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.
Hi Evan,
Can you include the full error you're receiving?
Thanks, --nate
On Mon, Oct 31, 2016 at 10:11 AM, evan clark eclark28@fau.edu 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/
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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.
Are your libX* libraries and headers the same version?
On Mon, Oct 31, 2016 at 10:17 AM, evan clark eclark28@fau.edu 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
Nate Coraor 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 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.
galaxy-dev@lists.galaxyproject.org