Various build issues on arch > possible fixes

[lifelessjellyfish]

Happy near year @pemsley

i wanted to build coot on arch but it failed on various points. After some trying i found some fixes for the packages:

• GMP failed ./configure -> fixed with "-c=99" flag
• readline failed make -> worked fine without the built-it-3-3 patches tho
• eigen failed cmake -> worked with "-DCMAKE_POLICY_VERSION_MINIMUM=3.5" flag

Also on arch the standard guile version is 3 and idk how to change the version on arch even with guile2.2 pacakge, so building it with the script would be comfier (maybe make make-guile flag always true on arch only?)

libCCP4 failed build

putenv() was defined differently as opposed to stdlib.h (i think). Added header and just skipped defining putenv()

--- "libccp4-8.0.0 (2)/ccp4/library_utils.c"	2022-05-23 18:11:07.000000000 +0200
+++ libccp4-8.0.0/ccp4/library_utils.c	2026-01-03 00:07:05.000000000 +0100
@@ -41,6 +41,7 @@
  *  @author  Charles Ballard
  */
 
+#include <stdlib.h>
 #include "ccp4_sysdep.h"
 #include <time.h>
 #include <math.h>
@@ -141,7 +142,7 @@
     defined (_WIN32) || defined __linux__
   /* putenv is the POSIX.1, draft 3 proposed mechanism */
 #if !(defined(__hpux) && defined(__HP_cc))
-  int putenv ();
+  //int putenv ();
 #endif
   char *param;

RDKit failed make -> errors and patches in ML/Cluster/Murtagh

the compiler needed the data types in those functions defined so i added them manually. They should be correct as the compiler was quiet after that fix.

diff --color -rua _2026-01-02__T20_14_46/rdkit-Release_2024_09_5/Code/ML/Cluster/Murtagh/hc.c _2026-01-02__T21_10_50/rdkit-Release_2024_09_5/Code/ML/Cluster/Murtagh/hc.c
--- _2026-01-02__T20_14_46/rdkit-Release_2024_09_5/Code/ML/Cluster/Murtagh/hc.c	2025-01-31 13:55:45.000000000 +0100
+++ _2026-01-02__T21_10_50/rdkit-Release_2024_09_5/Code/ML/Cluster/Murtagh/hc.c	2026-01-02 23:49:15.155585800 +0100
@@ -50,7 +50,7 @@
   static integer i2, j2, jj, im, jm;
   static doublereal xx;
   static integer ind, ncl;
-  extern integer ioffset_();
+  extern integer ioffset_(integer *, integer *, integer *);
   static integer ind1, ind2, ind3;
 
   /* Parameter adjustments */
diff --color -rua _2026-01-02__T20_14_46/rdkit-Release_2024_09_5/Code/ML/Cluster/Murtagh/hcdriver.c _2026-01-02__T21_10_50/rdkit-Release_2024_09_5/Code/ML/Cluster/Murtagh/hcdriver.c
--- _2026-01-02__T20_14_46/rdkit-Release_2024_09_5/Code/ML/Cluster/Murtagh/hcdriver.c	2025-01-31 13:55:45.000000000 +0100
+++ _2026-01-02__T21_10_50/rdkit-Release_2024_09_5/Code/ML/Cluster/Murtagh/hcdriver.c	2026-01-02 23:52:49.022316935 +0100
@@ -15,7 +15,7 @@
 {
   static logical *flag__;
   static doublereal *membr, *disnn;
-  extern /* Subroutine */ int hc_();
+  extern /* Subroutine */ int hc_(integer *, integer *, integer *, integer *, integer *, doublereal *, doublereal *, integer *, doublereal *, logical *, doublereal *);
   static integer *nn;
   flag__ = (logical *)malloc(*n * sizeof(logical));
   membr = (doublereal *)malloc(*n * sizeof(doublereal));
Only in _2026-01-02__T21_10_50/rdkit-Release_2024_09_5/Code/ML/Cluster/Murtagh: Makefile

I hope those small fixes are somewhat useful :3

[pemsley]

Thanks @lifelessjellyfish,

It has been a while since I compiled the dependencies on Arch Linux.

I will send Charles a link to this page.

I had chosen guile 2 because that worked with guile-gnome platform - and guile 3 did not (at the time). Maybe it does now.

[hgonomeg]

For Arch Linux, I recommend using the AUR package maintained by me.
I hope that helps. This way you use native system dependencies (and some from the AUR).

Personally I've also struggled with build-it-3-3.
I hope this helps / is relevant.