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

Nate Coraor <mailto:nate@bx.psu.edu> October 31, 2016 10:12 AM Hi Evan,

Can you include the full error you're receiving?

Thanks, --nate

evan clark <mailto:eclark28@fau.edu> 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.

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

Nate Coraor <mailto:nate@bx.psu.edu> October 31, 2016 10:25 AM Are your libX* libraries and headers the same version?

evan clark <mailto:eclark28@fau.edu> 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

Nate Coraor <mailto:nate@bx.psu.edu> October 31, 2016 10:12 AM Hi Evan,

Can you include the full error you're receiving?

Thanks, --nate

evan clark <mailto:eclark28@fau.edu> 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.