package or namespace load failed for 'sf' in dyn.load

[boboshaq]

Hi,
when I try install sf package I get error:

Error: package or namespace load failed for 'sf' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/user/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-sf/00new/sf/libs/sf.so':
  /home/user/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-sf/00new/sf/libs/sf.so: undefined symbol: _Z33OGRCreateCoordinateTransformationP19OGRSpatialReferenceS0_
Error: loading failed
Execution halted
ERROR: loading failed

I have Centos 7.7 with gdal-2.4.2, proj-6.2.0, pkgconfig-0.27.1, R-3.6.0.
What can I do, to install package "sf" successfully ?

[rsbivand]

Read the README about multiple installations of external libraries. You have multiple versions of GDAL on your system.

[boboshaq]

I read this post, but I don't understand what I should do to fix this problem.
I have those multiple libraries i /usr/lib64 :

libgeos-3.4.2.so
libgeos.so -> libgeos-3.4.2.so
libgeos_c.so -> libgeos_c.so.1.8.2
libgeos_c.so.1 -> libgeos_c.so.1.8.2
libgeos_c.so.1.8.2

I should just remove one of them?
How to remove GDAL instalation from system?

[boboshaq]

OK I delete all files created during installation proj and gdal from /usr/local/bin,etc,include,lib,lib64,share and I run installation again. It help me.

Instalation package SF on Centos 7 is very difficult, because proj and gdal are very old in repositories and You must install them from sources. Then You must edit /etc/ld.so.conf file and create PKG_CONFIG_PATH environment variable before instalation starts. Then, in R, You must specify paths to specific files from proj instalation folder, for eg.: install.packages("sf", configure.args = "--with-proj-include=/proj_home/include --with-proj-lib=/proj_home/lib --with-proj-api=no")
To understand this, it take me about 3 weeks !! Maybe You should create some HOWTO manual for installation SF on Centos 7.
Regards!

[beedawg1985]

@boboshaq Im attempting to install sf on Centos 7 and running into problems. I've overcome most but am left with:

Error: package or namespace load failed for ‘sf’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/.../x86_64-redhat-linux-gnu-library/3.6/sf/libs/sf.so':
  /lib64/libz.so.1: version `ZLIB_1.2.9' not found (required by /anaconda/envs/py35/lib/libpng16.so.16)

Did you find a way to get around this one?!

[boboshaq]

Hi,
It was a long time ago, so I don't remember exactly how I was doing it. I may tell you steps that I take.

1. install proj from sources
2. install gdal
3. edit /etc/ld.so.conf and put there path to libraries from proj (eg /../../proj/6.2.0/lib)
4. run command ldconfig or logout and login to get those settings visible
5. set environment variable PKG_CONFIG_PATH with path to file: proj.pc with should be in proj instalation home folder in /lib/pkgconfig (eg export PKG_CONFIG_PATH=/../../proj/6.2.0/lib/pkgconfig) - pkgconfig should been installed in system
6. open R and run install.packages command with options: --with-proj-include --with-proj-lib --with-proj-api=no (eg install.packages("sf", configure.args = "--with-proj-include=/path/to/proj/6.2.0/include --with-proj-lib=/path/to/proj/6.2.0/lib --with-proj-api=no"))

I assume that You have package ZLIB in version 1.2.9 in your system :)

[beedawg1985]

hey, thanks for this! I ended up creating a symlink to the new ZLIB library as detailed in this post: https://stackoverflow.com/questions/48306849/lib-x86-64-linux-gnu-libz-so-1-version-zlib-1-2-9-not-found

…

On Tue, Feb 25, 2020 at 4:05 PM boboshaq ***@***.***> wrote: Hi, It was a long time ago, so I don't remember exactly how I was doing it. I may tell you steps that I take. 1. install proj from sources 2. install gdal 3. edit /etc/ld.so.conf and put there path to libraries from proj (eg /../../proj/6.2.0/lib) 4. run command ldconfig or logout and login to get those settings visible 5. set environment variable PKG_CONFIG_PATH with path to file: proj.pc with should be in proj instalation home folder in /lib/pkgconfig (eg export PKG_CONFIG_PATH=/../../proj/6.2.0/lib/pkgconfig) - pkgconfig should been installed in system 6. open R and run install.packages command with options: --with-proj-include --with-proj-lib --with-proj-api=no (eg install.packages("sf", configure.args = "--with-proj-include=/path/to/proj/6.2.0/include --with-proj-lib=/path/to/proj/6.2.0/lib --with-proj-api=no")) I assume that You have package ZLIB in version 1.2.9 in your system :) — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1158?email_source=notifications&email_token=AHRKVKLNV2M3HYO6NBLXLOTREU6WHA5CNFSM4I3FU56KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEM4RMIQ#issuecomment-590943778>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHRKVKN2Q7CU6UHLSRGS7HDREU6WHANCNFSM4I3FU56A> .