I am trying to install the R (R version 3.2.4 Revised) package 'rgdal' onto my Linux, Ubuntu 14.04, but the package is having difficulties when it tries to load dependencies, specifically sqlite.
The error is as follows:
checking for gdal.h... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
/usr/lib/libgdal.so: undefined reference to `sqlite3_column_table_name'
collect2: error: ld returned 1 exit status
I updated GDAL/OGR per the instructions here, because I thought that may be the issue. Now when I type gdalinfo or ogrinfo into the terminal a similar error appears:
gdalinfo: symbol lookup error: /usr/lib/libgdal.so.1: undefined
symbol: sqlite3_column_table_name
When I look in my usr/local/lib the following sqlite libraries are present:
libsqlite3.a libsqlite3.la libsqlite3.so libsqlite3.so.0
libsqlite3.so.0.8.6
The funny thing is that this package was working fine in R last week and now is broken...
Any help appreciated! Thanks.
-Caitlin
Stumbled across this error when I was trying to upgrade GDAL. The fix was to ENABLE_COLUMN_METADATA when I was configuring sqlite for install with
sudo CFLAGS="-DSQLITE_ENABLE_COLUMN_METADATA=1" ./configure
See the sqlite Compile-time options for more details
Sounds like a problem with that shared library, have install/update anything in your system without using your Package Manager? (I believe its apt?)
The libgdal.so.1 in your system was compiled against some version of the libsqlite libraries, which now after you updated something else, have changed but libgdal is still the same file.
I have never used Ubuntu, but in the Linux i use (arch) this is the reason partial updates are discouraged (like updating only one program, for example)
So I would recommend to try a full system update, or at least update the sqllite libraries.
Related
When I tried to install r package "osmdata" (or any other package) with command
install.packages("osmdata")
it failed with error
"GLIBCXX_3.4.29' not found (required by /home...R/x86_64-unknown-linux-gnu-library/4.2/00LOCK-osmdata/00new/osmdata/libs/osmdata.so)
host system is debian, r is installed using package manager Guix.
The error means: osmdata.so was compiled with g++ version 11.1.0 (ABI mapping of GLIBCXX to g++ version is documented here), but the version of libstdc++.so.6 installed on the system is older, and doesn't provide GLIBCXX_3.4.29.
You need to get a version of osmdata.so appropriate for your system, or you need to build it from source, or you need to update your libstdc++.so.6.
P.S. Your question has nothing to do with glibc.
I solved it by installing package r-guix-install from Guix package manager and using this command
guix.install::guix.install("osmdata")
I have a new pc that I have installed ubuntu 20.04 on. I have added R4.0.0 and RStudio 1.2.5042. I need Rgdal and have tried installing it in a variety of ways - directly from CRAN within RStudio, from R in a terminal, and from github. They all fail with similar error messages. Attempting to install sf has a similar failure. It's message is from checking GDAL: checking whether PROJ is available for running: the sf message is free(): invalid pointer ./configure line 3594:102773 Aborted (core dumped) ./gdal_proj. It appears there is a problem with the gdal installation. gdalinfo --version returns GDAL 3.1.0 and after some usage options. FAILURE: no datasource specified; free(): invalid pointer.
I installed libspatialite-dev and libgeotiff-dev, and that fixed it.
Credit: https://www.mail-archive.com/gdal-dev#lists.osgeo.org/msg36151.html
Following the directions at this link solved the rgdal problem. Now have a different, non-gdal error with sf so need to research that.
Recently we have downgraded R(latest) to 3.3.0 to RHEL.
Which requires to install xlsx and other rJava dependent packages, though I have deep dived into every possible duplicate and tried all options.
Details:
Command Executed
R CMD javareconf
Error:
.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/lib64/R/lib64/R/lib/libR.a(CommandLineArgs.o): could not read symbols: Bad value
collect2: ld returned 1 exit status
make[2]: *** [libjri.so] Error 1
make[2]: Leaving directory /tmp/RtmpH1WhQR/R.INSTALL4a1266bbb309/rJava/jri/src'
`
Net search: I searched and found following link
https://github.com/BVLC/caffe/issues/2171 suggests to use
export CXXFLAGS=-fPIC
but no luck also I do not see CMakeCache.txt in the R folder, still not clear which piece I am missing and any help will be highly appreciated.
NOTE: This might seem to be a duplicate, but seriously I have already tried all the related/relevant posts on stackoverflow.
I resolved this, by manually placing the rJava folder(which I had in a different environment while we used R latest version), while entering into R add this following command before installing rJava dependant libraries:
.libPaths("/usr/lib64/R/library")
Change the path to the path where R is installed.
Hope this helps.
So I've been through a few problems trying to install rgdal. I'm running OS X 10.10.4
First I tried installing it from R :
install.packages("rgdal")
but the config file was not found :
configure: error: gdal-config not found or not executable.
So I installed gdal using Homebrew :
brew install gdal
Which installed a few dependencies alongside, like proj.
Problem is, R still can't install rgdal :
configure: error: proj_api.h not found in standard or given locations.
So I tried installing it manually, copying the rgdal_1.0-7.tar.gz from the temporary downloaded sources and unzipping it.
As ./config still seemed to fail finding proj_api.h, I searched it on my computer and found out it was in /usr/local/Cellar/proj/4.9.1/include, I tried
./configure CPPFLAGS="-I/usr/local/Cellar/proj/4.9.1/include"
... but it still doesn't work.
Now configure finds proj_api.h, but seems to be unable to find the functions defined in this header :
checking for proj_api.h... yes
checking for pj_init_plus in -lproj... no
configure: error: libproj not found in standard or given locations.
So now I don't know what to do anymore.
Any help would be great :)
I am trying to built a wireshark plugin code on my RHEL5 Virtual machine and while I am trying to compile it, I am getting the below error.
On ./configure command , below is the error message I receive and the make file is not being generated.
checking for Qt5Core - version >= 4.6.0... no
checking for QtCore - version >= 4.6.0... no
configure: error: Qt is not available
Please advise on how to go about this error. I have looked up for various rpm files and tried installing them but none works!
Try installing below packages as stated in this answer. Worked for me.
libqt4-dev (4:4.8.2+dfsg-11)
libqt4-dev-bin (4:4.8.2+dfsg-11)
libqt4-opengl-dev (4:4.8.2+dfsg-11)
libqtwebkit-dev (2.2.1-5)
qt4-linguist-tools (4:4.8.2+dfsg-11)
qt4-qmake (4:4.8.2+dfsg-11)
The error message you post is telling you that you need a version of Qt greater than or equal to 4.6.0. Since you are building software against Qt you will need the developer version of the package. There seems to be packages named qt47-devel that should be suitable.