For the record: Macaulay2 1.5 is about to be released.

[benjaminfjones]

comment:6

To review #12335 I need to install the spkg macaulay2-1.1-r7221.p0 into sage-5.0 but when I try I get:

Error: the autoconf program is not installed on your system.

/bin/sh: autoconf: not found
Please install or update autoconf: the version () should be at least 2.59.

It's mentioned in the error message that one can try:

make get-autoconf

but going to a sage shell and into the spkg src and running this command fails:

(sage-sh) jonesbe@sage:src$ make get-autoconf
make -f Makefile -C autoconf
make[1]: Entering directory `/home/jonesbe/sage/sage-5.0/spkg/build/macaulay2-1.1-r7221.p0/src/autoconf'
curl ftp://ftp.gnu.org/gnu/autoconf/autoconf-2.61.tar.gz -o "autoconf-2.61.tar.gz" && touch .fetched
/bin/sh: curl: not found
make[1]: *** [.fetched] Error 127
make[1]: Leaving directory `/home/jonesbe/sage/sage-5.0/spkg/build/macaulay2-1.1-r7221.p0/src/autoconf'
make: *** [get-autoconf] Error 2

[johnperry-math]

comment:7

Replying to @benjaminfjones:

To review #12335 I need to install the spkg macaulay2-1.1-r7221.p0 into sage-5.0 but when I try I get:

Error: the autoconf program is not installed on your system.

Is autoconf installed on your system? If not, does Sage include its own autoconf?

These may be dumb questions, but I can get past the autoconf, maybe because it's on my system. It breaks for me elsewhere.

[novoselt]

comment:8

I am trying to build M2 1.4 from source - it would be way better to upgrade spkg. My diary:

• I've installed autoconf on my system since it does not seem like Sage includes it in any way.
• bison and flex are available as experimental packages (why not optional?) and installed fine for me.
• I have MAKE="make -j2" and configure complains that make is not GNU, changing it to just "make" works fine.
• Next it complains about libcurses and libncurses. I have libncurses installed, but it is necessary to install development versions. I've done that.
• Now development version of libxml2...
• config finished without errors, make does not work:

error: for the third-party library or program source "gc"
       the source code is not present in the file "/home/novoselt/tests/Macaulay2-1.4-r12617/BUILD/normal/../../BUILD/tarfiles/gc-7.2alpha5-2010-09-03.tar.gz"
       so either download a "fat" tar file of the Macaulay2 source code
       or rerun the Macaulay2 "configure" command with the added option "--enable-download"
       to enable automatic downloading of the source code over the internet

[novoselt]

comment:9

I am not sure where fat source is, but I have downloaded files one by one until there were no complaints from here:
http://www.math.uiuc.edu/Macaulay2/Downloads/OtherSourceCode/1.4/index.html
I had to get 21 out of 29 currently posted there:

4ti2-1.3.2.tar.gz               gfan0.4plus.tar.gz   nauty24r2.tar.gz
cdd+-077a.tar.gz                glpk-4.44.tar.gz     normaliz2.5Source.zip
cddlib-094f.tar.gz              lapack-3.2.2.tgz     ntl-5.5.2.tar.gz
factory-3-1-1.tar.gz            libfac-3-1-1.tar.gz  pari-2.3.5.tar.gz
frobby_v0.8.2.tar.gz            lrslib-042c.tar.gz   readline61-001
gc-7.2alpha5-2010-09-03.tar.gz  mpfr-3.0.0.tar.gz    readline61-002
gdbm-1.8.3.tar.gz               mpir-2.1.2.tar.gz    readline-6.1.tar.gz

As I understand some of these should be substituted by Sage versions. From a license point of view, would it be OK to make an optional spkg with the rest included?

[novoselt]

comment:10

The end of make's output:

linalg.cpp:528:1: error: ‘FieldMatrix::FieldMatrix’ names the constructor, not the type
make[3]: *** [linalg.o] Error 1
make[3]: Leaving directory `/home/novoselt/tests/Macaulay2-1.4-r12617/BUILD/normal/libraries/gfan/build/gfan0.4plus'
make[2]: *** [.compiled-0.4plus] Error 2
make[2]: Leaving directory `/home/novoselt/tests/Macaulay2-1.4-r12617/BUILD/normal/libraries/gfan'
make[1]: *** [all-in-gfan] Error 2
make[1]: Leaving directory `/home/novoselt/tests/Macaulay2-1.4-r12617/BUILD/normal/libraries'
make: *** [all-in-libraries] Error 2
make: Leaving directory `/home/novoselt/tests/Macaulay2-1.4-r12617/BUILD/normal'

[novoselt]

comment:11

I made a new spkg based on Macaulay2-1.4, so far it fails to build because of 4ti2 and gfan. Both are installed in Sage (4ti2 as optional), but not detected by M2 - I've asked M2 developers what can be done. Including these into M2 package breaks during gfan installation, so I have no idea yet how close I am to a working package.