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Installing sf package in R under renv on Macos

 原文  2021-04-01 16:36:16  1   1    r/ macos/ renv

Question

I'm having problems in installing the sf package through renv . I have installed R from source in my Mac and everything is fine. I was able to install rgdal and sf through install.packages but can't make it with renv . The problem is that the installation script can't find the header proj_api.h even if I indicated the full path.

With

install.packages("sf")

everything works without further intervention. Within renv :

> renv::activate()
> renv::install("sf")
....
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’
....

The proj_api.h header is under /usr/local/include/ , so following the documentation I tried: 

options(configure.args = c(sf="--with-proj-include=/usr/local/include/"))

before installing, but with the same result. I have no idea of what to try next. I don't understand why with renv paths are not found and why without they are (locations are pretty standard). Can't understand also how is it possible that the header is not found even if I pass the full path.

The environment variables without renv :

__CF_USER_TEXT_ENCODING
                        0xAF76729:0x0:0x0
_CE_CONDA               
_CE_M                   
CLICOLOR                1
COLUMNS                 117
CONDA_EXE               /Users/52488/miniconda3/bin/conda
CONDA_PYTHON_EXE        /Users/52488/miniconda3/bin/python
CONDA_SHLVL             0
DISPLAY                 /private/tmp/com.apple.launchd.heGiCHqO77/org.xquartz:0
DYLD_FALLBACK_LIBRARY_PATH
                        /Users/52488/Rinstallation/R-4.0.4/lib:/Library/Java/JavaVirtualMachines/jdk-15.0.2.jdk/Contents/Home/lib/server
EDITOR                  vi
HOME                    /Users/52488
LC_ALL                  en_US.UTF-8
LC_CTYPE                UTF-8
LINES                   30
LN_S                    ln -s
LOGNAME                 52488
LSCOLORS                gxBxhxDxfxhxhxhxhxcxcx
MAKE                    make
PAGER                   /usr/bin/less
PATH                    /Users/52488/miniconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Applications/VMware
                        Fusion.app/Contents/Public:/opt/X11/bin
PWD                     /Users/52488
R_ARCH                  
R_BROWSER               /usr/bin/open
R_BZIPCMD               /usr/bin/bzip2
R_DOC_DIR               /Users/52488/Rinstallation/R-4.0.4/doc
R_GZIPCMD               /usr/bin/gzip
R_HOME                  /Users/52488/Rinstallation/R-4.0.4
R_INCLUDE_DIR           /Users/52488/Rinstallation/R-4.0.4/include
R_LIBS_SITE             
R_LIBS_USER             ~/Library/R/4.0/library
R_PAPERSIZE             a4
R_PDFVIEWER             /usr/local/bin/evince
R_PLATFORM              x86_64-apple-darwin17.0
R_PRINTCMD              lpr
R_RD4PDF                times,inconsolata,hyper
R_SESSION_TMPDIR        /var/folders/jb/vpf_9ht52zj_0qk_3r1f0dlw5gfss9/T//Rtmp40nNZi
R_SHARE_DIR             /Users/52488/Rinstallation/R-4.0.4/share
R_STRIP_SHARED_LIB      strip -x
R_STRIP_STATIC_LIB      strip -S
R_SYSTEM_ABI            macos,gcc,gxx,gfortran,gfortran
R_TEXI2DVICMD           /usr/local/bin/texi2dvi
R_UNZIPCMD              /usr/bin/unzip
R_ZIPCMD                /usr/bin/zip
SED                     /usr/bin/sed
SHELL                   /usr/local/bin/bash
SHLVL                   1
SSH_AUTH_SOCK           /private/tmp/com.apple.launchd.1OK1KoT1o5/Listeners
TAR                     /usr/bin/tar
TERM                    xterm-256color
TERM_PROGRAM            Apple_Terminal
TERM_PROGRAM_VERSION    433
TERM_SESSION_ID         2BA70166-937D-47AB-B6B6-23316D978294
TMPDIR                  /var/folders/jb/vpf_9ht52zj_0qk_3r1f0dlw5gfss9/T/
USER                    52488
XPC_FLAGS               0x0
XPC_SERVICE_NAME        0

With renv :

__CF_USER_TEXT_ENCODING
                        0xAF76729:0x0:0x0
_CE_CONDA               
_CE_M                   
CLICOLOR                1
COLUMNS                 117
CONDA_EXE               /Users/52488/miniconda3/bin/conda
CONDA_PYTHON_EXE        /Users/52488/miniconda3/bin/python
CONDA_SHLVL             0
DISPLAY                 /private/tmp/com.apple.launchd.heGiCHqO77/org.xquartz:0
DYLD_FALLBACK_LIBRARY_PATH
                        /Library/Frameworks/GDAL.framework/unix/lib:/Users/52488/Rinstallation/R-4.0.4/lib:/Library/Java/JavaVirtualMachines/jdk-15.0.2.jdk/Contents/Home/lib/server
EDITOR                  vi
HOME                    /Users/52488
LC_ALL                  en_US.UTF-8
LC_CTYPE                UTF-8
LINES                   30
LN_S                    ln -s
LOGNAME                 52488
LSCOLORS                gxBxhxDxfxhxhxhxhxcxcx
MAKE                    make
PAGER                   /usr/bin/less
PATH                    /Users/52488/miniconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Applications/VMware
                        Fusion.app/Contents/Public:/opt/X11/bin
PWD                     /Users/52488/Documents/staffing
R_ARCH                  
R_BROWSER               /usr/bin/open
R_BZIPCMD               /usr/bin/bzip2
R_DOC_DIR               /Users/52488/Rinstallation/R-4.0.4/doc
R_GZIPCMD               /usr/bin/gzip
R_HOME                  /Users/52488/Rinstallation/R-4.0.4
R_INCLUDE_DIR           /Users/52488/Rinstallation/R-4.0.4/include
R_LIBS_SITE             
R_LIBS_USER             /Users/52488/Documents/staffing/renv/library/R-4.0/x86_64-apple-darwin17.0:/private/var/folders/jb/vpf_9ht52zj_0qk_3r1f0dlw5gfss9/T/Rtmpm4f15L/renv-system-library
R_PAPERSIZE             a4
R_PDFVIEWER             /usr/local/bin/evince
R_PLATFORM              x86_64-apple-darwin17.0
R_PRINTCMD              lpr
R_RD4PDF                times,inconsolata,hyper
R_SESSION_TMPDIR        /var/folders/jb/vpf_9ht52zj_0qk_3r1f0dlw5gfss9/T//Rtmpm4f15L
R_SHARE_DIR             /Users/52488/Rinstallation/R-4.0.4/share
R_STRIP_SHARED_LIB      strip -x
R_STRIP_STATIC_LIB      strip -S
R_SYSTEM_ABI            macos,gcc,gxx,gfortran,gfortran
R_TEXI2DVICMD           /usr/local/bin/texi2dvi
R_UNZIPCMD              /usr/bin/unzip
R_ZIPCMD                /usr/bin/zip
RENV_DEFAULT_R_ENVIRON
                        <NA>
RENV_DEFAULT_R_ENVIRON_USER
                        <NA>
RENV_DEFAULT_R_LIBS     <NA>
RENV_DEFAULT_R_LIBS_SITE
                        
RENV_DEFAULT_R_LIBS_USER
                        ~/Library/R/4.0/library
RENV_DEFAULT_R_PROFILE
                        <NA>
RENV_DEFAULT_R_PROFILE_USER
                        <NA>
RENV_PROJECT            /Users/52488/Documents/staffing
RETICULATE_MINICONDA_PYTHON_ENVPATH
                        /Users/52488/Documents/staffing/renv/python/r-reticulate
SDKROOT                 /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
SED                     /usr/bin/sed
SHELL                   /usr/local/bin/bash
SHLVL                   1
SSH_AUTH_SOCK           /private/tmp/com.apple.launchd.1OK1KoT1o5/Listeners
TAR                     /usr/bin/tar
TERM                    xterm-256color
TERM_PROGRAM            Apple_Terminal
TERM_PROGRAM_VERSION    433
TERM_SESSION_ID         34A286FD-8106-4F78-88F9-8913E45EDCDE
TMPDIR                  /var/folders/jb/vpf_9ht52zj_0qk_3r1f0dlw5gfss9/T/
USER                    52488
XPC_FLAGS               0x0
XPC_SERVICE_NAME        0

Three variables differ, but it's pretty normal I guess:

[1] "PWD"              "R_LIBS_USER"      "R_SESSION_TMPDIR"

Of course there are the RENV* variables which are only present in the renv case.

Digging further and taking inspiration from this question , I checked the include path of gcc . There are differences depending on renv .

With renv :

> system("echo | gcc -Wp,-v -x c++ - -fsyntax-only", intern=TRUE)
clang -cc1 version 12.0.0 (clang-1200.0.32.29) default target x86_64-apple-darwin19.6.0
ignoring nonexistent directory "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/local/include"
ignoring nonexistent directory "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/Library/Frameworks"
#include "..." search starts here:
#include <...> search starts here:
 /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1
 /Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include
 /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
 /Library/Developer/CommandLineTools/usr/include
 /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks (framework directory)
End of search list.

Without renv :

> system("echo | gcc -Wp,-v -x c++ - -fsyntax-only", intern=TRUE)
clang -cc1 version 12.0.0 (clang-1200.0.32.29) default target x86_64-apple-darwin19.6.0
ignoring nonexistent directory "/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/local/include"
ignoring nonexistent directory "/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/Library/Frameworks"
#include "..." search starts here:
#include <...> search starts here:
 /usr/local/include
 /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1
 /Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include
 /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include
 /Library/Developer/CommandLineTools/usr/include
 /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Frameworks (framework directory)
End of search list.

It is apparent that inside renv the standard /usr/local/include is not present (there are also some differences in the other paths). Why is that? How can I fix it?

1 answers

solution1
 0  2021-11-02 15:15:22

I've went through this just now. I too had everything installed via install.packages('sf') and it worked just fine, until today I needed to work in renv environment.

This has helped me (assuming you have brew installed):

  1. brew install gdal --HEAD
  2. brew install gdal
  3. brew install proj

I don't know why sf actually worked before, probably R installs these binaries someplace r-internal.

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