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January 27, 2018 20:36
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R package rgdal fails to install via nix
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| let | |
| pkgs = import <nixpkgs> {}; | |
| stdenv = pkgs.stdenv; | |
| in with pkgs; { | |
| myProject = stdenv.mkDerivation { | |
| name = "myProject"; | |
| version = "1"; | |
| src = if pkgs.lib.inNixShell then null else nix; | |
| buildInputs = with rPackages; [ | |
| R | |
| ggplot2 | |
| dplyr | |
| maps | |
| Cairo | |
| knitr | |
| rgdal | |
| ]; | |
| }; | |
| } |
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| bash-3.2$ bash-3.2$ nix-shell . -I nixpkgs=/Users/dom/nixpkgs | |
| these derivations will be built: | |
| /nix/store/jk0rqmkm333pfiajrjvgd1ylfz4vf9yd-r-rgdal-1.2-16.drv | |
| building path(s) ‘/nix/store/0vn5702llamiw9h0w8g8izdd1na4vs50-r-rgdal-1.2-16’ | |
| unpacking sources | |
| unpacking source archive /nix/store/hmlpfphlllxw12m3rz5hr7748xhp64ac-rgdal_1.2-16.tar.gz | |
| source root is rgdal | |
| setting SOURCE_DATE_EPOCH to timestamp 1511308544 of file rgdal/MD5 | |
| patching sources | |
| configuring | |
| building | |
| running tests | |
| installing | |
| * installing *source* package 'rgdal' ... | |
| ** package 'rgdal' successfully unpacked and MD5 sums checked | |
| configure: CC: clang | |
| configure: CXX: clang++ | |
| configure: rgdal: 1.2-16 | |
| checking for /usr/bin/svnversion... yes | |
| ./configure: line 1733: svnversion: command not found | |
| configure: svn revision: 701 | |
| checking for gdal-config... /nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/bin/gdal-config | |
| checking gdal-config usability... yes | |
| configure: GDAL: 2.2.3 | |
| checking GDAL version >= 1.6.3... yes | |
| checking gdal: linking with --libs only... yes | |
| checking GDAL: /nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/share/gdal/pcs.csv readable... yes | |
| configure: -g -O2 -I/nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/include | |
| checking proj_api.h presence and usability... yes | |
| dyld: Library not loaded: /nix/store/wbbxlsnyp1vpwj7rp9d0l0m4d4z425gl-mariadb-connector-c-2.3.4/lib/libmariadb.2.dylib | |
| Referenced from: /nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/lib/libgdal.20.dylib | |
| Reason: image not found | |
| checking PROJ.4 version: ... ./configure: line 2030: test: -eq: unary operator expected | |
| ./configure: line 2035: test: -ge: unary operator expected | |
| < 4.8.0 | |
| ./configure: line 2063: test: -ge: unary operator expected | |
| proj_conf_test2.c:3:7: error: conflicting types for 'pj_open_lib' | |
| FILE *pj_open_lib(const char *, const char *); | |
| ^ | |
| /nix/store/l060rjvms9wbmnzvngjsrjbwg33c4kyr-proj-4.9.3/include/proj_api.h:169:8: note: previous declaration is here | |
| PAFile pj_open_lib(projCtx, const char *, const char *); | |
| ^ | |
| proj_conf_test2.c:7:34: error: too few arguments to function call, expected 3, have 2 | |
| fp = pj_open_lib("epsg", "rb"); | |
| ~~~~~~~~~~~ ^ | |
| /nix/store/l060rjvms9wbmnzvngjsrjbwg33c4kyr-proj-4.9.3/include/proj_api.h:169:1: note: 'pj_open_lib' declared here | |
| PAFile pj_open_lib(projCtx, const char *, const char *); | |
| ^ | |
| 2 errors generated. | |
| ./configure: line 2110: ./proj_conf_test2: No such file or directory | |
| checking PROJ.4: epsg found and readable... yes | |
| ./configure: line 2138: test: -ge: unary operator expected | |
| proj_conf_test3.c:3:7: error: conflicting types for 'pj_open_lib' | |
| FILE *pj_open_lib(const char *, const char *); | |
| ^ | |
| /nix/store/l060rjvms9wbmnzvngjsrjbwg33c4kyr-proj-4.9.3/include/proj_api.h:169:8: note: previous declaration is here | |
| PAFile pj_open_lib(projCtx, const char *, const char *); | |
| ^ | |
| proj_conf_test3.c:7:35: error: too few arguments to function call, expected 3, have 2 | |
| fp = pj_open_lib("conus", "rb"); | |
| ~~~~~~~~~~~ ^ | |
| /nix/store/l060rjvms9wbmnzvngjsrjbwg33c4kyr-proj-4.9.3/include/proj_api.h:169:1: note: 'pj_open_lib' declared here | |
| PAFile pj_open_lib(projCtx, const char *, const char *); | |
| ^ | |
| 2 errors generated. | |
| ./configure: line 2185: ./proj_conf_test3: No such file or directory | |
| checking PROJ.4: conus found and readable... yes | |
| configure: Package CPP flags: -I/nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/include | |
| configure: Package LIBS: -L/nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/lib -lgdal -lproj | |
| configure: creating ./config.status | |
| config.status: creating src/Makevars | |
| ** libs | |
| /nix/store/cslvigh4a1656g9z9j1ndvzalx7v2s4k-clang-wrapper-4.0.1/bin/c++ -std=gnu++11 -I/nix/store/vxni3jvvpz6xy0cd3w7gz0wjz61fymnx-R-3.4.3/lib/R/include -DNDEBUG -I/nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/include -I"/nix/store/ylk7gqpr4hyvkfmh8ymzf8gjpzvndkxr-r-sp-1.2-5/library/sp/include" -fPIC -g -O2 -c OGR_write.cpp -o OGR_write.o | |
| /nix/store/cslvigh4a1656g9z9j1ndvzalx7v2s4k-clang-wrapper-4.0.1/bin/c++ -std=gnu++11 -I/nix/store/vxni3jvvpz6xy0cd3w7gz0wjz61fymnx-R-3.4.3/lib/R/include -DNDEBUG -I/nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/include -I"/nix/store/ylk7gqpr4hyvkfmh8ymzf8gjpzvndkxr-r-sp-1.2-5/library/sp/include" -fPIC -g -O2 -c gdal-bindings.cpp -o gdal-bindings.o | |
| /nix/store/cslvigh4a1656g9z9j1ndvzalx7v2s4k-clang-wrapper-4.0.1/bin/cc -I/nix/store/vxni3jvvpz6xy0cd3w7gz0wjz61fymnx-R-3.4.3/lib/R/include -DNDEBUG -I/nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/include -I"/nix/store/ylk7gqpr4hyvkfmh8ymzf8gjpzvndkxr-r-sp-1.2-5/library/sp/include" -fPIC -g -O2 -c init.c -o init.o | |
| /nix/store/cslvigh4a1656g9z9j1ndvzalx7v2s4k-clang-wrapper-4.0.1/bin/cc -I/nix/store/vxni3jvvpz6xy0cd3w7gz0wjz61fymnx-R-3.4.3/lib/R/include -DNDEBUG -I/nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/include -I"/nix/store/ylk7gqpr4hyvkfmh8ymzf8gjpzvndkxr-r-sp-1.2-5/library/sp/include" -fPIC -g -O2 -c inverser.c -o inverser.o | |
| /nix/store/cslvigh4a1656g9z9j1ndvzalx7v2s4k-clang-wrapper-4.0.1/bin/cc -I/nix/store/vxni3jvvpz6xy0cd3w7gz0wjz61fymnx-R-3.4.3/lib/R/include -DNDEBUG -I/nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/include -I"/nix/store/ylk7gqpr4hyvkfmh8ymzf8gjpzvndkxr-r-sp-1.2-5/library/sp/include" -fPIC -g -O2 -c local_stubs.c -o local_stubs.o | |
| /nix/store/cslvigh4a1656g9z9j1ndvzalx7v2s4k-clang-wrapper-4.0.1/bin/c++ -std=gnu++11 -I/nix/store/vxni3jvvpz6xy0cd3w7gz0wjz61fymnx-R-3.4.3/lib/R/include -DNDEBUG -I/nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/include -I"/nix/store/ylk7gqpr4hyvkfmh8ymzf8gjpzvndkxr-r-sp-1.2-5/library/sp/include" -fPIC -g -O2 -c ogr_geom.cpp -o ogr_geom.o | |
| /nix/store/cslvigh4a1656g9z9j1ndvzalx7v2s4k-clang-wrapper-4.0.1/bin/cc -I/nix/store/vxni3jvvpz6xy0cd3w7gz0wjz61fymnx-R-3.4.3/lib/R/include -DNDEBUG -I/nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/include -I"/nix/store/ylk7gqpr4hyvkfmh8ymzf8gjpzvndkxr-r-sp-1.2-5/library/sp/include" -fPIC -g -O2 -c ogr_polygons.c -o ogr_polygons.o | |
| /nix/store/cslvigh4a1656g9z9j1ndvzalx7v2s4k-clang-wrapper-4.0.1/bin/c++ -std=gnu++11 -I/nix/store/vxni3jvvpz6xy0cd3w7gz0wjz61fymnx-R-3.4.3/lib/R/include -DNDEBUG -I/nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/include -I"/nix/store/ylk7gqpr4hyvkfmh8ymzf8gjpzvndkxr-r-sp-1.2-5/library/sp/include" -fPIC -g -O2 -c ogr_proj.cpp -o ogr_proj.o | |
| /nix/store/cslvigh4a1656g9z9j1ndvzalx7v2s4k-clang-wrapper-4.0.1/bin/c++ -std=gnu++11 -I/nix/store/vxni3jvvpz6xy0cd3w7gz0wjz61fymnx-R-3.4.3/lib/R/include -DNDEBUG -I/nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/include -I"/nix/store/ylk7gqpr4hyvkfmh8ymzf8gjpzvndkxr-r-sp-1.2-5/library/sp/include" -fPIC -g -O2 -c ogrdrivers.cpp -o ogrdrivers.o | |
| /nix/store/cslvigh4a1656g9z9j1ndvzalx7v2s4k-clang-wrapper-4.0.1/bin/c++ -std=gnu++11 -I/nix/store/vxni3jvvpz6xy0cd3w7gz0wjz61fymnx-R-3.4.3/lib/R/include -DNDEBUG -I/nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/include -I"/nix/store/ylk7gqpr4hyvkfmh8ymzf8gjpzvndkxr-r-sp-1.2-5/library/sp/include" -fPIC -g -O2 -c ogrsource.cpp -o ogrsource.o | |
| /nix/store/cslvigh4a1656g9z9j1ndvzalx7v2s4k-clang-wrapper-4.0.1/bin/c++ -std=gnu++11 -I/nix/store/vxni3jvvpz6xy0cd3w7gz0wjz61fymnx-R-3.4.3/lib/R/include -DNDEBUG -I/nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/include -I"/nix/store/ylk7gqpr4hyvkfmh8ymzf8gjpzvndkxr-r-sp-1.2-5/library/sp/include" -fPIC -g -O2 -c projectit.cpp -o projectit.o | |
| /nix/store/cslvigh4a1656g9z9j1ndvzalx7v2s4k-clang-wrapper-4.0.1/bin/c++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/nix/store/vxni3jvvpz6xy0cd3w7gz0wjz61fymnx-R-3.4.3/lib/R/lib -o rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -L/nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/lib -lgdal -lproj -L/nix/store/vxni3jvvpz6xy0cd3w7gz0wjz61fymnx-R-3.4.3/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation | |
| installing to /nix/store/0vn5702llamiw9h0w8g8izdd1na4vs50-r-rgdal-1.2-16/library/rgdal/libs | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| Error: package or namespace load failed for 'rgdal' in dyn.load(file, DLLpath = DLLpath, ...): | |
| unable to load shared object '/nix/store/0vn5702llamiw9h0w8g8izdd1na4vs50-r-rgdal-1.2-16/library/rgdal/libs/rgdal.so': | |
| dlopen(/nix/store/0vn5702llamiw9h0w8g8izdd1na4vs50-r-rgdal-1.2-16/library/rgdal/libs/rgdal.so, 6): Library not loaded: /nix/store/wbbxlsnyp1vpwj7rp9d0l0m4d4z425gl-mariadb-connector-c-2.3.4/lib/libmariadb.2.dylib | |
| Referenced from: /nix/store/2ci05xq0q9h86yqfg99g2jdvynkcfjm3-gdal-2.2.3/lib/libgdal.20.dylib | |
| Reason: image not found | |
| Error: loading failed | |
| Execution halted | |
| ERROR: loading failed | |
| * removing '/nix/store/0vn5702llamiw9h0w8g8izdd1na4vs50-r-rgdal-1.2-16/library/rgdal' | |
| builder for ‘/nix/store/jk0rqmkm333pfiajrjvgd1ylfz4vf9yd-r-rgdal-1.2-16.drv’ failed with exit code 1 | |
| error: build of ‘/nix/store/jk0rqmkm333pfiajrjvgd1ylfz4vf9yd-r-rgdal-1.2-16.drv’ failed | |
| /nix/var/nix/profiles/default/bin/nix-shell: failed to build all dependencies | |
| bash-3.2$ |
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