Compiling dependencies in galaxy yields error

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Compiling dependencies in galaxy yields error

evan clark
I was installing a tool from the galaxy toolshed and one of the
dependencies was missing due to a bad link. I modified the install files
to use the same version of the the software except from a local
directory, however galaxy renders a large error when compiling. If I
compile the source in the same location outside of galaxy it compiles
and installs correctly. The specific package I am attempting to install
is ghostscript for homer package.
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Re: Compiling dependencies in galaxy yields error

Nate Coraor (nate@bx.psu.edu)
Hi Evan,

Can you include the full error you're receiving?

Thanks,
--nate

On Mon, Oct 31, 2016 at 10:11 AM, evan clark <[hidden email]> wrote:
I was installing a tool from the galaxy toolshed and one of the dependencies was missing due to a bad link. I modified the install files to use the same version of the the software except from a local directory, however galaxy renders a large error when compiling. If I compile the source in the same location outside of galaxy it compiles and installs correctly. The specific package I am attempting to install is ghostscript for homer package.
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/


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Re: Compiling dependencies in galaxy yields error

evan clark
All LibX are installed

freetype/src/base/ftrfork.c:407:3: warning: no previous prototype for \u2018ft_raccess_rule_by_darwin_vfs\u2019 [-Wmissing-prototypes]
   ft_raccess_rule_by_darwin_vfs( FT_Library  library,
   ^
freetype/src/psaux/afmparse.c:563:3: warning: no previous prototype for \u2018afm_parser_read_int\u2019 [-Wmissing-prototypes]
   afm_parser_read_int( AFM_Parser  parser,
   ^
freetype/src/raster/ftraster.c:3244:3: warning: no previous prototype for \u2018Render_Glyph\u2019 [-Wmissing-prototypes]
   Render_Glyph( RAS_ARG )
   ^
freetype/src/raster/ftraster.c:3392:3: warning: no previous prototype for \u2018Render_Gray_Glyph\u2019 [-Wmissing-prototypes]
   Render_Gray_Glyph( RAS_ARG )
   ^
freetype/src/type1/t1load.c:230:3: warning: no previous prototype for \u2018mm_axis_unmap\u2019 [-Wmissing-prototypes]
   mm_axis_unmap( PS_DesignMap  axismap,
   ^
freetype/src/type1/t1load.c:266:3: warning: no previous prototype for \u2018mm_weights_unmap\u2019 [-Wmissing-prototypes]
   mm_weights_unmap( FT_Fixed*  weights,
   ^
freetype/src/type1/t1gload.c:58:3: warning: no previous prototype for \u2018T1_Parse_Glyph_And_Get_Char_String\u2019 [-Wmissing-prototypes]
   T1_Parse_Glyph_And_Get_Char_String( T1_Decoder  decoder,
   ^
./base/gxcmap.c: In function \u2018cmap_cmyk_direct\u2019:
./base/gxcmap.c:936:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxcmap.c: In function \u2018cmap_separation_direct\u2019:
./base/gxcmap.c:1185:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxcmap.c: In function \u2018devicen_icc_cmyk\u2019:
./base/gxcmap.c:1305:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxcmap.c: In function \u2018cmap_devicen_halftoned\u2019:
./base/gxcmap.c:1356:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxcmap.c: In function \u2018cmap_devicen_direct\u2019:
./base/gxcmap.c:1402:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxcmap.c: In function \u2018gx_device_uses_std_cmap_procs\u2019:
./base/gxcmap.c:1984:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxdcolor.c: In function \u2018gx_dc_devn_write\u2019:
./base/gxdcolor.c:627:9: warning: unused variable \u2018k\u2019 [-Wunused-variable]
     int k;
         ^
./base/gxht_thresh.c: In function \u2018gx_ht_threshold_landscape_sub\u2019:
./base/gxht_thresh.c:400:5: warning: \u2018align\u2019 attribute directive ignored [-Wattributes]
     __align16 byte contone[LAND_BITS];
     ^
./base/gxht_thresh.c: In function \u2018gx_ht_threshold_landscape\u2019:
./base/gxht_thresh.c:491:5: warning: \u2018align\u2019 attribute directive ignored [-Wattributes]
     __align16 byte contone[LAND_BITS];
     ^
./base/gxht_thresh.c: In function \u2018gxht_thresh_image_init\u2019:
./base/gxht_thresh.c:578:15: warning: variable \u2018oy\u2019 set but not used [-Wunused-but-set-variable]
     fixed ox, oy;
               ^
./base/gximono.c: In function \u2018image_render_mono_ht\u2019:
./base/gximono.c:1103:10: warning: \u2018xrun\u2019 may be used uninitialized in this function [-Wmaybe-uninitialized]
     code = gxht_thresh_planes(penum, xrun, dest_width, dest_height,
          ^
./base/gxi12bit.c: In function \u2018gs_image_class_2_fracs\u2019:
./base/gxi12bit.c:147:17: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
             int code;
                 ^
./base/gxi12bit.c: In function \u2018image_render_icc16\u2019:
./base/gxi12bit.c:596:27: warning: variable \u2018pcs\u2019 set but not used [-Wunused-but-set-variable]
     const gs_color_space *pcs;
                           ^
./base/gxiscale.c: In function \u2018gs_image_class_0_interpolate\u2019:
./base/gxiscale.c:86:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxiscale.c: In function \u2018initial_decode\u2019:
./base/gxiscale.c:444:19: warning: variable \u2018index_space\u2019 set but not used [-Wunused-but-set-variable]
     unsigned char index_space;
                   ^
./base/gxiscale.c:443:25: warning: unused variable \u2018w\u2019 [-Wunused-variable]
     stream_cursor_write w;
                         ^
./base/gxiscale.c:441:28: warning: unused variable \u2018lop\u2019 [-Wunused-variable]
     gs_logical_operation_t lop = penum->log_op;
                            ^
./base/gxiscale.c:439:28: warning: unused variable \u2018pis\u2019 [-Wunused-variable]
     const gs_imager_state *pis = penum->pis;
                            ^
./base/gxiscale.c: In function \u2018image_render_interpolate_icc\u2019:
./base/gxiscale.c:907:70: warning: suggest parentheses around \u2018&&\u2019 within \u2018||\u2019 [-Wparentheses]
     need_decode = !((penum->device_color || penum->icc_setup.is_lab) &&
                                                                      ^
./base/gxiscale.c:934:13: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
         int code;
             ^
./base/gxiscale.c: In function \u2018image_render_interpolate_landscape_icc\u2019:
./base/gxiscale.c:1351:70: warning: suggest parentheses around \u2018&&\u2019 within \u2018||\u2019 [-Wparentheses]
     need_decode = !((penum->device_color || penum->icc_setup.is_lab) &&
                                                                      ^
./base/gxiscale.c:1378:13: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
         int code;
             ^
./base/gdevdbit.c: In function \u2018gx_default_copy_alpha_hl_color\u2019:
./base/gdevdbit.c:203:11: warning: variable \u2018end_ptr\u2019 set but not used [-Wunused-but-set-variable]
     byte *end_ptr;
           ^
In file included from ./base/gdevddrw.c:401:0:
./base/gxdtfill.h: In function \u2018gx_fill_trapezoid_ns_lc\u2019:
./base/gxdtfill.h:146:13: warning: variable \u2018ry\u2019 set but not used [-Wunused-but-set-variable]
         int ry;
             ^
In file included from ./base/gdevddrw.c:411:0:
./base/gxdtfill.h: In function \u2018gx_fill_trapezoid_as_lc\u2019:
./base/gxdtfill.h:146:13: warning: variable \u2018ry\u2019 set but not used [-Wunused-but-set-variable]
         int ry;
             ^
./base/gdevdrop.c: In function \u2018mem_default_strip_copy_rop\u2019:
./base/gdevdrop.c:832:14: warning: \u2018source_row_raster\u2019 may be used uninitialized in this function [-Wmaybe-uninitialized]
         code = (*dev_proc(&mdev, strip_copy_rop))
              ^
./base/gdevmr8n.c: In function \u2018mem_gray8_rgb24_strip_copy_rop\u2019:
./base/gdevmr8n.c:134:9: warning: case value \u2018204\u2019 not in enumerated type \u2018gs_rop3_t {aka enum <anonymous>}\u2019 [-Wswitch]
         case rop3_S:
         ^
./base/gdevmr8n.c:138:9: warning: case value \u2018240\u2019 not in enumerated type \u2018gs_rop3_t {aka enum <anonymous>}\u2019 [-Wswitch]
         case rop3_T:
         ^
In file included from ./base/gp_unix.c:19:0:
./base/pipe_.h:41:1: warning: function declaration isn\u2019t a prototype [-Wstrict-prototypes]
 extern FILE *popen( /* const char *, const char * */ );
 ^
./base/mkromfs.c:211:1: warning: no previous prototype for \u2018lprintf_file_only\u2019 [-Wmissing-prototypes]
 lprintf_file_only(FILE * f, const char *file)
 ^
./obj/aux/gp_unifs.o: In function `gp_open_scratch_file_generic':
gp_unifs.c:(.text+0x83): warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib/../lib64/libXext.so: undefined reference to `_XEatDataWords'
collect2: error: ld returned 1 exit status
make: *** [bin/gs] Error 1

October 31, 2016 10:12 AM
Hi Evan,

Can you include the full error you're receiving?

Thanks,
--nate


October 31, 2016 10:11 AM
I was installing a tool from the galaxy toolshed and one of the dependencies was missing due to a bad link. I modified the install files to use the same version of the the software except from a local directory, however galaxy renders a large error when compiling. If I compile the source in the same location outside of galaxy it compiles and installs correctly. The specific package I am attempting to install is ghostscript for homer package.


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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Re: Compiling dependencies in galaxy yields error

Nate Coraor (nate@bx.psu.edu)
Are your libX* libraries and headers the same version?

On Mon, Oct 31, 2016 at 10:17 AM, evan clark <[hidden email]> wrote:
All LibX are installed

freetype/src/base/ftrfork.c:407:3: warning: no previous prototype for \u2018ft_raccess_rule_by_darwin_vfs\u2019 [-Wmissing-prototypes]
   ft_raccess_rule_by_darwin_vfs( FT_Library  library,
   ^
freetype/src/psaux/afmparse.c:563:3: warning: no previous prototype for \u2018afm_parser_read_int\u2019 [-Wmissing-prototypes]
   afm_parser_read_int( AFM_Parser  parser,
   ^
freetype/src/raster/ftraster.c:3244:3: warning: no previous prototype for \u2018Render_Glyph\u2019 [-Wmissing-prototypes]
   Render_Glyph( RAS_ARG )
   ^
freetype/src/raster/ftraster.c:3392:3: warning: no previous prototype for \u2018Render_Gray_Glyph\u2019 [-Wmissing-prototypes]
   Render_Gray_Glyph( RAS_ARG )
   ^
freetype/src/type1/t1load.c:230:3: warning: no previous prototype for \u2018mm_axis_unmap\u2019 [-Wmissing-prototypes]
   mm_axis_unmap( PS_DesignMap  axismap,
   ^
freetype/src/type1/t1load.c:266:3: warning: no previous prototype for \u2018mm_weights_unmap\u2019 [-Wmissing-prototypes]
   mm_weights_unmap( FT_Fixed*  weights,
   ^
freetype/src/type1/t1gload.c:58:3: warning: no previous prototype for \u2018T1_Parse_Glyph_And_Get_Char_String\u2019 [-Wmissing-prototypes]
   T1_Parse_Glyph_And_Get_Char_String( T1_Decoder  decoder,
   ^
./base/gxcmap.c: In function \u2018cmap_cmyk_direct\u2019:
./base/gxcmap.c:936:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxcmap.c: In function \u2018cmap_separation_direct\u2019:
./base/gxcmap.c:1185:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxcmap.c: In function \u2018devicen_icc_cmyk\u2019:
./base/gxcmap.c:1305:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxcmap.c: In function \u2018cmap_devicen_halftoned\u2019:
./base/gxcmap.c:1356:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxcmap.c: In function \u2018cmap_devicen_direct\u2019:
./base/gxcmap.c:1402:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxcmap.c: In function \u2018gx_device_uses_std_cmap_procs\u2019:
./base/gxcmap.c:1984:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxdcolor.c: In function \u2018gx_dc_devn_write\u2019:
./base/gxdcolor.c:627:9: warning: unused variable \u2018k\u2019 [-Wunused-variable]
     int k;
         ^
./base/gxht_thresh.c: In function \u2018gx_ht_threshold_landscape_sub\u2019:
./base/gxht_thresh.c:400:5: warning: \u2018align\u2019 attribute directive ignored [-Wattributes]
     __align16 byte contone[LAND_BITS];
     ^
./base/gxht_thresh.c: In function \u2018gx_ht_threshold_landscape\u2019:
./base/gxht_thresh.c:491:5: warning: \u2018align\u2019 attribute directive ignored [-Wattributes]
     __align16 byte contone[LAND_BITS];
     ^
./base/gxht_thresh.c: In function \u2018gxht_thresh_image_init\u2019:
./base/gxht_thresh.c:578:15: warning: variable \u2018oy\u2019 set but not used [-Wunused-but-set-variable]
     fixed ox, oy;
               ^
./base/gximono.c: In function \u2018image_render_mono_ht\u2019:
./base/gximono.c:1103:10: warning: \u2018xrun\u2019 may be used uninitialized in this function [-Wmaybe-uninitialized]
     code = gxht_thresh_planes(penum, xrun, dest_width, dest_height,
          ^
./base/gxi12bit.c: In function \u2018gs_image_class_2_fracs\u2019:
./base/gxi12bit.c:147:17: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
             int code;
                 ^
./base/gxi12bit.c: In function \u2018image_render_icc16\u2019:
./base/gxi12bit.c:596:27: warning: variable \u2018pcs\u2019 set but not used [-Wunused-but-set-variable]
     const gs_color_space *pcs;
                           ^
./base/gxiscale.c: In function \u2018gs_image_class_0_interpolate\u2019:
./base/gxiscale.c:86:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxiscale.c: In function \u2018initial_decode\u2019:
./base/gxiscale.c:444:19: warning: variable \u2018index_space\u2019 set but not used [-Wunused-but-set-variable]
     unsigned char index_space;
                   ^
./base/gxiscale.c:443:25: warning: unused variable \u2018w\u2019 [-Wunused-variable]
     stream_cursor_write w;
                         ^
./base/gxiscale.c:441:28: warning: unused variable \u2018lop\u2019 [-Wunused-variable]
     gs_logical_operation_t lop = penum->log_op;
                            ^
./base/gxiscale.c:439:28: warning: unused variable \u2018pis\u2019 [-Wunused-variable]
     const gs_imager_state *pis = penum->pis;
                            ^
./base/gxiscale.c: In function \u2018image_render_interpolate_icc\u2019:
./base/gxiscale.c:907:70: warning: suggest parentheses around \u2018&&\u2019 within \u2018||\u2019 [-Wparentheses]
     need_decode = !((penum->device_color || penum->icc_setup.is_lab) &&
                                                                      ^
./base/gxiscale.c:934:13: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
         int code;
             ^
./base/gxiscale.c: In function \u2018image_render_interpolate_landscape_icc\u2019:
./base/gxiscale.c:1351:70: warning: suggest parentheses around \u2018&&\u2019 within \u2018||\u2019 [-Wparentheses]
     need_decode = !((penum->device_color || penum->icc_setup.is_lab) &&
                                                                      ^
./base/gxiscale.c:1378:13: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
         int code;
             ^
./base/gdevdbit.c: In function \u2018gx_default_copy_alpha_hl_color\u2019:
./base/gdevdbit.c:203:11: warning: variable \u2018end_ptr\u2019 set but not used [-Wunused-but-set-variable]
     byte *end_ptr;
           ^
In file included from ./base/gdevddrw.c:401:0:
./base/gxdtfill.h: In function \u2018gx_fill_trapezoid_ns_lc\u2019:
./base/gxdtfill.h:146:13: warning: variable \u2018ry\u2019 set but not used [-Wunused-but-set-variable]
         int ry;
             ^
In file included from ./base/gdevddrw.c:411:0:
./base/gxdtfill.h: In function \u2018gx_fill_trapezoid_as_lc\u2019:
./base/gxdtfill.h:146:13: warning: variable \u2018ry\u2019 set but not used [-Wunused-but-set-variable]
         int ry;
             ^
./base/gdevdrop.c: In function \u2018mem_default_strip_copy_rop\u2019:
./base/gdevdrop.c:832:14: warning: \u2018source_row_raster\u2019 may be used uninitialized in this function [-Wmaybe-uninitialized]
         code = (*dev_proc(&mdev, strip_copy_rop))
              ^
./base/gdevmr8n.c: In function \u2018mem_gray8_rgb24_strip_copy_rop\u2019:
./base/gdevmr8n.c:134:9: warning: case value \u2018204\u2019 not in enumerated type \u2018gs_rop3_t {aka enum <anonymous>}\u2019 [-Wswitch]
         case rop3_S:
         ^
./base/gdevmr8n.c:138:9: warning: case value \u2018240\u2019 not in enumerated type \u2018gs_rop3_t {aka enum <anonymous>}\u2019 [-Wswitch]
         case rop3_T:
         ^
In file included from ./base/gp_unix.c:19:0:
./base/pipe_.h:41:1: warning: function declaration isn\u2019t a prototype [-Wstrict-prototypes]
 extern FILE *popen( /* const char *, const char * */ );
 ^
./base/mkromfs.c:211:1: warning: no previous prototype for \u2018lprintf_file_only\u2019 [-Wmissing-prototypes]
 lprintf_file_only(FILE * f, const char *file)
 ^
./obj/aux/gp_unifs.o: In function `gp_open_scratch_file_generic':
gp_unifs.c:(.text+0x83): warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib/../lib64/libXext.so: undefined reference to `_XEatDataWords'
collect2: error: ld returned 1 exit status
make: *** [bin/gs] Error 1

October 31, 2016 10:12 AM
Hi Evan,

Can you include the full error you're receiving?

Thanks,
--nate


October 31, 2016 10:11 AM
I was installing a tool from the galaxy toolshed and one of the dependencies was missing due to a bad link. I modified the install files to use the same version of the the software except from a local directory, however galaxy renders a large error when compiling. If I compile the source in the same location outside of galaxy it compiles and installs correctly. The specific package I am attempting to install is ghostscript for homer package.



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

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Re: Compiling dependencies in galaxy yields error

evan clark
I am unsure as it does compile properly outside of galaxy. How do I check these and make sure they are the same?

October 31, 2016 10:25 AM
Are your libX* libraries and headers the same version?


October 31, 2016 10:17 AM
All LibX are installed

freetype/src/base/ftrfork.c:407:3: warning: no previous prototype for \u2018ft_raccess_rule_by_darwin_vfs\u2019 [-Wmissing-prototypes]
   ft_raccess_rule_by_darwin_vfs( FT_Library  library,
   ^
freetype/src/psaux/afmparse.c:563:3: warning: no previous prototype for \u2018afm_parser_read_int\u2019 [-Wmissing-prototypes]
   afm_parser_read_int( AFM_Parser  parser,
   ^
freetype/src/raster/ftraster.c:3244:3: warning: no previous prototype for \u2018Render_Glyph\u2019 [-Wmissing-prototypes]
   Render_Glyph( RAS_ARG )
   ^
freetype/src/raster/ftraster.c:3392:3: warning: no previous prototype for \u2018Render_Gray_Glyph\u2019 [-Wmissing-prototypes]
   Render_Gray_Glyph( RAS_ARG )
   ^
freetype/src/type1/t1load.c:230:3: warning: no previous prototype for \u2018mm_axis_unmap\u2019 [-Wmissing-prototypes]
   mm_axis_unmap( PS_DesignMap  axismap,
   ^
freetype/src/type1/t1load.c:266:3: warning: no previous prototype for \u2018mm_weights_unmap\u2019 [-Wmissing-prototypes]
   mm_weights_unmap( FT_Fixed*  weights,
   ^
freetype/src/type1/t1gload.c:58:3: warning: no previous prototype for \u2018T1_Parse_Glyph_And_Get_Char_String\u2019 [-Wmissing-prototypes]
   T1_Parse_Glyph_And_Get_Char_String( T1_Decoder  decoder,
   ^
./base/gxcmap.c: In function \u2018cmap_cmyk_direct\u2019:
./base/gxcmap.c:936:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxcmap.c: In function \u2018cmap_separation_direct\u2019:
./base/gxcmap.c:1185:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxcmap.c: In function \u2018devicen_icc_cmyk\u2019:
./base/gxcmap.c:1305:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxcmap.c: In function \u2018cmap_devicen_halftoned\u2019:
./base/gxcmap.c:1356:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxcmap.c: In function \u2018cmap_devicen_direct\u2019:
./base/gxcmap.c:1402:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxcmap.c: In function \u2018gx_device_uses_std_cmap_procs\u2019:
./base/gxcmap.c:1984:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxdcolor.c: In function \u2018gx_dc_devn_write\u2019:
./base/gxdcolor.c:627:9: warning: unused variable \u2018k\u2019 [-Wunused-variable]
     int k;
         ^
./base/gxht_thresh.c: In function \u2018gx_ht_threshold_landscape_sub\u2019:
./base/gxht_thresh.c:400:5: warning: \u2018align\u2019 attribute directive ignored [-Wattributes]
     __align16 byte contone[LAND_BITS];
     ^
./base/gxht_thresh.c: In function \u2018gx_ht_threshold_landscape\u2019:
./base/gxht_thresh.c:491:5: warning: \u2018align\u2019 attribute directive ignored [-Wattributes]
     __align16 byte contone[LAND_BITS];
     ^
./base/gxht_thresh.c: In function \u2018gxht_thresh_image_init\u2019:
./base/gxht_thresh.c:578:15: warning: variable \u2018oy\u2019 set but not used [-Wunused-but-set-variable]
     fixed ox, oy;
               ^
./base/gximono.c: In function \u2018image_render_mono_ht\u2019:
./base/gximono.c:1103:10: warning: \u2018xrun\u2019 may be used uninitialized in this function [-Wmaybe-uninitialized]
     code = gxht_thresh_planes(penum, xrun, dest_width, dest_height,
          ^
./base/gxi12bit.c: In function \u2018gs_image_class_2_fracs\u2019:
./base/gxi12bit.c:147:17: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
             int code;
                 ^
./base/gxi12bit.c: In function \u2018image_render_icc16\u2019:
./base/gxi12bit.c:596:27: warning: variable \u2018pcs\u2019 set but not used [-Wunused-but-set-variable]
     const gs_color_space *pcs;
                           ^
./base/gxiscale.c: In function \u2018gs_image_class_0_interpolate\u2019:
./base/gxiscale.c:86:9: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
     int code;
         ^
./base/gxiscale.c: In function \u2018initial_decode\u2019:
./base/gxiscale.c:444:19: warning: variable \u2018index_space\u2019 set but not used [-Wunused-but-set-variable]
     unsigned char index_space;
                   ^
./base/gxiscale.c:443:25: warning: unused variable \u2018w\u2019 [-Wunused-variable]
     stream_cursor_write w;
                         ^
./base/gxiscale.c:441:28: warning: unused variable \u2018lop\u2019 [-Wunused-variable]
     gs_logical_operation_t lop = penum->log_op;
                            ^
./base/gxiscale.c:439:28: warning: unused variable \u2018pis\u2019 [-Wunused-variable]
     const gs_imager_state *pis = penum->pis;
                            ^
./base/gxiscale.c: In function \u2018image_render_interpolate_icc\u2019:
./base/gxiscale.c:907:70: warning: suggest parentheses around \u2018&&\u2019 within \u2018||\u2019 [-Wparentheses]
     need_decode = !((penum->device_color || penum->icc_setup.is_lab) &&
                                                                      ^
./base/gxiscale.c:934:13: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
         int code;
             ^
./base/gxiscale.c: In function \u2018image_render_interpolate_landscape_icc\u2019:
./base/gxiscale.c:1351:70: warning: suggest parentheses around \u2018&&\u2019 within \u2018||\u2019 [-Wparentheses]
     need_decode = !((penum->device_color || penum->icc_setup.is_lab) &&
                                                                      ^
./base/gxiscale.c:1378:13: warning: variable \u2018code\u2019 set but not used [-Wunused-but-set-variable]
         int code;
             ^
./base/gdevdbit.c: In function \u2018gx_default_copy_alpha_hl_color\u2019:
./base/gdevdbit.c:203:11: warning: variable \u2018end_ptr\u2019 set but not used [-Wunused-but-set-variable]
     byte *end_ptr;
           ^
In file included from ./base/gdevddrw.c:401:0:
./base/gxdtfill.h: In function \u2018gx_fill_trapezoid_ns_lc\u2019:
./base/gxdtfill.h:146:13: warning: variable \u2018ry\u2019 set but not used [-Wunused-but-set-variable]
         int ry;
             ^
In file included from ./base/gdevddrw.c:411:0:
./base/gxdtfill.h: In function \u2018gx_fill_trapezoid_as_lc\u2019:
./base/gxdtfill.h:146:13: warning: variable \u2018ry\u2019 set but not used [-Wunused-but-set-variable]
         int ry;
             ^
./base/gdevdrop.c: In function \u2018mem_default_strip_copy_rop\u2019:
./base/gdevdrop.c:832:14: warning: \u2018source_row_raster\u2019 may be used uninitialized in this function [-Wmaybe-uninitialized]
         code = (*dev_proc(&mdev, strip_copy_rop))
              ^
./base/gdevmr8n.c: In function \u2018mem_gray8_rgb24_strip_copy_rop\u2019:
./base/gdevmr8n.c:134:9: warning: case value \u2018204\u2019 not in enumerated type \u2018gs_rop3_t {aka enum <anonymous>}\u2019 [-Wswitch]
         case rop3_S:
         ^
./base/gdevmr8n.c:138:9: warning: case value \u2018240\u2019 not in enumerated type \u2018gs_rop3_t {aka enum <anonymous>}\u2019 [-Wswitch]
         case rop3_T:
         ^
In file included from ./base/gp_unix.c:19:0:
./base/pipe_.h:41:1: warning: function declaration isn\u2019t a prototype [-Wstrict-prototypes]
 extern FILE *popen( /* const char *, const char * */ );
 ^
./base/mkromfs.c:211:1: warning: no previous prototype for \u2018lprintf_file_only\u2019 [-Wmissing-prototypes]
 lprintf_file_only(FILE * f, const char *file)
 ^
./obj/aux/gp_unifs.o: In function `gp_open_scratch_file_generic':
gp_unifs.c:(.text+0x83): warning: the use of `mktemp' is dangerous, better use `mkstemp'
/usr/lib/../lib64/libXext.so: undefined reference to `_XEatDataWords'
collect2: error: ld returned 1 exit status
make: *** [bin/gs] Error 1


October 31, 2016 10:12 AM
Hi Evan,

Can you include the full error you're receiving?

Thanks,
--nate


October 31, 2016 10:11 AM
I was installing a tool from the galaxy toolshed and one of the dependencies was missing due to a bad link. I modified the install files to use the same version of the the software except from a local directory, however galaxy renders a large error when compiling. If I compile the source in the same location outside of galaxy it compiles and installs correctly. The specific package I am attempting to install is ghostscript for homer package.


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