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r-spatial / sf

Simple Features for R
https://r-spatial.github.io/sf/
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liblwgeom support on macOS #349

Closed pat-s closed 7 years ago

pat-s commented 7 years ago

Related: #347, #266

I did brew install liblwgeom && brew link --force liblwgeom and during sf source install liblwgeom is found. However, lwgeom_version in -llwgeom is not found. 

checking liblwgeom.h usability... yes
checking liblwgeom.h presence... yes
checking for liblwgeom.h... yes
checking for lwgeom_version in -llwgeom... no

sf v0.4.3

Any ideas where to look here? I do not know where -llwgeom is referring to..

edzer commented 7 years ago

My guess is that the version of lwgeom is too old, but I haven't tried or looked into.

pat-s commented 7 years ago

It seems patching the brew formula might not be that easy -> brew edit liblwgeom 10-13:

Strip all the PostgreSQL functions from PostGIS configure.ac, to allow building liblwgeom.dylib without needing PostgreSQL NOTE: this will need to be maintained per postgis version Somehow, this still works for 2.1.5, which is awesome!

edzer commented 7 years ago

I see, on ubuntu 16.04:

> library(sf)
Linking to GEOS 3.5.1, GDAL 2.1.3, proj.4 4.9.2, lwgeom 2.3.2 r15302

(seems that lwgeom versions follow postgis version)

pat-s commented 7 years ago

(seems that lwgeom versions follow postgis version)

jep, its dev repository is within the postgis one: https://github.com/postgis/postgis/tree/svn-trunk/liblwgeom

edzer commented 7 years ago

So we can close this one, right?

pat-s commented 7 years ago

I would like to leave it open until there is a working solution for the liblwgeom install - the current brew version does not work (probably its too old as you suggested). I will later try to install from source / patch the brew formula.

ping @bhaskarvk

edzer commented 7 years ago

I like to see open issues as issues that need work on the side of sf. As this is an issue with brew and MacOS, I'm closing here, but would welcome it if you report back here when you've settled that.

pat-s commented 7 years ago

brew install postgis solves the problem as it does the linking to -llwgeom

checking liblwgeom.h usability... yes
checking liblwgeom.h presence... yes
checking for liblwgeom.h... yes
checking for lwgeom_version in -llwgeom... yes

I also checked that st_make_valid() is working.

It would be good if a message could be thrown that it depends on brew install postgis if one tries to use st_make_valid() on macOS. Currently it looks likes this: 

st_make_valid(poly) -> poly_V
Error in CPL_make_valid(x) :
  st_make_valid requires compilation against liblwgeom

and if one does brew install liblwgeom it will not work. So the current message is right in terms of dependency but misleading when one wants to solve the issue -> see PR #350

NateMietk commented 7 years ago

I successfully installed using brew install postgis, but I still generate the Error in CPL_make_valid(x) : st_make_valid requires compilation against liblwgeom error. I have confirmed that I have liblwgeom installed and have reinstalled sf, nothing seems to be working. Any suggestions here?

pat-s commented 7 years ago

Works for me. Do you have different settings?

devtools::session_info("sf")
Session info ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.4.1 (2017-06-30)
 system   x86_64, darwin16.7.0        
 ui       RStudio (1.1.362)           
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       Europe/Berlin               
 date     2017-09-15                  

Packages -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 package   * version date       source        
 DBI         0.7     2017-06-18 CRAN (R 3.4.0)
 graphics  * 3.4.1   2017-08-18 local         
 grDevices * 3.4.1   2017-08-18 local         
 grid        3.4.1   2017-08-18 local         
 magrittr    1.5     2014-11-22 CRAN (R 3.3.2)
 methods   * 3.4.1   2017-08-18 local         
 Rcpp        0.12.12 2017-07-15 CRAN (R 3.4.1)
 sf        * 0.5-4   2017-08-28 CRAN (R 3.4.1)
 stats     * 3.4.1   2017-08-18 local         
 tools       3.4.1   2017-08-18 local         
 udunits2    0.13    2016-11-17 CRAN (R 3.3.2)
 units       0.4-6   2017-08-27 CRAN (R 3.4.1)
 utils     * 3.4.1   2017-08-18 local       
Linking to GEOS 3.6.2, GDAL 2.2.1, proj.4 4.9.3, lwgeom 2.3.2 r15302

x = st_sfc(st_polygon(list(rbind(c(0,0),c(0.5,0),c(0.5,0.5),c(0.5,0),c(1,0),c(1,1),c(0,1),c(0,0)))))
st_make_valid(x)

Geometry set for 1 feature 
geometry type:  GEOMETRYCOLLECTION
dimension:      XY
bbox:           xmin: 0 ymin: 0 xmax: 1 ymax: 1
epsg (SRID):    NA
proj4string:    NA
GEOMETRYCOLLECTION (POLYGON ((0.5 0, 0 0, 0 1, ...
NateMietk commented 7 years ago

Using your example I generate the same Error in CPL_make_valid(x) : st_make_valid requires compilation against liblwgeom. My devtools::session_info("sf") shows the same information:

 setting  value                       
 version  R version 3.4.1 (2017-06-30)
 system   x86_64, darwin15.6.0        
 ui       RStudio (1.0.143)           
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/Denver              
 date     2017-09-15                  

Packages -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 package   * version date       source        
 DBI         0.7     2017-06-18 CRAN (R 3.4.0)
 graphics  * 3.4.1   2017-07-07 local         
 grDevices * 3.4.1   2017-07-07 local         
 grid        3.4.1   2017-07-07 local         
 magrittr    1.5     2014-11-22 CRAN (R 3.4.0)
 methods   * 3.4.1   2017-07-07 local         
 Rcpp        0.12.12 2017-07-15 CRAN (R 3.4.1)
 sf          0.5-4   2017-08-28 CRAN (R 3.4.1)
 stats     * 3.4.1   2017-07-07 local         
 tools       3.4.1   2017-07-07 local         
 udunits2    0.13    2016-11-17 CRAN (R 3.4.0)
 units       0.4-6   2017-08-27 CRAN (R 3.4.1)
 utils     * 3.4.1   2017-07-07 local
pat-s commented 7 years ago

A possible error source could be that you are not running macOS Sierra but El Capitan as far as I can see?

Did sf successfully compile against liblwgeomduring installation?

install.packages("sf")
[...]
checking liblwgeom.h usability... yes
checking liblwgeom.h presence... yes
checking for liblwgeom.h... yes
checking for lwgeom_version in -llwgeom... yes
NateMietk commented 7 years ago

Doesn't look that way - it seems to be searching for an el-capitan folder. I didn't think OS Sierra would have made a difference! I'll just use a docker container until Sierra is compatible with sf. Thanks!

Installing package into ‘/Users/nami1114/Library/R/3.4/library’
(as ‘lib’ is unspecified)
Warning in install.packages :
  cannot open URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/PACKAGES.rds': HTTP status was '404 Not Found'
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/sf_0.5-4.tgz'
Content type 'application/x-gzip' length 35969512 bytes (34.3 MB)
==================================================
downloaded 34.3 MB

The downloaded binary packages are in
    /var/folders/jw/l23y3f2j7m7b5mchg3mdg8g87kc8gr/T//RtmpYl7luO/downloaded_packages
pat-s commented 7 years ago

I'll just use a docker container until Sierra is compatible with sf.

Don't understand what you mean. sf is compatible with Sierra. However, there are problems on El Capitan obviously.

Try to explicitly install from source and not use the binary: install.packages("sf", type="source")

NateMietk commented 7 years ago

Sorry. Misunderstood. I am using macOS Sierra, NOT El Captain. The install from the source does not work, thanks for the suggestion.

I have been using a docker container in the meantime to get around this issue.

pat-s commented 7 years ago

Did you update your system since your last post? Your sessionInfo() output tells that you are running ElCapitan:

system x86_64, darwin15.6.0

Sierra has darwin16.x.x.

Also, the logs of the source installation (install.packages(sf)) would be helpful here.

pat-s commented 7 years ago

its not about liblwgeomat all but your gdal config is not properly setup.

Follow the instructions of the README: 

brew unlink gdal
brew tap osgeo/osgeo4mac && brew tap --repair
brew install proj
brew install geos
brew install udunits
brew install gdal2 --with-armadillo --with-complete --with-libkml --with-unsupported
brew link --force gdal2