sci-chemistry:prekin-6.51.081122-r1:20200325-010430.log

sci-chemistry:prekin-6.51.081122-r1:20200325-010430.log (text/plain), 16.76 KB, created by Toralf Förster on 2020-03-25 08:09:11 UTC

 * Package:    sci-chemistry/prekin-6.51.081122-r1
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking prekin.6.51.081122.src.tgz to /var/tmp/portage/sci-chemistry/prekin-6.51.081122-r1/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/prekin-6.51.081122-r1/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/prekin-6.51.081122-r1/work/prekin.6.51.081122 ...
 * Applying 6.51.081122-Makefile.patch ...
 [ ok ]
 * Applying 6.51.081122-overflow.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/prekin-6.51.081122-r1/work/prekin.6.51.081122 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-chemistry/prekin-6.51.081122-r1/work/prekin.6.51.081122 ...
make -j1 nogui 
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native  -falign-functions=32:25:16 -fno-common -Wformat -Werror=format-security -I/usr/X11R6/include   -D NOGUI -I/usr/X11R6/include   -c -o PKINANGL.o PKINANGL.c
PKINANGL.c:1443:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
 1443 | constructcircle(float Cxyz[SEGMENTS][3], float Axyz[3], float Bxyz[3], float radius)
      | ^~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native  -falign-functions=32:25:16 -fno-common -Wformat -Werror=format-security -I/usr/X11R6/include   -D NOGUI -I/usr/X11R6/include   -c -o PKINCRTL.o PKINCRTL.c
PKINCRTL.c: In function ‘flowControl’:
PKINCRTL.c:59:20: warning: implicit declaration of function ‘TickCount’ [-Wimplicit-function-declaration]
   59 | OldTickCounts[0] = TickCount();
      |                    ^~~~~~~~~
PKINCRTL.c:1277:11: warning: implicit declaration of function ‘getkeydownstate’ [-Wimplicit-function-declaration]
 1277 |       if( getkeydownstate() ) /*PKMCMAIN.C PKPCMAIN.C*/
      |           ^~~~~~~~~~~~~~~
PKINCRTL.c:1697:8: warning: implicit declaration of function ‘AdjustMenus’ [-Wimplicit-function-declaration]
 1697 |        AdjustMenus();          /*____MENU.c*/
      |        ^~~~~~~~~~~
PKINCRTL.c:1418:41: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=]
 1418 |        if(Nprotein > 0) sprintf(word,"%s, %d Protein",word,Nprotein);
      |                                         ^~
PKINCRTL.c:1418:38: note: directive argument in the range [1, 2147483647]
 1418 |        if(Nprotein > 0) sprintf(word,"%s, %d Protein",word,Nprotein);
      |                                      ^~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
                 from PKIN.h:17,
                 from PKINCRTL.c:3:
/usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 12 and 276 bytes into a destination of size 256
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PKINCRTL.c:1419:42: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=]
 1419 |        if(Nhetgroup > 0) sprintf(word,"%s, %d Het Group",word,Nhetgroup);
      |                                          ^~
PKINCRTL.c:1419:39: note: directive argument in the range [1, 2147483647]
 1419 |        if(Nhetgroup > 0) sprintf(word,"%s, %d Het Group",word,Nhetgroup);
      |                                       ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
                 from PKIN.h:17,
                 from PKINCRTL.c:3:
/usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 14 and 278 bytes into a destination of size 256
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PKINCRTL.c:1420:39: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=]
 1420 |        if(Nwater > 0) sprintf(word,"%s, %d Water",word,Nwater);
      |                                       ^~
PKINCRTL.c:1420:36: note: directive argument in the range [1, 2147483647]
 1420 |        if(Nwater > 0) sprintf(word,"%s, %d Water",word,Nwater);
      |                                    ^~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
                 from PKIN.h:17,
                 from PKINCRTL.c:3:
/usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 10 and 274 bytes into a destination of size 256
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from PKINCRTL.c:3:
PKIN.h:128:14: warning: ‘%s’ directive writing up to 255 bytes into a region of size between 230 and 488 [-Wformat-overflow=]
  128 | #define CRLF "\n"
      |              ^~~~
PKINCRTL.c:1542:23: note: in expansion of macro ‘CRLF’
 1542 |         sprintf(temps,CRLF"chain #%d, ID: %s of type %s%s: %d \"residues\""
      |                       ^~~~
PKINCRTL.c:1691:46: note: format string is defined here
 1691 |             CRLF"After reading these messages, go to the File menu and either"
      |                                              ^~
In file included from /usr/include/stdio.h:867,
                 from PKIN.h:17,
                 from PKINCRTL.c:3:
/usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 39 or more bytes (assuming 552) into a destination of size 512
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native  -falign-functions=32:25:16 -fno-common -Wformat -Werror=format-security -I/usr/X11R6/include   -D NOGUI -I/usr/X11R6/include   -c -o PKINCSBS.o PKINCSBS.c
PKINCSBS.c: In function ‘pperptobase’:
PKINCSBS.c:2808:49: error: format not a string literal and no format arguments [-Werror=format-security]
 2808 |             sprintf(colr,colorscale[Ncolorscale].color); /*high value default*/
      |                          ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
PKINCSBS.c:2813:45: error: format not a string literal and no format arguments [-Werror=format-security]
 2813 |                   sprintf(colr,colorscale[j].color);
      |                                ~~~~~~~~~~~~~^~~~~~
PKINCSBS.c: In function ‘Bcoloredoutput’:
PKINCSBS.c:3196:45: error: format not a string literal and no format arguments [-Werror=format-security]
 3196 |        sprintf(color,colorscale[Ncolorscale].color); /*high value default*/
      |                      ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
PKINCSBS.c:3201:44: error: format not a string literal and no format arguments [-Werror=format-security]
 3201 |              sprintf(color,colorscale[ncol].color);
      |                            ~~~~~~~~~~~~~~~~^~~~~~
PKINCSBS.c: In function ‘writesctoscratch’:
PKINCSBS.c:1084:55: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
 1084 |            if(extra[0] != '\0')sprintf(extra1,"%sB%.2f",extra,B[k]);
      |                                                       ^
In file included from /usr/include/stdio.h:867,
                 from PKIN.h:17,
                 from PKINCSBS.c:3:
/usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 330 bytes into a destination of size 20
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PKINCSBS.c:1093:23: warning: ‘%s’ directive writing up to 19 bytes into a region of size 16 [-Wformat-overflow=]
 1093 |        sprintf(extra,"%s %s",extra1,ShortNameStr);
      |                       ^~     ~~~~~~
In file included from /usr/include/stdio.h:867,
                 from PKIN.h:17,
                 from PKINCSBS.c:3:
/usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 276 bytes into a destination of size 16
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PKINCSBS.c:1109:55: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
 1109 |            if(extra[0] != '\0')sprintf(extra2,"%sB%.2f",extra,B[j]);
      |                                                       ^
In file included from /usr/include/stdio.h:867,
                 from PKIN.h:17,
                 from PKINCSBS.c:3:
/usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 330 bytes into a destination of size 20
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PKINCSBS.c:1118:23: warning: ‘%s’ directive writing up to 19 bytes into a region of size 16 [-Wformat-overflow=]
 1118 |        sprintf(extra,"%s %s",extra2,ShortNameStr);
      |                       ^~     ~~~~~~
In file included from /usr/include/stdio.h:867,
                 from PKIN.h:17,
                 from PKINCSBS.c:3:
/usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 276 bytes into a destination of size 16
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PKINCSBS.c: In function ‘writescratch’:
PKINCSBS.c:1760:52: warning: ‘%.2f’ directive writing between 3 and 313 bytes into a region of size between 3 and 18 [-Wformat-overflow=]
 1760 |            if(extra[0] != '\0')sprintf(extra1,"%s B%.2f",extra,B[k]);
      |                                                    ^~~~
PKINCSBS.c:1760:47: note: assuming directive output of 4 bytes
 1760 |            if(extra[0] != '\0')sprintf(extra1,"%s B%.2f",extra,B[k]);
      |                                               ^~~~~~~~~~
In file included from /usr/include/stdio.h:867,
                 from PKIN.h:17,
                 from PKINCSBS.c:3:
/usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 6 and 331 bytes into a destination of size 20
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PKINCSBS.c:1769:23: warning: ‘%s’ directive writing up to 19 bytes into a region of size 16 [-Wformat-overflow=]
 1769 |        sprintf(extra,"%s %s",extra1,ShortNameStr);
      |                       ^~     ~~~~~~
In file included from /usr/include/stdio.h:867,
                 from PKIN.h:17,
                 from PKINCSBS.c:3:
/usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 276 bytes into a destination of size 16
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PKINCSBS.c:1785:52: warning: ‘%.2f’ directive writing between 3 and 313 bytes into a region of size between 3 and 18 [-Wformat-overflow=]
 1785 |            if(extra[0] != '\0')sprintf(extra2,"%s B%.2f",extra,B[j]);
      |                                                    ^~~~
PKINCSBS.c:1785:47: note: assuming directive output of 4 bytes
 1785 |            if(extra[0] != '\0')sprintf(extra2,"%s B%.2f",extra,B[j]);
      |                                               ^~~~~~~~~~
In file included from /usr/include/stdio.h:867,
                 from PKIN.h:17,
                 from PKINCSBS.c:3:
/usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 6 and 331 bytes into a destination of size 20
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PKINCSBS.c:1794:23: warning: ‘%s’ directive writing up to 19 bytes into a region of size 16 [-Wformat-overflow=]
 1794 |        sprintf(extra,"%s %s",extra2,ShortNameStr);
      |                       ^~     ~~~~~~
In file included from /usr/include/stdio.h:867,
                 from PKIN.h:17,
                 from PKINCSBS.c:3:
/usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 276 bytes into a destination of size 16
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PKINCSBS.c:1903:37: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 15 [-Wformat-overflow=]
 1903 |              else sprintf(extra,"%s %d",MolNameStr,level);
      |                                     ^~
In file included from /usr/include/stdio.h:867,
                 from PKIN.h:17,
                 from PKINCSBS.c:3:
/usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 28 bytes into a destination of size 16
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PKINCSBS.c: In function ‘writeatomscratch’:
PKINCSBS.c:2414:55: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
 2414 |            if(extra[0] != '\0')sprintf(extra2,"%sB%.2f",extra,B[j]);
      |                                                       ^
In file included from /usr/include/stdio.h:867,
                 from PKIN.h:17,
                 from PKINCSBS.c:3:
/usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 330 bytes into a destination of size 20
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PKINCSBS.c:2423:25: warning: ‘%s’ directive writing up to 19 bytes into a region of size 16 [-Wformat-overflow=]
 2423 |          sprintf(extra,"%s %s",extra2,ShortNameStr);
      |                         ^~     ~~~~~~
In file included from /usr/include/stdio.h:867,
                 from PKIN.h:17,
                 from PKINCSBS.c:3:
/usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 276 bytes into a destination of size 16
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc1: some warnings being treated as errors
make: *** [<builtin>: PKINCSBS.o] Error 1
 * ERROR: sci-chemistry/prekin-6.51.081122-r1::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-chemistry/prekin-6.51.081122-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-chemistry/prekin-6.51.081122-r1::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-chemistry:prekin-6.51.081122-r1:20200325-010430.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/prekin-6.51.081122-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/prekin-6.51.081122-r1/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-chemistry/prekin-6.51.081122-r1/work/prekin.6.51.081122'
 * S: '/var/tmp/portage/sci-chemistry/prekin-6.51.081122-r1/work/prekin.6.51.081122'