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fethalen / Patchwork

Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data
GNU General Public License v3.0
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PackageCompiler: compiling nonincremental system image ERROR #53

Closed qilu521 closed 6 months ago

qilu521 commented 1 year ago

Here's what happened when I Compile Patchwork [18m:45s] PackageCompiler: compiling nonincremental system image /opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/ld: warning: /root/software/ju lia-1.8.2/lib/julia/libstdc++.so: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010001 /opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/ld: warning: /root/software/ju lia-1.8.2/lib/julia/libstdc++.so: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010002 /opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/ld: warning: /root/software/ju lia-1.8.2/lib/julia/libatomic.so.1: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010001 /opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/ld: warning: /root/software/ju lia-1.8.2/lib/julia/libatomic.so.1: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010002 /opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/ld: warning: /root/software/ju lia-1.8.2/lib/julia/libstdc++.so.6: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010001 /opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/ld: warning: /root/software/ju lia-1.8.2/lib/julia/libstdc++.so.6: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010002

[root@localhost patchwork]# julia --project=. src/compile.jl . src/precompiled.jl OUTPUT_DIR PackageCompiler: bundled artifacts: ├── Bzip2_jll - 1.444 MiB ├── Cairo_jll - 11.884 MiB ├── Expat_jll - 786.043 KiB ├── FFMPEG_jll - 26.314 MiB ├── Fontconfig_jll - 1.597 MiB ├── FreeType2_jll - 4.090 MiB ├── FriBidi_jll - 324.047 KiB ├── GLFW_jll - 554.408 KiB ├── GR_jll - 24.410 MiB ├── Gettext_jll - 13.968 MiB ├── Glib_jll - 16.549 MiB ├── Graphite2_jll - 302.039 KiB ├── HarfBuzz_jll - 2.960 MiB ├── JpegTurbo_jll - 4.167 MiB ├── LAME_jll - 904.166 KiB ├── LERC_jll - 629.045 KiB ├── LZO_jll - 899.784 KiB ├── Libffi_jll - 97.715 KiB ├── Libgcrypt_jll - 5.030 MiB ├── Libglvnd_jll - 4.996 MiB ├── Libgpg_error_jll - 1.590 MiB ├── Libiconv_jll - 1.955 MiB ├── Libmount_jll - 15.725 MiB ├── Libtiff_jll - 8.200 MiB ├── Libuuid_jll - 7.658 MiB ├── NodeJS │ └── nodejs_app - 70.889 MiB ├── Ogg_jll - 562.720 KiB ├── OpenSSL_jll - 12.358 MiB ├── OpenSpecFun_jll - 577.252 KiB ├── Opus_jll - 2.709 MiB ├── Pixman_jll - 5.407 MiB ├── Qt5Base_jll - 67.711 MiB ├── Vega │ └── vegalite_app - 139.263 MiB ├── VegaLite │ └── vegalite_app - [already bundled] ├── Wayland_jll - 1.325 MiB ├── Wayland_protocols_jll - 465.663 KiB ├── XML2_jll - 8.998 MiB ├── XSLT_jll - 1.687 MiB ├── Xorg_libX11_jll - 51.291 MiB ├── Xorg_libXau_jll - 134.889 KiB ├── Xorg_libXcursor_jll - 678.776 KiB ├── Xorg_libXdmcp_jll - 302.636 KiB ├── Xorg_libXext_jll - 2.235 MiB ├── Xorg_libXfixes_jll - 612.308 KiB ├── Xorg_libXi_jll - 5.838 MiB ├── Xorg_libXinerama_jll - 177.771 KiB ├── Xorg_libXrandr_jll - 1.273 MiB ├── Xorg_libXrender_jll - 1.432 MiB ├── Xorg_libpthread_stubs_jll - 5.074 KiB ├── Xorg_libxcb_jll - 11.389 MiB ├── Xorg_libxkbfile_jll - 1.513 MiB ├── Xorg_xcb_util_image_jll - 187.199 KiB ├── Xorg_xcb_util_jll - 142.044 KiB ├── Xorg_xcb_util_keysyms_jll - 82.065 KiB ├── Xorg_xcb_util_renderutil_jll - 116.603 KiB ├── Xorg_xcb_util_wm_jll - 701.915 KiB ├── Xorg_xkbcomp_jll - 770.177 KiB ├── Xorg_xkeyboard_config_jll - 5.271 MiB ├── Xorg_xtrans_jll - 241.450 KiB ├── Zstd_jll - 1.493 MiB ├── fzf_jll - 3.595 MiB ├── libaom_jll - 15.624 MiB ├── libass_jll - 1.088 MiB ├── libfdk_aac_jll - 8.467 MiB ├── libpng_jll - 976.110 KiB ├── libvorbis_jll - 1.119 MiB ├── x264_jll - 4.934 MiB ├── x265_jll - 5.982 MiB └── xkbcommon_jll - 1.373 MiB Total artifact file size: 597.765 MiB ✔ [03m:21s] PackageCompiler: compiling base system image (incremental=false) Precompiling project... 203 dependencies successfully precompiled in 566 seconds ✔ [18m:45s] PackageCompiler: compiling nonincremental system image /opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/ld: warning: /root/software/ju lia-1.8.2/lib/julia/libstdc++.so: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010001 /opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/ld: warning: /root/software/ju lia-1.8.2/lib/julia/libstdc++.so: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010002 /opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/ld: warning: /root/software/ju lia-1.8.2/lib/julia/libatomic.so.1: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010001 /opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/ld: warning: /root/software/ju lia-1.8.2/lib/julia/libatomic.so.1: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010002 /opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/ld: warning: /root/software/ju lia-1.8.2/lib/julia/libstdc++.so.6: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010001 /opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/ld: warning: /root/software/ju lia-1.8.2/lib/julia/libstdc++.so.6: unsupported GNU_PROPERTY_TYPE (5) type: 0xc0010002

fethalen commented 6 months ago

The updated compilation procedure should solve the issues you were having. If not, consider reopening this issue.