Sf: proj_api.h not found in standard or given locations

[lurch999]

Centos7 OS
R version 3.6.0
Proj4 6.1.9 installed to default /usr/local location with ./configure, make, sudo make install
GDAL 3.0.0 installed to default /usr/local location with ./configure, make, sudo make install
GEOS 3.7.2 installed to default /usr/local location with ./configure, make, sudo make install
/etc/ld.so.conf.d/libgdal-x86_64.conf contains /usr/local/lib
then sudo ldconfig

remotes::install_github("r-spatial/sf", configure.args = "--with-gdal-config=/usr/local/bin/gdal-config --with-geos-config=/usr/local/bin/geos-config --with-proj-include=/usr/local/include/ --with-proj-lib=/usr/local/lib/")

Downloading GitHub repo r-spatial/sf@masterroj-lib=/usr/local/lib/")
Running R CMD build...

• checking for file ‘/tmp/Rtmp7lzWH1/remotesd64758beac60/r-spatial-sf-ee35c42/DESCRIPTION’ ... OK
• 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_0.7-5.tar.gz’
  Installing package into ‘/usr/lib64/R/library’
  (as ‘lib’ is unspecified)
• installing source package ‘sf’ ...
  ** using staged installation
  configure: CC: gcc -m64 -std=gnu99
  configure: CXX: g++ -m64 -std=gnu++11
  configure: gdal-config set to /usr/local/bin/gdal-config
  checking gdal-config exists... yes
  checking gdal-config executable... yes
  checking gdal-config usability... yes
  configure: GDAL: 3.0.0
  checking GDAL version >= 2.0.1... yes
  checking for gcc... gcc -m64 -std=gnu99
  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 -m64 -std=gnu99 accepts -g... yes
  checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
  checking how to run the C preprocessor... gcc -m64 -std=gnu99 -E
  checking for grep that handles long lines and -e... /bin/grep
  checking for egrep... /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
  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.
  ERROR: configuration failed for package ‘sf’
• removing ‘/usr/lib64/R/library/sf’
  Error in i.p(...) :
  (converted from warning) installation of package ‘/tmp/Rtmp7lzWH1/filed6474cb52a8/sf_0.7-5.tar.gz’ had non-zero exit status

I'm stumped! I see proj_api.h here: /usr/local/include/proj_api.h

Suggestions please?

[edzer]

Proj4 6.1.9 does not exist.

[edzer]

What I see is

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
...

Is it possible that you don't have e.g. this working:

root@43c5e412d3ee:/# pkg-config proj --libs
-L/usr/local/lib -lproj

please check & report back.

[lurch999]

Sorry, I meant Proj4 version 6.1.0
Is this on one line?
pkg-config proj --libs -L/usr/local/lib -lproj
If so, it errors in Centos:

pkg-config --libs -L/usr/local/lib -lproj
Unknown option -L/usr/local/lib

[rsbivand]

Not one line, run:

pkg-config --libs

with

-L/usr/local/lib -lproj

the expected output.

[lurch999]

Okay, thanks. Here's the output:

# pkg-config --libs
Must specify package names on the command line

[edzer]

No: please try

pkg-config proj --libs

[lurch999]

# pkg-config proj --libs
Package proj was not found in the pkg-config search path.
Perhaps you should add the directory containing `proj.pc'
to the PKG_CONFIG_PATH environment variable
No package 'proj' found

[lurch999]

# pkg-config proj --libs
Package proj was not found in the pkg-config search path.
Perhaps you should add the directory containing `proj.pc'
to the PKG_CONFIG_PATH environment variable
No package 'proj' found

Which is weird because:

# echo $PKG_CONFIG_PATH
/usr/local/lib/pkgconfig/
# ls $PKG_CONFIG_PATH
gdal.pc  proj.pc

[edzer]

Well, at least it gives you a direction to search for a solution.

[lurch999]

Interesting, I had thought R picked up my Bash environment variables by default but it doesn't.
Doing the following led me to build 'sf' successfully:

> print(Sys.setenv(PKG_CONFIG_PATH = "/usr/local/lib/pkgconfig/"))

Thanks for your patience and help!

[edzer]

R picks up environment variables, when they are properly set in the environment in which R is started.