Closed rsbivand closed 4 years ago
Could you give me the full output of the configure
step?
> remotes::install_github("r-spatial/sf", configure.args="--with-proj-api=yes")
Downloading GitHub repo r-spatial/sf@master
checking for file ‘/tmp/Rtmp0sA3nB/remotese702814a77fa/r-spatial-sf-5144b56/D checking for file ‘/tmp/Rtmp0sA3nB/remotese702814a77fa/r-spatial-sf-5144b56/D checking for file ‘/tmp/Rtmp0sA3nB/remotese702814a77fa/r-spatial-sf-5144b56/D✔ checking for file ‘/tmp/Rtmp0sA3nB/remotese702814a77fa/r-spatial-sf-5144b56/DESCRIPTION’
─ preparing ‘sf’:
✔ checking DESCRIPTION meta-information ... OK
─ cleaning src
─ running ‘cleanup’
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘sf_0.8-1.tar.gz’
Installing package into ‘/home/rsb/lib/r_libs’
(as ‘lib’ is unspecified)
* installing *source* package ‘sf’ ...
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++11
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.4.4
checking GDAL version >= 2.0.1... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking gdal.h usability... yes
checking gdal.h presence... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /usr/local/share/gdal/pcs.csv readable... yes
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available fur running:... yes
configure: pkg-config proj exists, will use it
checking proj.h usability... yes
checking proj.h presence... yes
checking for proj.h... yes
configure: PROJ: 5.2.0
checking PROJ: checking whether PROJ and sqlite3 are available for linking:... yes
checking for geos-config... /usr/local/bin/geos-config
checking geos-config usability... yes
configure: GEOS: 3.8.0
checking GEOS version >= 3.4.0... yes
checking geos_c.h usability... yes
checking geos_c.h presence... yes
checking for geos_c.h... yes
checking geos: linking with -L/usr/local/lib -lgeos_c... yes
configure: Package CPP flags: -I/usr/local/include -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include
configure: Package LIBS: -L/usr/local/lib -lproj -L/usr/local/lib -lgdal -L/usr/local/lib -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
Is that enough?
Yes. Should work now, could you try again?
Tomorrow morning, ok?
Roger Bivand Falsensvei 32 5063 Bergen
man. 27. jan. 2020, 22.09 skrev Edzer Pebesma notifications@github.com:
Yes. Should work now, could you try again?
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New attempt successful, closing:
> remotes::install_github("r-spatial/sf", configure.args="--with-proj-api=yes")
Downloading GitHub repo r-spatial/sf@master
checking for file ‘/tmp/Rtmpit7gpC/remotescfd6606e1ce/r-spatial-sf-dcaa100/DE✔ checking for file ‘/tmp/Rtmpit7gpC/remotescfd6606e1ce/r-spatial-sf-dcaa100/DESCRIPTION’
─ preparing ‘sf’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ running ‘cleanup’
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘sf_0.8-1.tar.gz’
Installing package into ‘/home/rsb/lib/r_libs’
(as ‘lib’ is unspecified)
* installing *source* package ‘sf’ ...
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++11
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.4.4
checking GDAL version >= 2.0.1... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking gdal.h usability... yes
checking gdal.h presence... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /usr/local/share/gdal/pcs.csv readable... yes
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available fur running:... yes
configure: pkg-config proj exists, will use it
checking proj_api.h usability... yes
checking proj_api.h presence... yes
checking for proj_api.h... yes
configure: PROJ: 5.2.0
checking for pj_init_plus in -lproj... yes
checking PROJ: epsg found and readable... yes
checking for geos-config... /usr/local/bin/geos-config
checking geos-config usability... yes
configure: GEOS: 3.8.0
checking GEOS version >= 3.4.0... yes
checking geos_c.h usability... yes
checking geos_c.h presence... yes
checking for geos_c.h... yes
checking geos: linking with -L/usr/local/lib -lgeos_c... yes
configure: Package CPP flags: -I/usr/local/include -I/usr/local/include -I/usr/local/include
configure: Package LIBS: -L/usr/local/lib -lproj -L/usr/local/lib -lgdal -L/usr/local/lib -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c bbox.cpp -o bbox.o
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c gdal.cpp -o gdal.o
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c gdal_geom.cpp -o gdal_geom.o
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c gdal_read.cpp -o gdal_read.o
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c gdal_utils.cpp -o gdal_utils.o
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c gdal_write.cpp -o gdal_write.o
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c geos.cpp -o geos.o
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c hex.cpp -o hex.o
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c ops.cpp -o ops.o
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c polygonize.cpp -o polygonize.o
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c proj.cpp -o proj.o
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c proj_info.cpp -o proj_info.o
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c raster2sf.cpp -o raster2sf.o
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c sfg.cpp -o sfg.o
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c signed_area.cpp -o signed_area.o
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c stars.cpp -o stars.o
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c wkb.cpp -o wkb.o
g++ -std=gnu++11 -I"/home/rsb/topics/R/R362-share/lib64/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -I"/home/rsb/lib/r_libs/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c zm_range.cpp -o zm_range.o
g++ -std=gnu++11 -shared -L/home/rsb/topics/R/R362-share/lib64/R/lib -L/usr/local/lib64 -o sf.so RcppExports.o bbox.o gdal.o gdal_geom.o gdal_read.o gdal_utils.o gdal_write.o geos.o hex.o ops.o polygonize.o proj.o proj_info.o raster2sf.o sfg.o signed_area.o stars.o wkb.o zm_range.o -L/usr/local/lib -lproj -L/usr/local/lib -lgdal -L/usr/local/lib -lgeos_c -L/home/rsb/topics/R/R362-share/lib64/R/lib -lR
installing to /home/rsb/lib/r_libs/00LOCK-sf/00new/sf/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
in method for ‘dbWriteTable’ with signature ‘"PostgreSQLConnection","character","sf"’: no definition for class “PostgreSQLConnection”
in method for ‘dbDataType’ with signature ‘"PostgreSQLConnection","sf"’: no definition for class “PostgreSQLConnection”
in method for ‘coerce’ with signature ‘"Spatial","sf"’: no definition for class “Spatial”
in method for ‘coerce’ with signature ‘"Spatial","sfc"’: no definition for class “Spatial”
in method for ‘coerce’ with signature ‘"sf","Spatial"’: no definition for class “Spatial”
in method for ‘coerce’ with signature ‘"sfc","Spatial"’: no definition for class “Spatial”
in method for ‘coerce’ with signature ‘"XY","Spatial"’: no definition for class “Spatial”
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sf)
Thanks, the proj header detecting is now really getting messy. I propose the following approach, dropping conditioning on pkgconf proj
being available (when installing PROJ from git/master, it isn't):
OK, I'll stay with the current settings in rgdal for now. It would be good if gdal-config
could report its PROJ build choices, but that is maybe too blue-sky.
Maybe re-open, fails for PROJ >= now:
configure: CC: gcc
configure: CXX: g++ -std=gnu++11
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.1.0
checking GDAL version >= 2.0.1... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking gdal.h usability... yes
checking gdal.h presence... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /usr/local/share/gdal/pcs.csv readable... no
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available fur running:... yes
configure: pkg-config proj exists, will use it
checking proj_api.h usability... no
checking proj_api.h presence... no
checking for proj_api.h... no
configure: error: proj_api.h not found in standard or given locations.
$ pkg-config proj --modversion
7.0.0$ ls /usr/local/include/proj*.h
/usr/local/include/proj_api.h /usr/local/include/proj.h
/usr/local/include/proj_constants.h /usr/local/include/proj_symbol_rename.h
/usr/local/include/proj_experimental.h
(living dangerously ...)
Add: | test "${PROJV1}" = "7"
on line 344 in configure.ac.
I have "configure: error: libproj not found in standard or given locations." error message. Could you help me, plz
$ remotes::install_github("r-spatial/sf", configure.args="--with-proj-api=yes")
Downloading GitHub repo r-spatial/sf@master
✓ checking for file ‘/private/var/folders/v7/w8cdtg0934j1jms2wgqyyx3r0000gn/T/RtmpfsnT7n/remotes7d14113c5f17/r-spatial-sf-8cc2adf/DESCRIPTION’ ...
─ preparing ‘sf’:
✓ checking DESCRIPTION meta-information ...
─ cleaning src
─ running ‘cleanup’
─ checking for LF line-endings in source and make files and shell scripts (1.1s)
─ checking for empty or unneeded directories
─ building ‘sf_0.9-1.tar.gz’
* installing *source* package ‘sf’ ...
** using staged installation
configure: CC: clang
configure: CXX: clang++ -std=gnu++11
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.4.4
checking GDAL version >= 2.0.1... yes
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking gdal.h usability... yes
checking gdal.h presence... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /usr/local/Cellar/gdal/2.4.4_2/share/gdal/pcs.csv readable... yes
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available fur running:... yes
configure: GDAL: 2.4.4
checking proj.h usability... yes
checking proj.h presence... yes
checking for proj.h... yes
checking PROJ: checking whether PROJ and sqlite3 are available for linking:... no
configure: error: libproj not found in standard or given locations.
ERROR: configuration failed for package ‘sf’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sf’
Error: Failed to install 'sf' from GitHub:
(converted from warning) installation of package ‘/var/folders/v7/w8cdtg0934j1jms2wgqyyx3r0000gn/T//RtmpfsnT7n/file7d1456df1f68/sf_0.9-1.tar.gz’ had non-zero exit status
This is my session info
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.3
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_2.2.2 usethis_1.5.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4 rstudioapi_0.11 magrittr_1.5 pkgload_1.0.2
[5] R6_2.4.1 rlang_0.4.5 fansi_0.4.1 tools_3.6.3
[9] pkgbuild_1.0.6 grid_3.6.3 sessioninfo_1.1.1 cli_2.0.2
[13] withr_2.1.2 remotes_2.1.1 htmltools_0.4.0 crosstalk_1.1.0.1
[17] ellipsis_0.3.0 leafsync_0.1.0 rprojroot_1.3-2 leaflet_2.0.3
[21] assertthat_0.2.1 digest_0.6.25 crayon_1.3.4 processx_3.4.2
[25] callr_3.4.3 RColorBrewer_1.1-2 ps_1.3.2 htmlwidgets_1.5.1
[29] fs_1.4.0 curl_4.3 testthat_2.3.2 memoise_1.1.0
[33] glue_1.3.2 compiler_3.6.3 backports_1.1.5 desc_1.2.0
[37] prettyunits_1.1.1
@ChoWonmin see https://github.com/r-spatial/sf/issues/1327 and only use CRAN binaries on OSX unless you need the newest sf and are willing to invest a lot of time to learn how to build a lot of software from compiled code source (not R code).
With --with-proj-api as
remotes::install_github("r-spatial/sf", configure.args="--with-proj-api=yes")
and PROJ 520: