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add configure of edstats

[#4738] force use of libccp4f.a for Darwin_intel_compilers

remove makecif from build

Fixed a typo in --disable-srs option.

tidy wrapping of pisaII

update for new pisa configuration

version numbers to 6.2.992

add ccp4srs under lib

add gesamt in src

[#4667] ccp4/configure now checks whether the variable TCL_INCDIR is set to
a directory including tcl.h.

do not try to configure or make clipper_progs if it is not there

add with-mmdb and with-ccif to libccp4 configure

update list of files to be touched in ccif

[#4641] correct typo, cnsfrommodel to cncsfrommodel

guard ssm

add test for existance of share/ccp4i and DiffractionImage

need --with-mmdb for crank software

for DiffractionImage, having set xopts then use it

try to get TCL_INCDIR for mapslicer, so then use it for idiffdisp

now access lapack from /lib/Makefile, so change path for lapackdir to just lapack

do not want shared library build for ccif by default

reenter aimless block as I canot get older version to work

set CXXFLAGS on command line for configures

lots of problems with line splitting for AIMLESS section

ccp4i now in share

if we do not have clipper then do not configure it

add treatment of rxdispencer and tidy xopts

lib should be in the path for cctbx_sources

add prefix for ccif, and move to having standalone libraries

add aimless

[#4435] add prosmart in src

LDFLAGS options for leiden software are wrong

[#4498] attempt to use netlib lapack

[#4474] at least for the semi static libccp4map.so we require the linking in of libccp4c

update for 6.2.0

[#4442] reorder icpc and ifort tests for changes in compiler options

Updated Phaser to version 2.3.0

update phaser version for passing to pointless

input lapack libs into leiden suite

syntax error

add Darwin32 and Darwin64

first stab at spinning out crank software

[#4384] use ranlib -c to include .mod information

[#4300] continues refinement of ORIGIN

[#4300] round 1 of setting up the relative paths rpath for linux

add cprodrg

X11 libraries are lipo-ed for Darwin

update for problems in merge

merge branch-7-9-2010

[#4317] compiler check

should be static-libgcc not static_libgcc for othercell

keep up to date with phaser version

[#4250] no -fno-stack-protector for gfortran 4.0.x

[#4222] replace curly braces by brackets for some versions of the bourne shell

LD is not defined for icc on os x

bug 4116, intel compilers cannot do libcheck at -O2

merge in series-6_1 to release-6_1_3

bug 4047, handle different modes of gcc compilation on os x

bug 3996, more changes required

bug 3996, directly link the object files into the archive to get around relocation problems associated with whole-archive on non fPIC objects

snow leopard and other changes from the series-6_1 branch

bug 3993, downgrade optimisation for crunch2 using ifort 11.1 on linux

add crt1.10.6.o to list of ignored files

bug 3905, set with-ccp4 for superpose

bug 3905, set with-ccp4 for superpose

bug 3983, correct logic in existance of intel compilers tests

merge in 6.1.1 to 6.1.2 changes from the series-6_1 branch

bug 3929, turn off inter procedure optimisation, but raise general opt from O1 to O2 for linux intel compilers

bug 3902, use enable-shared-lib to control shared library build for ccif

bug 3892, copy ccp4i/bin elements to /Users/Shared/ccp4/bin

bug 3797, add object file names to link lines

bug 3862, remove the bounds checking as scala is running out of space

merge in 6.1.1 changes

with this code, the interface checking is a step too far

wrong location for the last bit, as it set the options for the default run of linux_intel_compilers

start bringing in fpe, unitialised, bounds and interface checks for the intel fortran compiler by subverting warnings option

changes required to get the 10.1 test to work on serv3

best to set this first

bug 3663, begin correct for limits.h

bug 3571, need to include the ccp4 libraries when we are building in the .a ccp4 environment

Fixed this again..

Updated with fix for 3647

Fix for 3647 on gcc 4.3.x

bug 3656, make sure the compilation and xmkmf are singing from the same song sheet

bug 3654, pass static instruction on

lower optimisation to -O1 for Intel 11 (Bug 3534)

merge in branch release-6_1_0 changes

lower optimisation to -O1 for Intel 11 (Bug 3534)

better as does XFFLAGS, XCFLAGS and XCXXFLAGS

static-libgcc for linux build

changes for Intel 11 compilers (Bug 3534)

Fix for bug # 3482 - switches off stack smashing detection in gfortran, which
is on by default for ubuntu. Not finished yet though, as this probably needs to
be switched on for c compilation too...

add parrot static line and paths for ibm compilers

by default only have generic ppcv setting for ibm compilers on os x

bug 3358, disable shared build of lixml2 and gc7

update mmdb objects list for xlc shared library

Hide the flag --with-rxdispencer, it shouldn't be needed any more
and is known to cause problems on 64-bit Ubuntu, see bug 3397

bug 3068, _LDFLAGS updates for cmaplocal cmakereference rotgen and ipmosflm

Bug #3286: $CCP4/share/python needed by Diffraction Image installation.

Typo in earlier modification: use "test -z" rather than just "-z".

Bug #3286: two changes for "onlylib" option:
1. Only add "share" to the list of DIRS if not configuring onlylib, and
2. Only configure clipper programs if not configuring onlylib.

bug 3285, add disable-diffractionImg to config.status generation

missing directory separator in path when touching libxml2 files

outside-build branch: building outside the source tree for elements not including rapper and pdb_extract

bug 3243, set options for phaser build

bug 3243, only use libdir in configure, also these may not be consistent with each other

Fix missing ";;" in case statement, which appears to have been omitted from
earlier revision 1.467.

bug 3243, set prefix option and build bin and lib files into it, version that leaves xplot84driver, nice_font.bin and font.bin behind

bug 3253, add crtxi.o and crtxn.o to list of files to be avoided

bug 3250, match 4.x test in 3.x gcc section of linux build

merge in 6.0.99e changes

Bug #3232: try reversing the order that lib64 and lib are checked for the
Tcl/Tk config scripts, to see if we can get a 64-bit version first.

bug 3220, set absolute paths for libccif.dylib, libccp4c.dylib and libmmdb.dylib

bug 3121, skip crt3.o as well, for some OS X setups

Added warning message to inform user that the tclConfig.sh/tkConfig.sh files were guessed. Bugzilla #3199

Reverting to including TK_LIBS variable in testcomp compile

Took out the  libraries from the testcomp.c compilation. They aren't necessary. Bugzilla #3199

bug 3069, use gcc as linker for libccp4map.so under linux, also do not add -lccp4c (at least for static build of ccp4)

Sfcheck 7.3 needs F90

update of pointless

correcting location of cctbx built stuff in phaser directory

Sfcheck 7.3 needs F90

bug 3147, /var/tmp is another location we should ignore

bug 3147, /var/tmp is another location we should ignore

merge in bug 3147 changes

bug 3147, correction for TMPDIR from Claus

bug 3147, skip crti.o and crtend.o

bug 3147, catch more of the crt files, plus try and catch the compiler temporary files by assuming they are in tmp

bug 3041, pass CCC to pdb_extract

bug 2940, allow /usr/lib64/c++init.o to be included in CXX_LIB for refmac5.5 compilation on irix

bug 3115, remove tlsgroups

merge in series-6_0_99d

bug 3069, MAPSLICER_XCFLAGS for intel compilers

bug 3070, search in lib and lib64 for the TclConfig

bug 3068, get static linking sorted for superpose, clipper_progs, rapper, pisa, pointless

bug 3068, use XLDFLAGS instead of CC etc to set static

bug 2993, downgrade proclean to -O0 on Darwin_intel_compilers

bug 2846, -O0 no longer required for vecref following fix to vecref.f

another sets of corrections for bug 2962

BALBESTARGETS need fortran90

bug 2806, missing directory separator

bug 2912, search for f90 on osf1

bug 2806, test for presence of ctime, and use cpp_c_headers if missing

Revert 1.440 - 1.442 following proper fix to findncs.f (Bug 2954).

Bug #2958: part of Claus Flensburg fix for pdb_extract build.

adding with-pic on the Diffraction Image configure as it seems to fix the compilation problem on 64 bits machines

bug 2909, add prerelease to build

Lower optimisation for findncs on Intel 10.0 as well

missing \ in V1.440

Lower optimisation for findncs on Intel 9 (Bug 2889).

keep pace with the step change in phaser to 2.1.3

Added catch for gfortran 4.1.0 compiler so that refmac compiles with optimization -O0 (off) Bugzilla #2898

Fix for linux64/32/* error (added ;;)

bug 2894, add linux32 system type for -m32 specification.  Note: explicit setting of CC, CXX, FC also works

Cosmetic: make message about which programs need F90 support more version
neutral, since it will get out-of-date quickly.

bug 2646, 2882 updates for compiler specific fortran flags

update for 6.1 test releases

bug 2868, activate generalisation for Darwin_intel_compilers F_LIBS

bug 2868, updates for Darwin

add general catch all to determine F_LIBS, active for irix and irix64

general catch all for CXX_LIBS

bug 2867, use -ptused and -no_prelink on irix

bug 2857, update to touch configure files in gc7.0

bug 2858, set --build_boost_python_extensions=0 for cctbx under IRIX

bug 2862, reduce opt level for sfcheck under gfortran 4.3.0 on os x to -O0

update configure options to pointless for phaser 2.1.2

bug 2846, correct typos

bug 2846, set -O0 for vecref with ifort version 10.1

bug 2845, require -D_f90 for f90 compiler on IRIX usage of M4 in unix.m4

bugs 2843, 2844, add search for f90 compiler for irix and irix64

bug 2817, have to skip -lcrt1.10.5.o on leopard

turned on the build of the tcl module to be able to have idiffdisp running directly

correcting option setting for intel 10 compilers the check was the wrong way round

Changing the detection of version 10

add fftw to pointless build options, and make extended use of the xopts parameter

libxml2 and gc6.8 contain configure.in not configure.ac

bug 2751, try and locate the cctbx build

bug 2790, further logic in enable tests

add full path of cctbx and phaser

Switch diffraction image on by default and have an option to disable it if necessary

Switch diffraction image on by default and have an option to disable it if necessary

Added share directory to configuration

there is no ltmain.sh or ltconfig in the pisa source tree

bug 2751, call to pointless configure

bug 2749, add pisa configure call, needs extending to test for ssm configure and testing of course

bug 2747, add rapper to core configure

bug 2725, add call to clipper_progs configure to main configure

deprecated directory added to configure but not make (deliberate!)

fixed typos

Last set of changes merged from the release-6_0_patch branch.

fixing bug 2591

fix bug 2588, another way to look for specific libraries for
intel compilers

Bug #2565: update default setting of INSTALL_PROGRAM and INSTALL_DATA to
be "cp -p" wherever it was previously "cp", to preserve timestamp of copied
files.

silly typo when setting XCXXFLAGS

bring in patch branch changes

modify F90 warning message to include molrep 10.1

add molrep to list of programs requiring F90

add uber configure options for rampage

reinstate 1.372.2.18 to 1.372.2.19 changes

add elements to configure for rampage update

Allow answer Y as well for licence query

Extend LDFLAG to include libdir as well as LIB_DIR
This means you should be able to link against installed libraries
as well as recently built ones.

add --prefix to control installation location, but still allow libdir and bindir override.  Also, bug 1937 - check that includedir exists, creating it if it does not

Intel compiler found bug in F90 test program

Test f90 compilation and adjust refmac targets appropriately

Bug #1838: explicitly check TMPDIR variable from the environment, and use
this as the internal default within configure, to fix bug #1838.

fortran optimisation level reduced to -O1 for Intel9 compilers on Itanium

Bug #1868: patch from Matsuura to fix MIPSpro C++ compiler detection.
Looks similar to r1.381 in the main branch.

generally add -Vaxlib to ifort and ifc so better not set FC value to early for linux_intel_compilers

bug1805, increase sweep of icc checks

bug 1836, turn off shared build for libjwc_f on all Darwin

Updated version to 6.0.2

add Darwin_intel_compilers option

bug 1707, trap for gfortran 4.1.0

bug 1709, correction to MIPSpro 7.4 pattern matching

bug 1709, correction to MIPSpro 7.4 pattern matching

For linux, SETFLAGS should go after definitions of XFFLAGS and FOPTIM
that it uses. Fell over with lgglib missing -fPIC.

For linux, move SETFLAGS after definitions of XFFLAGS and FOPTIM
that it uses. It failed with lgglib lacking -fPIC.

Copy revision 1.372.2.7 to main branch

Adding target for the Diffraction Image Library need the tag --enable-diffractionImg to enable its built

Including Matsuura changes for IRIX compiler recognitions

lower molrep -O for mactel and gfortran 4.0.3

Use mkdir -p for --bindir and --libdir

Use mkdir -p for bindir and libdir

need to allow for gfortran -m64

fix should be for 7.4 compiler not OS

fix should be for 7.4 compiler not OS

bug 1656, add libc_in_namespace_std for IRIX 7

bug 1656, add libc_in_namespace_std for IRIX 7

add some architecture determination, primarily for i386 Darwin

add some architecture determination, primarily for i386 Darwin

test not assignment for g2c header

add 375 revision to patch branch

need to add -lstdc++ for libmmdb.dylib linking

copy 1.373-375 changes into patch branch

for os x gcc gives cleaner linking that g++

disable all shared builds for libjwc_f on Darwin

if I have got this right, then for Darwin g77 a check will be made for g2c.h

cannot have dynamic fortran libraries for ibm compilers

Fix a bug encountered on OSF1 V5.1, where the leading $ causes problems
(even if the code isn't executed) unless the expression is quoted.

correct syntax error in onlylibs section

Corrected minor typo in licensing section.

Charles' fix for Intel 9 compilers merged in. Tested on Intel 8 and Intel 9 and seems fine. Looks like there may be problem with Intel 7. See bugzilla #1496.

under os x the fortran and C++ compilers may be in different areas, so get paths for C++ compiler libraries

Fixed Charles' typo in icpc -cxxlib-icc line.

icc 9.0 fixes for gcc 4.0 and ia64 platform

downgrade lgglib opt level for gfortran

not necessarily using g77 as default linux

under os x g++4 with g77 requires SystemStubs

allow fixed path gfortran

Changes to build shared libccp4map (for ccp4mapwish/mapslicer), even if
shared libs are not requested (see bug #1466).

Restore CVS keyword which was lost in revision 1.247.

Extensive update to mapslicer configuration section. Now attempts to use
TCL_INCLUDE_SPEC from tclConfig.sh (if present) to locate tcl.h, if other
attempts fail (bug #1466).

use dumpversion for locale independence

misformed case statement

try gcc4 with g77 without g2c.h

allow g77 options for gcc4 on linux

Bug #1373: -fPIC may be detrimental when compiling non-shared versions of
the netlib lapack/blas libraries; configuration of these libraries now
checks for and removed -fPIC when switching off shared build.

Fix to onlylibs changes: quote variable when using test -z.

Changes to make the --onlylibs option work correctly:
1. Disable licence check for onlylibs
2. Disable x-windows and phaser for onlylibs
3. Make a dummy src/Makefile.in for onlylibs (to fool top-level Makefile at
   build time)

tidy the comments printed out concerning enable and disable-x

bug 1163: updated to correct this, and set --enable-x as default

Implement non_shared for sunos(32)
Won't work for sunos64 because only .so distributed for many
libraries e.g. libm and libc
More details in Bugzilla (lost number but search on sun)

add/change echo's in X-windows section so we know where we are

cctbx no longer static libraries

bug 1300, split g77 options on C compiler

licence sections updated for 6.0

SETFLAGS update for gfortran

get XLDFLAGS to include -lm for osf v5

correct LDFLAGS for OS X 10.4

better test for gcc 4.0

correct SUNSpro fortran library list

correct syntax for sunox lapack C interface

first stab at gfortran support for linux and Darwin, assume gcc 4 uses gfortran

bug 1223, add ieee for floating exceptions under osf1

extend 1.334 to Darwin_ibm_compilers and lapack tests

os x 10.4 does not require cc_dynamic

bug 368, use lgglib_FLAGS to lower optimisation to -O0 for ifort

-Kc++ causes problems with the 7.0 icc compiler, and we use icpc anyway

bug 1177, 1178 - add -fno-move-all-moveables to stereo and mlphare

bug 1174, version prior to syntax correction committed in error

bugs 1173, 1174 - check for C linkage of liblapack and use icpc for C++ intel compilers

bug 1172, seperate out CXX and C builds, also add F_LIBS, C_LIBS, CXX_LIBS

bug 1162, updates required for shared libs using icc

bug 1152, add in linux

bug 1152, correctly output LDCFLAGS and add Darwin_ibm_compilers

bug 1152, use LDCFLAGS as osf1 complains of multiply defined symbols

bug 1133, test for 64-bit ABI on linux

configure should "touch" clipper configure.in, not configure.ac (Ezra
Peisach, bug #1060).

duplicate cctbxopts for phaser build

Add --bindir and --libdir to the configure lines for fftw, clipper
and ssm. These override the more general --exec_prefix and --prefix

bring cctbxopt options together

tidy linuxppc32 linuxppc64 divide

64 bit for linux

bug 1033 - similar for osf1

bug 1033 - need -lftn for irix

bug 1035 - test with and without XLDFLAGS extension

use gnu/linux calling convention for linuxppc

add -Kc++ for ifort 8.1 compiler

first round of changes for ia64 efc and ifort, also add XLDFLAGS to blas/lapack test compilations for cblas case

changes for ifort on altrix

change opt level for pmf for xlf compiler on OS X

update flags for mac xlf compilation

force -static for molrep - bug 999

replace fft by fftbig

pass platform-specific cctbx options to Makefile header

some tidying

first run through linuxppc with ibm compilers

As for last revision, but for Intel 8
Sorry about the hard-coded path.

Specify system Fortran libraries for BP3 build for Intel 7 compilers.
These libraries are different for Intel 8, which is yet to be addressed.

start move to sfftw

add checks that cctbx and phaser packages have been downloaded
into the expected destinations

add cctbx and phaser

add -lBLAS to XLAPACK_LIB for Darwin_ibm_compilers

changes for AIX 5.2

MDW: changes for AIX 5.2

a couple of OSF1 options for BP3
the -lfor is because BP3 links in the Fortran lapack/blas libraries

make fftw, clipper and ssm the default

extra IRIX options for C++ (for bp3 but applied generally)

add ssm

add clarification to mapslicer error message

pp54: configuration for pdb_extract needed to be moved higher up

Mapslicer configuration: allow user to explicitly define TCL_CONFIG,
TCL_INCDIR, TK_CONFIG and TK_INCDIR in the environment, and test and use
these instead.

Updated message from LAPACK configuration (all precisions are now built).

Test for m4 was broken on Irix and SunOS.

Added a test to check that m4 is working.

touch the ccif configuration files

implement default option for licence agreement

Mapslicer configuration: usr/local should actually be /usr/local

minor correction for install_name on OS X

seems grep isnt standard accross osf1 and irix and linux.
so replaced the grep with a a new file name.

changes for Sun: remove sunmath and add -dalign to sunperf,
                 define SUNOS64_5 for 64-bit XCCPJIFFY compilation

have to use the objects for xlf on mac os x, this may well be a problem if changes are made to the files

typo in writing --disable-pdb_extract to config.status
use f90 on SunOS - this avoids call to ieee_retrospective and hence
   FAILED in ccp4i
reduce optimisation for rantan and refmac, due to problems in
   iropt on compilation

new licensing stuff!

pp54: Fixed issues regarding pdb_extract when configuring with "--onlylibs" and osf1: pdb_extract is not configured to build when --only-libs is used as configure flag

ibm compiler now called xlc++ on Darwin

PP: fixed mistake in location of pdb_extract configuration

PP: Modification to pdb_extract configuration. Call 'make configure' to check compiler in case linux_intel_compilers are used

default to gmake under FreeBSD

add g77 support on FreeBSD - bug 416

change veclib to vecLib for OS X - bug 426

force multiple substitution evals into subshell, for FreeBSD - bug 416

downgrade refmac5 and molrep compilation levels to -O1 on Darwin - bug 360

update for ifort compiler under ia64, not option name change

Minor modification to test of compilation settings for mapslicer (don't
write stderr to stdout).

Mapslicer configuration: try to compile a test program to check the
settings obtained from tclConfig.sh and tkConfig.sh.

downgrade optimization level for distang to O1 under efc -bug 403

to quote CV, this is very dangerous and should not be done - bug 5

use which ifort etc for intel compiler version, this is consistent with old setup and could do with an overhaul

If --onlylibs specified then automatically disable mapslicer and
pdb_extract. Also minor cleanup to printing of mapslicer configuration.

reinstate shared build for mosflm, alter jpg ltconfig

Darwin test for 3.1 only

Added check for bison when running configure. PDB_EXTRACT is dependent on bison.

Modified to disable build of pdb_extract for osf1 v4

start to update configure for AIX

work around for linux linking problem involving undefined reference to main

Sun compiler 5.5 has libsunmath instead of libsunperf

shift XLDFLAGS to end of LDFLAGS list

Tidying up processing of --non_shared option

Added --disable-pdb_extract option - this option does not build pdb_extract suite

more tidying of cc_dynamic for OS X

mplot g77 3.4 problem, drop to -O1

additional test for os X vecLib to satisfy g77 3.4

the redhat 9 problem goes away with updates to glibc from redhat

apple with xl compilers:
add cc_dynamic for restFP and saveFP, previously only with LAPACK
disable ccp4f dylib build as we access common blocks directly

more OS X xlf update, plus disable shared build for mosflm

setting of XMKMF added for Darwin_ibm_compilers

reduce opt level for ibm compilers

vecLib relocation

a work around for redhat 9 if compiling with shared libs. ccif does not
compile for some reason. this fudge directs configure to compile ccif as
static.

core configure Darwin xlc changes, may be commented out for release

changes and a test to cope with --non_shared on linux and the need for -lblas
that some of the original test programs were not showing. the code for the test
is taken from the problem prog = scala! seems to work.

work around for -fno-common problem with g77 on Mac OS X

changes to allow compilation with fftw in suite

changes for fftw configure

Allow --with-shared-libs as alias for --with-shared-lib.

adding --non_shared to configure for linux

remove line break from ecc shared library build

add test for g++3

Patch from Clemens: check for presence of libtool to avoid errors.

Define rxdispencer directory and add to Makefile for distclean etc.

add touch sequence for libjwc_c and libjwc_f

ccp4mapwish: also collect TK_XINCLUDES from tkConfig.sh.

first bash at SGI Japan's Altrix changes

Mapslicer/ccp4mapwish: search for tclConfig.sh and tkConfig.sh and use the
values found in these files when building and linking ccp4mapwish.

attempt at MAPSLICER_SHARE for Suns

-Nl45 obsolete for suns and now cause problems

better test for vecLib on Darwin

*** empty log message ***

minor correction

update in clipper package list

Default settings of SHARED_LIB_F/CFLAGS for Irix are only picked up if shared libs are requested.

fftw_prefix and prefix_fftw

correction of fftw_prefix:+set test

set prefix and exec_prefix for headers and libraries

corrections in paths for clipper configure

hooks for clipper and fftw directories in make procedure

debug prints removed

hooks added for clipper and fftw, specifically --enable-clipper
and --with-fftw=

CXX and CC were reversed in SHARE_LIBS

corrections for Mac

SHARED_LIB_FLAGS split into SHARED_LIB_CFLAGS and SHARED_LIB_FFLAGS to
overcome problem with Mac OS X

set -O2 for Darwin COPTIM

updating configure for intel shared.

icc fix and reationalisation of flags for static compile of ifc

corrected ifc to icc check
also arp_waters - if it has -static it wont run on RH8
                  if it has -C it turns off optimisation

shift with-ccp4-prefix to lib not lib/src for Rotgen configure

chopped line joined

touch configuration files in Rotgen

-mips3 for XCFLAGS and XCXXFLAGS

OSF1 4.0: if shared libs requested then remove -lcxx from XLDFLAGS,
otherwise mmdb applications (ncont etc) fail at runtime with unrecognised
symbols.

first stab at linux_intel_compilers. It seems to work fairly well for non
shared and no x stuff.

add -lm for Sun linking

CXX set for linux, also various XCXXFLAGS.
Note: no g++3 types set...

treat CXXFLAGS like CFLAGS and FFLAGS

tcl 8.4 is out in the wild (well mac anyway)

Link in maths library for IRIX build.
Link in -lcxx to libmmdb.so for OSF1.

no longer use relative paths much of the x-builds.  Access Rotgen
configure script

add -lstdc++ for linux

linux link flags for static as well as shared!

XCXXFLAGS set for Darwin (will have to set for all G77)

Set XCXXFLAGS explicitly for linux
Update checks on existence of old libraries

need to order libraries correctly for static build

library split into 3 - changes to some configure variables

some Darwin stuff