Cygwin: installing Seismic Unix - error during make install

Question

I am trying to install the software "Seismic Unix" for Cygwin on Windows.

Under normal circumstances the issue described below would probably be fixed with downloading Cygwin again and doing just a simple reinstallation of all packages - the problem is: I can't really do that, because I am on a research ship in the South Atlantic right now and am sharing a bandwidth of 190 kb/s with 50 people. Therefore the best I can do is to download or update single packages. In order to do this, however, I first need to know what causes my error messages.

The issue arises when I am trying to make install. The error message reads:

fcat.c: In function ‘main’:
fcat.c:35:14: error: storage size of ‘buf’ isn’t known
  struct stat buf;
              ^~~
In file included from fcat.c:26:0:
/usr/local/su2/include/cwp.h:713:15: warning: implicit declaration of function  open64’ [-Wimplicit-function-declaration]
 #define open  open64
               ^
fcat.c:43:8: note: in expansion of macro ‘open’
   fd = open(av[ic], O_RDONLY);
        ^~~~
/usr/local/su2/include/cwp.h:720:15: warning: implicit declaration of function  fstat64’ [-Wimplicit-function-declaration]
 #define fstat fstat64
               ^
fcat.c:45:3: note: in expansion of macro ‘fstat’
   fstat(fd, &buf);
   ^~~~~
fcat.c:35:14: warning: unused variable ‘buf’ [-Wunused-variable]
  struct stat buf;
              ^~~
make[2]: *** [Makefile:24: /usr/local/su2/bin/fcat] Error 1
make[2]: Leaving directory '/usr/local/su2/src/cwp/main'
make[1]: *** [Makefile:8: INSTALL] Error 2
make[1]: Leaving directory '/usr/local/su2/src/cwp'
make: *** [Makefile:85: cwpstuff] Error 2
 

/usr/local/su2/ is the directory of Seismic Unix. I have a long range of packages installed that works for a similar software (called Madagascar), but apparently not for Seismic Unix. I found some posts that explained this error message arises sometimes, when gcc is not found/up to date. I checked this several times and it is up to date. Furthermore, I tried to use "rebaseall" in the Ash terminal of Cygwin, because this apparently fixes problems with single packages installed after the main installation, but so far nothing works.

Does anyone have some ideas that could help me?

Edit: thanks to steeldriver I am past the issue with make install. The config for Cygwin file that Seismic Unix install on Windows is talking about is actually in the /config folder and called Makefile.config_Cygwin_32 (see comments). That gets me past most make xxxinstall commands.

However, now there is another error message with the last step: make sfinstall. I get the following error:

make[4]: Entering directory '/usr/local/su2/src/Sfio/src/lib/sfio/Stdio_s'
cc -c -I. -I.. -O -Dvt_threaded=0  stdfgetc.c
In file included from /usr/include/sys/errno.h:11:0,
                 from /usr/include/errno.h:9,
                 from ../vthread.h:14,
                 from ../sfhdr.h:58,
                 from stdio_s.h:11,
                 from stdfgetc.c:1:
/usr/include/sys/reent.h:285:26: error: conflicting types for ‘__FILE’
 typedef struct __sFILE64 __FILE;
                          ^~~~~~
In file included from stdfgetc.c:1:0:
stdio_s.h:8:25: note: previous declaration of ‘__FILE’ was here
 typedef struct _sfio_s *__FILE;
                         ^~~~~~
make[4]: *** [Makefile:25: stdfgetc.o] Error 1
make[4]: Leaving directory '/usr/local/su2/src/Sfio/src/lib/sfio/Stdio_s'
make[3]: *** [Makefile:146: mkstdio_s] Error 2
make[3]: Leaving directory '/usr/local/su2/src/Sfio/src/lib/sfio'
make[2]: *** [Makefile:79: install] Error 2
make[2]: Leaving directory '/usr/local/su2/src/Sfio/src/lib/sfio'
make[1]: *** [Makefile:7: INSTALL] Error 2
make[1]: Leaving directory '/usr/local/su2/src/Sfio'
make: *** [Makefile:129: sfinstall] Error 2

Does anybody know what to do here? After I didn't at first I tried every step again with a freshly untarred source tarball, but the error message still stands.

Answer 1

The following procedure works on 64 bit cygwin

cp configs/Makefile.config_Cygwin_32 Makefile.config

patch the Makefile.config as

--- configs/Makefile.config_Cygwin_32   2015-03-17 16:36:38.000000000 +0100
+++ Makefile.config     2018-01-28 19:37:35.224138200 +0100
@@ -34,7 +34,7 @@
 LINEHDRFLAG =
 XDRFLAG = # -DSUXDR
 ENDIANFLAG = -DCWP_LITTLE_ENDIAN
-LARGE_FILE_FLAG = # -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
+LARGE_FILE_FLAG =  -D_FILE_OFFSET_BITS=64 # -D_LARGEFILE64_SOURCE

 CWP_FLAGS = $(LARGE_FILE_FLAG) $(ENDIANFLAG) $(XDRFLAG) $(LINEHDRFLAG)

@@ -59,10 +59,10 @@
 # use both X11 path conventions
 #-----------------------------------------------------------------------

-IX11 = /usr/X11/include
-LX11 = /usr/X11/lib
-IMOTIF = /usr/X11R6/include
-LMOTIF = /usr/X11R6/lib
+IX11 = /usr/include/X11
+LX11 = /usr/lib
+IMOTIF = /usr/include/X11
+LMOTIF = /usr/lib

 LD_LIBRARY_PATH += $(CWPROOT)/lib:${LX11}:${LMOTIF}

@@ -91,7 +91,7 @@

 CC = gcc
 #OPTC = -g  -std=c99 -Wall -pedantic -Wno-long-long
-OPTC = -O  -std=c99 -Wall -pedantic -Wno-long-long
+OPTC = -O   -Wall -pedantic -Wno-long-long
 CFLAGS = -I$I $(OPTC) $(CWP_FLAGS) -D_BSD_SOURCE -D_POSIX_SOURCE

 FC = gfortran

Additional patch for make sfinstall

    --- Sfio/src/lib/sfio/Stdio_b/sfstdio.h~        2018-01-28 20:36:09.022523600 +0100
+++ Sfio/src/lib/sfio/Stdio_b/sfstdio.h 2018-01-28 21:21:12.331496700 +0100
@@ -26,7 +26,7 @@

  /* Linux7.2 requires __FILE in wchar.h - we fake it here */
  #include       "FEATURE/sfio"
 -#if _typ___FILE
 +#if defined(_typ___FILE) && !defined(__CYGWIN__)
  typedef FILE   *__FILE;
  #endif

--- Sfio/src/lib/sfio/Stdio_s/stdio_s.h~        2002-09-14 03:01:15.000000000 +0200
+++ Sfio/src/lib/sfio/Stdio_s/stdio_s.h 2018-01-28 20:33:16.400954500 +0100
@@ -4,7 +4,7 @@

 #include       "FEATURE/sfio"

-#if _typ___FILE /* Redhat7.3 requires __FILE in wchar.h */
+#if defined(_typ___FILE) && !defined(__CYGWIN__) /* Redhat7.3 requires __FILE in wchar.h */
 typedef struct _sfio_s *__FILE;
 #endif