rgdal 1.5-8 released on CRAN
Roy, I'm not OSX but generally I see them as conceptually similar and where I have stumbled (at what appears to be 'this stage') is in permissions so I would check the 'geneaology' of permissions and your ownership there upon the entire path of permissions that allows dynlib to execute comprehensively. And as you pass the rgdal hurdle so the same for gdal, geos. As applies to OSX, this may appear as voodoo, but if there is a sudo analog in OSX, try it. My voodoo (that is possibly disconcerting to those who view computers as logical systems. I would have advocated base 3 were I there at the beginning...) Chris On Sat, May 30, 2020 at 2:12 PM Roy Mendelssohn - NOAA Federal via
R-sig-Geo <r-sig-geo at r-project.org> wrote:
Hi All: Okay after some fiddling I was able to get it to sort of successfully compile, where I am having problems is in finding the dynamic libraries, such as I get this error:
dyld: Library not loaded: @rpath/libproj.19.dylib
and
Error: package or namespace load failed for ?rgdal? in dyn.load(file,
DLLpath = DLLpath, ...):
unable to load shared object
'/Users/rmendels/Library/R/4.0/library/00LOCK-rgdal/00new/rgdal/libs/rgdal.so':
dlopen(/Users/rmendels/Library/R/4.0/library/00LOCK-rgdal/00new/rgdal/libs/rgdal.so, 6): Library not loaded: @rpath/libgdal.26.dylib
Referenced from:
/Users/rmendels/Library/R/4.0/library/00LOCK-rgdal/00new/rgdal/libs/rgdal.so
Reason: image not found Error: loading failed
It has to do with these are defined in terms of @rpath. I thought defining this in $LD_LIBRARY_PATH would do it, but I have:
echo $LD_LIBRARY_PATH /Users/rmendels/Library/R/4.0/library:/Users/rmendels/anaconda3/lib
I also tried setting $DYLD_LIBRARY_PATH same problem. If someone can tell me how to set it so @rpath finds the dynamic libraries I might be able to get this to work. Thanks, -Roy
On May 30, 2020, at 8:04 AM, chris english <
englishchristophera at gmail.com> wrote:
my setup - albeit on 20.04 as reported by sf
library(sf)
Linking to GEOS 3.9.0dev, GDAL 3.1.0, PROJ 7.0.1 Note I'm using release gdal, that I none the less built from source as I
had to enable Mr. Sid for some particular
data. Couldn't get GDAL 3.2.*dev working but still toying around with
it. Roger's discussion of the history of all
of this on r-spatial and the path forward is very much worth the read as
and relates to his following message here.
On Sat, May 30, 2020 at 10:33 AM Roy Mendelssohn - NOAA Federal <
roy.mendelssohn at noaa.gov> wrote:
Yes thanks. As I said in reply to Roger I am far from an expert in
these things, but if I can get it to build, then I will try to post somewhere for others to use.
-Roy
On May 30, 2020, at 7:03 AM, chris english <
englishchristophera at gmail.com> wrote:
Roy, From a related prior post Roger shared this link to rgdal-1.5-9,
http://spatial.nhh.no/R/rgdal/ . I followed discussions
from the 'sf' github readme and purged all prior proj/geos/gdal
iterations that have lingered around over the past five
years and built them from source on ubuntu 20.04. This upgrade to
20.04 was perhaps my first mistake in a month
long effort to bring back my full spatial capabilities as it doesn't
become the official LTS until sometime mid this month.
I don't know how Anaconda packages and may require sym links or
copying files from down in the depths to visible,
but it worked before and can be made to work again. HTH- Chris On Sat, May 30, 2020 at 8:08 AM Roger Bivand <Roger.Bivand at nhh.no>
wrote:
On Fri, 29 May 2020, Thiago V. dos Santos wrote:
Dear Roger, Many thanks for the effort keeping rgdal up-to-date with proj6. I'd like to report that I am unable to install rgdal 1.5.8 on my
macOS
system. I am reporting this error here on the list because I thought
it
would be the best channel in terms of reaching future users
experiencing
the same error. Please apologize if my rationale is not right, and ignore this message. GDAL was installed via MacPorts and is at its latest version, 3.1.0
(at
the time of this writing). Proj6 has also been installed via
Macports.
This is how I am trying to install it:
export PKG_CONFIG_PATH=/opt/local/lib/proj6/lib/pkgconfig
R
install.packages('rgdal', type="source", configure.args=c(
'--with-proj-include=/opt/local/lib/proj6/include',
'--with-proj-lib=/opt/local/lib/proj6/lib'))
and this is the output I get:
R version 4.0.0 (2020-04-24) -- "Arbor Day"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
install.packages('rgdal', type="source", configure.args=c(
+ '--with-proj-include=/opt/local/lib/proj6/include',
+ '--with-proj-lib=/opt/local/lib/proj6/lib'))
Installing package into ?/Users/thiago/Documents/R-packages?
(as ?lib? is unspecified)
trying URL '
Content type 'application/x-gzip' length 2299235 bytes (2.2 MB) ================================================== downloaded 2.2 MB * installing *source* package ?rgdal? ... ** package ?rgdal? successfully unpacked and MD5 sums checked ** using staged installation configure: R_HOME: /Library/Frameworks/R.framework/Resources configure: CC: /opt/local/bin/gcc configure: CXX: /opt/local/bin/g++ configure: C++11 support available configure: rgdal: 1.5-8 checking for /usr/bin/svnversion... yes configure: svn revision: 990 checking for gdal-config... /opt/local/bin/gdal-config checking gdal-config usability... yes configure: GDAL: 3.1.0 checking GDAL version >= 1.11.4... yes checking GDAL version <= 2.5 or >= 3.0... yes checking gdal: linking with --libs only... yes checking GDAL: gdal-config data directory readable... yes checking GDAL: /opt/local/share/gdal/stateplane.csv readable... yes configure: pkg-config proj exists, will use it
So far so good, but you chose to override pkg-config proj by passing configure arguments. You should let pkg-config proj provide those
values.
configure: PROJ version: 6.3.2 configure: proj CPP flags: -DPROJ_H_API
-I/opt/local/lib/proj6/include
configure: PROJ LIBS: -L/opt/local/lib/proj6/lib checking PROJ header API:... proj.h checking for gcc... /opt/local/bin/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 /opt/local/bin/gcc accepts -g... yes checking for /opt/local/bin/gcc option to accept ISO C89... none
needed
checking how to run the C preprocessor... /opt/local/bin/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... 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 proj.h usability... yes checking proj.h presence... yes checking for proj.h... yes
Also OK.
checking for proj_context_create in -lproj... no configure: error: proj_context_create not found in libproj.
The directory where libproj should be does not contain it - whether
you
got it wrong, pkg-config got it wrong, or for some other reason, the library was not found.
ERROR: configuration failed for package ?rgdal? * removing ?/Users/thiago/Documents/R-packages/rgdal? * restoring previous ?/Users/thiago/Documents/R-packages/rgdal? The downloaded source packages are in
?/private/var/folders/_z/01gg71zs19g816v6m2dddt8w0000gn/T/RtmpvZAChj/downloaded_packages?
Warning message:
In install.packages("rgdal", type = "source", configure.args =
c("--with-proj-include=/opt/local/lib/proj6/include", :
installation of package ?rgdal? had non-zero exit status I found this error to be quite mysterious, and could not find any previous discussion about it.
Try to avoid googling, it is usually misleading. Running ./configure
in
the untarred source package directory, and running ./configure --help
to
show the arguments to configure can be much more helpful. Crucially,
they
are up to date, while most search hits are old, and they are ordered
by
hit counts, which is certainly no guarantee of precision.
Are you familiar with it? Is there any other argument that I can
pass to
install.packages to solve it?
Try not setting configure arguments and let pkg-config proj do the
work if
you feel you can trust it. If, however, you have multiple installs of
GDAL
and/or PROJ, the proj.pc file may point to a deleted install. Download
and
untar the source package, and run just ./configure with its
argumments, or
setting PKG_CONFIG_PATH= until you find a recipe that works that far. Roger
Greetings, -- Thiago V. dos Santos ThiagoDosSantos.com MudancasClimaticasBrasil.com On Thursday, May 28, 2020, 08:53:50 AM GMT-3, Roger Bivand <
roger.bivand at nhh.no> wrote:
With sp 1.4-2 and rgdal 1.5-8, those using GDAL 3 and PROJ 6
(including
users of the CRAN Windows binary when it comes) will be part of the
big
migration to WKT2 from Proj4 strings for CRS representation. See
or for a better rendering of "\phi" and bib-handling:
for background and https://www.r-spatial.org/r/2020/03/17/wkt.html
for the
full sf and sp story. You will see lots of warnings, they should grab your attention, that
is
what they are for. We need your attention to be as sure as we can be
that
your results - if affected by the transition - have been checked by
you.
I plan to flip the warnings to default off from rgdal 1.6-*, and sp
1.5-*.
In some weeks but before flipping the defaults, I'll follow up
showing
ways of muting them, but we really need to be confident that this necessary and future-proofing change isn't silently destroying your
work
first. So please don't treat the many warnings as just pesky and
nagging -
they are priming your immune system to check for unwanted
consequences of
your legacy CRS representation choices. I'd also like to thank the maintainers of packages importing from/depending on sp/rgdal for largely positive responses to issues
raised
and emails sent, often less polite than they might have been, but
grabbing
attention was more important. From over 70 broken reverse dependency packages we are now well under 20, and I've contacted all of those,
with
only a couple not responding. Edzer has seen similar responsiveness
for
the parallel migration of sf. Enjoy! Roger
-- Roger Bivand Department of Economics, Norwegian School of Economics, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; e-mail: Roger.Bivand at nhh.no https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en_______________________________________________
R-sig-Geo mailing list R-sig-Geo at r-project.org
********************** "The contents of this message do not reflect any position of the U.S.
Government or NOAA."
********************** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center ***Note new street address*** 110 McAllister Way Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov www: https://www.pfeg.noaa.gov/ "Old age and treachery will overcome youth and skill." "From those who have been given much, much will be expected" "the arc of the moral universe is long, but it bends toward justice"
-MLK Jr.
********************** "The contents of this message do not reflect any position of the U.S. Government or NOAA." ********************** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center ***Note new street address*** 110 McAllister Way Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov www: https://www.pfeg.noaa.gov/ "Old age and treachery will overcome youth and skill." "From those who have been given much, much will be expected" "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
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