About error in installing terra package in R-4.2.0 in Anaconda ,Centos 7

General
1

Hell, I am trying to install R and R studio using Anaconda in the linux server. I am facing issue with installing terra package as the when ever I try to install it following error occurs

Error Message: configure: error: GDALAllRegister not found in libgdal.
The detail is here. Need some suggestions

install.packages("terra")
also installing the dependency ‘Rcpp’

trying URL 'https://cran.rstudio.com/src/contrib/Rcpp_1.0.10.tar.gz'
Content type 'application/x-gzip' length 2936173 bytes (2.8 MB)

downloaded 2.8 MB

trying URL 'https://cran.rstudio.com/src/contrib/terra_1.7-29.tar.gz'
Content type 'application/x-gzip' length 806064 bytes (787 KB)

downloaded 787 KB

  • installing source package ‘Rcpp’ ...
    ** package ‘Rcpp’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    x86_64-conda-linux-gnu-c++ -std=gnu++14 -I"/data19/wrk/bikash/anaconda3/envs/r_4.2/lib/R/include" -DNDEBUG -I../inst/include/ -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data19/wrk/bikash/anaconda3/envs/r_4.2/include -I/data19/wrk/bikash/anaconda3/envs/r_4.2/include -Wl,-rpath-link,/data19/wrk/bikash/anaconda3/envs/r_4.2/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data19/wrk/bikash/anaconda3/envs/r_4.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659512907744/work=/usr/local/src/conda/r-base-4.2.0 -fdebug-prefix-map=/data19/wrk/bikash/anaconda3/envs/r_4.2=/usr/local/src/conda-prefix -c api.cpp -o api.o
    x86_64-conda-linux-gnu-c++ -std=gnu++14 -I"/data19/wrk/bikash/anaconda3/envs/r_4.2/lib/R/include" -DNDEBUG -I../inst/include/ -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data19/wrk/bikash/anaconda3/envs/r_4.2/include -I/data19/wrk/bikash/anaconda3/envs/r_4.2/include -Wl,-rpath-link,/data19/wrk/bikash/anaconda3/envs/r_4.2/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data19/wrk/bikash/anaconda3/envs/r_4.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659512907744/work=/usr/local/src/conda/r-base-4.2.0 -fdebug-prefix-map=/data19/wrk/bikash/anaconda3/envs/r_4.2=/usr/local/src/conda-prefix -c attributes.cpp -o attributes.o
    x86_64-conda-linux-gnu-c++ -std=gnu++14 -I"/data19/wrk/bikash/anaconda3/envs/r_4.2/lib/R/include" -DNDEBUG -I../inst/include/ -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data19/wrk/bikash/anaconda3/envs/r_4.2/include -I/data19/wrk/bikash/anaconda3/envs/r_4.2/include -Wl,-rpath-link,/data19/wrk/bikash/anaconda3/envs/r_4.2/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data19/wrk/bikash/anaconda3/envs/r_4.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659512907744/work=/usr/local/src/conda/r-base-4.2.0 -fdebug-prefix-map=/data19/wrk/bikash/anaconda3/envs/r_4.2=/usr/local/src/conda-prefix -c barrier.cpp -o barrier.o
    x86_64-conda-linux-gnu-c++ -std=gnu++14 -I"/data19/wrk/bikash/anaconda3/envs/r_4.2/lib/R/include" -DNDEBUG -I../inst/include/ -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data19/wrk/bikash/anaconda3/envs/r_4.2/include -I/data19/wrk/bikash/anaconda3/envs/r_4.2/include -Wl,-rpath-link,/data19/wrk/bikash/anaconda3/envs/r_4.2/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data19/wrk/bikash/anaconda3/envs/r_4.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659512907744/work=/usr/local/src/conda/r-base-4.2.0 -fdebug-prefix-map=/data19/wrk/bikash/anaconda3/envs/r_4.2=/usr/local/src/conda-prefix -c date.cpp -o date.o
    x86_64-conda-linux-gnu-c++ -std=gnu++14 -I"/data19/wrk/bikash/anaconda3/envs/r_4.2/lib/R/include" -DNDEBUG -I../inst/include/ -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data19/wrk/bikash/anaconda3/envs/r_4.2/include -I/data19/wrk/bikash/anaconda3/envs/r_4.2/include -Wl,-rpath-link,/data19/wrk/bikash/anaconda3/envs/r_4.2/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data19/wrk/bikash/anaconda3/envs/r_4.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659512907744/work=/usr/local/src/conda/r-base-4.2.0 -fdebug-prefix-map=/data19/wrk/bikash/anaconda3/envs/r_4.2=/usr/local/src/conda-prefix -c module.cpp -o module.o
    x86_64-conda-linux-gnu-c++ -std=gnu++14 -I"/data19/wrk/bikash/anaconda3/envs/r_4.2/lib/R/include" -DNDEBUG -I../inst/include/ -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /data19/wrk/bikash/anaconda3/envs/r_4.2/include -I/data19/wrk/bikash/anaconda3/envs/r_4.2/include -Wl,-rpath-link,/data19/wrk/bikash/anaconda3/envs/r_4.2/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /data19/wrk/bikash/anaconda3/envs/r_4.2/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1659512907744/work=/usr/local/src/conda/r-base-4.2.0 -fdebug-prefix-map=/data19/wrk/bikash/anaconda3/envs/r_4.2=/usr/local/src/conda-prefix -c rcpp_init.cpp -o rcpp_init.o
    x86_64-conda-linux-gnu-c++ -std=gnu++14 -shared -L/data19/wrk/bikash/anaconda3/envs/r_4.2/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/data19/wrk/bikash/anaconda3/envs/r_4.2/lib -Wl,-rpath-link,/data19/wrk/bikash/anaconda3/envs/r_4.2/lib -L/data19/wrk/bikash/anaconda3/envs/r_4.2/lib -o Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o -L/data19/wrk/bikash/anaconda3/envs/r_4.2/lib/R/lib -lR
    installing to /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/R/library/00LOCK-Rcpp/00new/Rcpp/libs
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded from temporary location
    ** checking absolute paths in shared objects and dynamic libraries
    ** testing if installed package can be loaded from final location
    ** testing if installed package keeps a record of temporary installation path
  • DONE (Rcpp)
  • installing source package ‘terra’ ...
    ** package ‘terra’ successfully unpacked and MD5 sums checked
    ** using staged installation
    configure: CC: /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/x86_64-conda-linux-gnu-cc
    configure: CXX: x86_64-conda-linux-gnu-c++ -std=gnu++14
    checking for gdal-config... /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/gdal-config
    checking gdal-config usability... yes
    configure: GDAL: 3.5.3
    checking GDAL version >= 2.0.1... yes
    checking for x86_64-conda-linux-gnu-gcc... /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/x86_64-conda-linux-gnu-cc
    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 the compiler supports GNU C... yes
    checking whether /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/x86_64-conda-linux-gnu-cc accepts -g... yes
    checking for /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/x86_64-conda-linux-gnu-cc option to enable C11 features... none needed
    checking for stdio.h... yes
    checking for stdlib.h... yes
    checking for string.h... yes
    checking for inttypes.h... yes
    checking for stdint.h... yes
    checking for strings.h... yes
    checking for sys/stat.h... yes
    checking for sys/types.h... yes
    checking for unistd.h... yes
    checking for gdal.h... yes
    checking GDAL: linking with --libs only... no
    checking GDAL: linking with --libs and --dep-libs... no
    /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/./libkea.so.1.5: undefined reference to H5::H5Location::createDataSet(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, H5::DataType const&, H5::DataSpace const&, H5::DSetCreatPropList const&, H5::DSetAccPropList const&, H5::LinkCreatPropList const&) const' /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/libgdal.so: undefined reference to H5::H5File::H5File(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, unsigned int, H5::FileCreatPropList const&, H5::FileAccPropList const&)'
    /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/./libkea.so.1.5: undefined reference to H5::H5Object::createAttribute(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, H5::DataType const&, H5::DataSpace const&, H5::PropList const&) const' /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/./libkea.so.1.5: undefined reference to H5::H5Location::openGroup(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) const'
    /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/./libkea.so.1.5: undefined reference to H5::H5Location::createGroup(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long) const' /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/libgdal.so: undefined reference to posix_spawnp@GLIBC_2.15'
    /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/./libkea.so.1.5: undefined reference to H5::CompType::insertMember(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long, H5::DataType const&) const' /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/./libnetcdf.so.19: undefined reference to H5Pset_fapl_ros3'
    /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/./libkea.so.1.5: undefined reference to H5::H5Location::getObjnameByIdx[abi:cxx11](unsigned long long) const' /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/libgdal.so: undefined reference to memcpy@GLIBC_2.14'
    /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/./libkea.so.1.5: undefined reference to H5::Attribute::write(H5::DataType const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/./libkea.so.1.5: undefined reference to H5::DataSet::operator=(H5::DataSet const&)'
    /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/./libkea.so.1.5: undefined reference to H5::Exception::getDetailMsg[abi:cxx11]() const' /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/./libkea.so.1.5: undefined reference to H5::H5Object::openAttribute(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) const'
    /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/./libkea.so.1.5: undefined reference to H5::H5Location::openDataSet(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, H5::DSetAccPropList const&) const' /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/./libkea.so.1.5: undefined reference to H5::H5Location::move(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) const'
    /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/./libkea.so.1.5: undefined reference to H5::H5Location::unlink(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, H5::LinkAccPropList const&) const' collect2: error: ld returned 1 exit status /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: warning: libjpeg.so.9, needed by /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/libgdal.so, may conflict with libjpeg.so.8 /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/libgdal.so: undefined reference to posix_spawnp@GLIBC_2.15'
    /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /data19/wrk/bikash/anaconda3/envs/r_4.2/lib/libgdal.so: undefined reference to memcpy@GLIBC_2.14' /data19/wrk/bikash/anaconda3/envs/r_4.2/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: /opt/hdf5-1.12.0/lib/libhdf5_hl.so.200: undefined reference to HDfprintf'
    collect2: error: ld returned 1 exit status
    configure: Install failure: compilation and/or linkage problems.
    configure: error: GDALAllRegister not found in libgdal.
    ERROR: configuration failed for package ‘terra’
  • removing ‘/data19/wrk/bikash/anaconda3/envs/r_4.2/lib/R/library/terra’
    Warning in install.packages :
    installation of package ‘terra’ had non-zero exit status

The downloaded source packages are in
‘/tmp/RtmpNG1oHf/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done

2

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