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Hello,
I failed to install beachmat package in R 4.4.2. Tried to find a similar issue but could not find. Any comment could be helpful for me.
Thank you.
Log is below.
> BiocManager::install("beachmat")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.irsn.fr
Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.2 (2024-10-31)
Installing package(s) 'beachmat'
trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/beachmat_2.22.0.tar.gz'
Content type 'application/x-gzip' length 378908 bytes (370 KB)
==================================================
downloaded 370 KB
* installing *source* package ‘beachmat’ ...
** package ‘beachmat’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 8.5.0 20210514 (Red Hat 8.5.0-18)’
using C++17
g++ -std=gnu++17 -I"/apps/r/rcran/4.4.2/lib64/R/include" -DNDEBUG -I../inst/include -I'/apps/r/rcran/4.4.2/lib64/R/library/Rcpp/include' -I'/apps/r/rcran/4.4.2/lib64/R/library/assorthead/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/apps/r/rcran/4.4.2/lib64/R/include" -DNDEBUG -I../inst/include -I'/apps/r/rcran/4.4.2/lib64/R/library/Rcpp/include' -I'/apps/r/rcran/4.4.2/lib64/R/library/assorthead/include' -I/usr/local/include -fpic -g -O2 -c delayed_isometric_binary.cpp -o delayed_isometric_binary.o
In file included from /apps/r/rcran/4.4.2/lib64/R/library/assorthead/include/tatami/tatami.hpp:33,
from /apps/r/rcran/4.4.2/lib64/R/library/assorthead/include/tatami_r/UnknownMatrix.hpp:5,
from /apps/r/rcran/4.4.2/lib64/R/library/assorthead/include/tatami_r/tatami_r.hpp:4,
from ../inst/include/Rtatami.h:8,
from delayed_isometric_binary.cpp:1:
/apps/r/rcran/4.4.2/lib64/R/library/assorthead/include/tatami/subset/DelayedSubsetBlock.hpp: In constructor ‘tatami::DelayedSubsetBlock_internal::AcrossDense<oracle_, Value_, Index_>::AcrossDense(const tatami::Matrix<Value_, Index_>*, Index_, bool, tatami::MaybeOracle<oracle_, Index_>, Args_&& ...)’:
/apps/r/rcran/4.4.2/lib64/R/library/assorthead/include/tatami/subset/DelayedSubsetBlock.hpp:115:68: error: class template argument deduction failed:
auto ptr = new SubsetOracle(std::move(oracle), my_shift);
^
/apps/r/rcran/4.4.2/lib64/R/library/assorthead/include/tatami/subset/DelayedSubsetBlock.hpp:115:68: error: no matching function for call to ‘SubsetOracle()’
/apps/r/rcran/4.4.2/lib64/R/library/assorthead/include/tatami/subset/DelayedSubsetBlock.hpp:94:5: note: candidate: ‘template<class Index_> SubsetOracle(std::shared_ptr<const tatami::Oracle<Index_> >, Index_)-> tatami::DelayedSubsetBlock_internal::SubsetOracle<Index_>’
SubsetOracle(std::shared_ptr<const Oracle<Index_> > oracle, Index_ shift) : my_oracle(std::move(oracle)), my_shift(shift) {}
^~~~~~~~~~~~
/apps/r/rcran/4.4.2/lib64/R/library/assorthead/include/tatami/subset/DelayedSubsetBlock.hpp:94:5: note: template argument deduction/substitution failed:
/apps/r/rcran/4.4.2/lib64/R/library/assorthead/include/tatami/subset/DelayedSubsetBlock.hpp:115:68: note: candidate expects 2 arguments, 0 provided
auto ptr = new SubsetOracle(std::move(oracle), my_shift);
^
/apps/r/rcran/4.4.2/lib64/R/library/assorthead/include/tatami/subset/DelayedSubsetBlock.hpp: In constructor ‘tatami::DelayedSubsetBlock_internal::AcrossSparse<oracle_, Value_, Index_>::AcrossSparse(const tatami::Matrix<Value_, Index_>*, Index_, bool, tatami::MaybeOracle<oracle_, Index_>, Args_&& ...)’:
/apps/r/rcran/4.4.2/lib64/R/library/assorthead/include/tatami/subset/DelayedSubsetBlock.hpp:136:68: error: class template argument deduction failed:
auto ptr = new SubsetOracle(std::move(oracle), my_shift);
^
/apps/r/rcran/4.4.2/lib64/R/library/assorthead/include/tatami/subset/DelayedSubsetBlock.hpp:136:68: error: no matching function for call to ‘SubsetOracle()’
/apps/r/rcran/4.4.2/lib64/R/library/assorthead/include/tatami/subset/DelayedSubsetBlock.hpp:94:5: note: candidate: ‘template<class Index_> SubsetOracle(std::shared_ptr<const tatami::Oracle<Index_> >, Index_)-> tatami::DelayedSubsetBlock_internal::SubsetOracle<Index_>’
SubsetOracle(std::shared_ptr<const Oracle<Index_> > oracle, Index_ shift) : my_oracle(std::move(oracle)), my_shift(shift) {}
^~~~~~~~~~~~
/apps/r/rcran/4.4.2/lib64/R/library/assorthead/include/tatami/subset/DelayedSubsetBlock.hpp:94:5: note: template argument deduction/substitution failed:
/apps/r/rcran/4.4.2/lib64/R/library/assorthead/include/tatami/subset/DelayedSubsetBlock.hpp:136:68: note: candidate expects 2 arguments, 0 provided
auto ptr = new SubsetOracle(std::move(oracle), my_shift);
^
make: *** [/apps/r/rcran/4.4.2/lib64/R/etc/Makeconf:204: delayed_isometric_binary.o] Error 1
ERROR: compilation failed for package ‘beachmat’
* removing ‘/apps/r/rcran/4.4.2/lib64/R/library/beachmat’
The downloaded source packages are in
‘/tmp/Rtmp4nHLxZ/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(...) :
installation of package ‘beachmat’ had non-zero exit status
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