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rix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>; Rhs = Eigen::Matrix<double, -1, 1>; int Options = 0; int ProductTag = 6; LhsShape = Eigen::DenseShape; RhsShape = Eigen::DenseShape; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, Option>::Rhs>::Scalar = double; typename Eigen::Product<Lhs, Rhs, Option>::Rhs = Eigen::Matrix<double, -1, 1>; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, Option>::Lhs>::Scalar = double; typename Eigen::Product<Lhs, Rhs, Option>::Lhs = Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>; Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, Option>, ProductTag, LhsShape, RhsShape>::XprType = Eigen::Product<Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>, Eigen::Matrix<double, -1, 1>, 0>]’
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:35:90:   required from ‘Eigen::internal::evaluator<Eigen::Product<Lhs, Rhs, Option> >::evaluator(const XprType&) [with Lhs = Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>; Rhs = Eigen::Matrix<double, -1, 1>; int Options = 0; Eigen::internal::evaluator<Eigen::Product<Lhs, Rhs, Option> >::XprType = Eigen::Product<Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>, Eigen::Matrix<double, -1, 1>, 0>]’
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/Product.h:132:22:   required from ‘Eigen::internal::dense_product_base<Lhs, Rhs, Option, 6>::operator const Scalar() const [with Lhs = Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>; Rhs = Eigen::Matrix<double, -1, 1>; int Option = 0; Eigen::internal::dense_product_base<Lhs, Rhs, Option, 6>::Scalar = double]’
./stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:23:56:   required from ‘double stan::mcmc::dense_e_metric<Model, BaseRNG>::T(stan::mcmc::dense_e_point&) [with Model = stan::model::model_base; BaseRNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >]’
./stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:10:   required from here
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Block<Eigen::Transpose<Eigen::Matrix<double, 1, -1> >, -1, 1, true>, 0>’:
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Block<Eigen::Transpose<Eigen::Matrix<double, 1, -1> >, -1, 1, true>, 1>’
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Block<Eigen::Transpose<Eigen::Matrix<double, 1, -1> >, -1, 1, true>, 3>’
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Block<Eigen::Transpose<Eigen::Matrix<double, 1, -1> >, -1, 1, true> >’
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Block<Eigen::Transpose<Eigen::Matrix<double, 1, -1> >, -1, 1, true> >’
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/MapBase.h:37:34:   required from ‘class Eigen::MapBase<Eigen::Block<Eigen::Transpose<Eigen::Matrix<double, 1, -1> >, -1, 1, true>, 0>’
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/MapBase.h:221:34:   [ skipping 20 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:251:64:   required from ‘static void Eigen::internal::generic_product_impl<Lhs, Rhs, Eigen::DenseShape, Eigen::DenseShape, 6>::evalTo(Dst&, const Lhs&, const Rhs&) [with Dst = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Lhs = Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>; Rhs = Eigen::Matrix<double, -1, 1>]’
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:124:75:   required from ‘Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, Option>, ProductTag, LhsShape, RhsShape>::product_evaluator(const XprType&) [with Lhs = Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>; Rhs = Eigen::Matrix<double, -1, 1>; int Options = 0; int ProductTag = 6; LhsShape = Eigen::DenseShape; RhsShape = Eigen::DenseShape; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, Option>::Rhs>::Scalar = double; typename Eigen::Product<Lhs, Rhs, Option>::Rhs = Eigen::Matrix<double, -1, 1>; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, Option>::Lhs>::Scalar = double; typename Eigen::Product<Lhs, Rhs, Option>::Lhs = Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>; Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, Option>, ProductTag, LhsShape, RhsShape>::XprType = Eigen::Product<Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>, Eigen::Matrix<double, -1, 1>, 0>]’
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:35:90:   required from ‘Eigen::internal::evaluator<Eigen::Product<Lhs, Rhs, Option> >::evaluator(const XprType&) [with Lhs = Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>; Rhs = Eigen::Matrix<double, -1, 1>; int Options = 0; Eigen::internal::evaluator<Eigen::Product<Lhs, Rhs, Option> >::XprType = Eigen::Product<Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>, Eigen::Matrix<double, -1, 1>, 0>]’
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/Product.h:132:22:   required from ‘Eigen::internal::dense_product_base<Lhs, Rhs, Option, 6>::operator const Scalar() const [with Lhs = Eigen::Product<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<Eigen::Matrix<double, -1, 1> > >, Eigen::Matrix<double, -1, -1>, 0>; Rhs = Eigen::Matrix<double, -1, 1>; int Option = 0; Eigen::internal::dense_product_base<Lhs, Rhs, Option, 6>::Scalar = double]’
./stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:23:56:   required from ‘double stan::mcmc::dense_e_metric<Model, BaseRNG>::T(stan::mcmc::dense_e_point&) [with Model = stan::model::model_base; BaseRNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >]’
./stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:10:   required from here
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
g++ -std=gnu++14 -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o rstan.so Module.o chains.o init.o misc.o pointer-tools.o sparse_extractors.o stan_fit_base.o stan_fit_rccp.o stanc.o stan/lang/ast_def.o stan/lang/grammars/bare_type_grammar_inst.o stan/lang/grammars/block_var_decls_grammar_inst.o stan/lang/grammars/expression07_grammar_inst.o stan/lang/grammars/expression_grammar_inst.o stan/lang/grammars/functions_grammar_inst.o stan/lang/grammars/indexes_grammar_inst.o stan/lang/grammars/local_var_decls_grammar_inst.o stan/lang/grammars/program_grammar_inst.o stan/lang/grammars/semantic_actions_def.o stan/lang/grammars/statement_2_grammar_inst.o stan/lang/grammars/statement_grammar_inst.o stan/lang/grammars/term_grammar_inst.o stan/lang/grammars/whitespace_grammar_inst.o -L/usr/lib64/R/lib -lR
ar -rs ../inst/lib//libStanServices.a stan_fit.o stan_fit_base.o
ar: creating ../inst/lib//libStanServices.a
installing to /build/r-rstan/src/00LOCK-rstan/00new/rstan/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error in as.POSIXlt.character(x, tz, ...) : 
  character string is not in a standard unambiguous format
Error: unable to load R code in package ‘rstan’
Execution halted
ERROR: lazy loading failed for package ‘rstan’

�[1m�[34m  ->�(B�[m�[1m Extracting V1.10.tar.gz with bsdtar�(B�[m
�[1m�[32m==>�(B�[m�[1m Starting build()...�(B�[m
/startdir/PKGBUILD: line 17: cd: LRA-V1.10: No such file or directory
�[1m�[31m==> ERROR:�(B�[m�[1m A failure occurred in build().�(B�[m

* installing *source* package ‘Herper’ ...
** using staged installation
Error : Invalid DESCRIPTION file

Authors@R field gives more than one person with maintainer role:
  Matt Paul <[email protected]> [aut, cre] (<https://orcid.org/0000-0002-3020-7729>)
  Thomas Carroll <[email protected]> [aut, cre] (<https://orcid.org/0000-0002-0073-1714>)

See section 'The DESCRIPTION file' in the 'Writing R Extensions'

gcc -I"/usr/include/R/" -DNDEBUG  -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I'/usr/lib/R/library/Rcpp/include' -I'/usr/lib/R/library/S4Vectors/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/usr/include/R/" -DNDEBUG  -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I'/usr/lib/R/library/Rcpp/include' -I'/usr/lib/R/library/S4Vectors/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c ByteStringVector.c -o ByteStringVector.o
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG  -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I'/usr/lib/R/library/Rcpp/include' -I'/usr/lib/R/library/S4Vectors/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c ExplicitRepC.cpp -o ExplicitRepC.o
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG  -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -I'/usr/lib/R/library/Rcpp/include' -I'/usr/lib/R/library/S4Vectors/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
FeatureWeightsPosDepC.cpp: In instantiation of ‘bool getWeightsPerPosition(T, SEXPREC**, kh_pdfw_t*, kh_pdfi_t*, bool, int, uint64_t, uint64_t, T*) [with T = unsigned char; SEXP = SEXPREC*; uint64_t = long unsigned int]’:
FeatureWeightsPosDepC.cpp:103:41:   required from here
FeatureWeightsPosDepC.cpp:59:17: error: ‘Free’ was not declared in this scope; did you mean ‘free’?
   59 |             Free(keys);
      |             ~~~~^~~~~~
      |             free
FeatureWeightsPosDepC.cpp:76:17: error: ‘Free’ was not declared in this scope; did you mean ‘free’?
   76 |             Free(keys);
      |             ~~~~^~~~~~
      |             free
FeatureWeightsPosDepC.cpp:86:9: error: ‘Free’ was not declared in this scope; did you mean ‘free’?
   86 |     Free(keys);
      |     ~~~~^~~~~~
      |     free
FeatureWeightsPosDepC.cpp: In instantiation of ‘bool getWeightsPerPosition(T, SEXPREC**, kh_pdfw_t*, kh_pdfi_t*, bool, int, uint64_t, uint64_t, T*) [with T = short unsigned int; SEXP = SEXPREC*; uint64_t = long unsigned int]’:
FeatureWeightsPosDepC.cpp:109:41:   required from here
FeatureWeightsPosDepC.cpp:59:17: error: ‘Free’ was not declared in this scope; did you mean ‘free’?
   59 |             Free(keys);
      |             ~~~~^~~~~~
      |             free
FeatureWeightsPosDepC.cpp:76:17: error: ‘Free’ was not declared in this scope; did you mean ‘free’?
   76 |             Free(keys);
      |             ~~~~^~~~~~
      |             free
FeatureWeightsPosDepC.cpp:86:9: error: ‘Free’ was not declared in this scope; did you mean ‘free’?
   86 |     Free(keys);
      |     ~~~~^~~~~~
      |     free
FeatureWeightsPosDepC.cpp: In instantiation of ‘bool getWeightsPerPosition(T, SEXPREC**, kh_pdfw_t*, kh_pdfi_t*, bool, int, uint64_t, uint64_t, T*) [with T = unsigned int; SEXP = SEXPREC*; uint64_t = long unsigned int]’:
FeatureWeightsPosDepC.cpp:116:41:   required from here
FeatureWeightsPosDepC.cpp:59:17: error: ‘Free’ was not declared in this scope; did you mean ‘free’?
   59 |             Free(keys);
      |             ~~~~^~~~~~
      |             free
FeatureWeightsPosDepC.cpp:76:17: error: ‘Free’ was not declared in this scope; did you mean ‘free’?
   76 |             Free(keys);
      |             ~~~~^~~~~~
      |             free
FeatureWeightsPosDepC.cpp:86:9: error: ‘Free’ was not declared in this scope; did you mean ‘free’?
   86 |     Free(keys);
      |     ~~~~^~~~~~
      |     free
FeatureWeightsPosDepC.cpp: In instantiation of ‘bool getWeightsPerPosition(T, SEXPREC**, kh_pdfw_t*, kh_pdfi_t*, bool, int, uint64_t, uint64_t, T*) [with T = long unsigned int; SEXP = SEXPREC*; uint64_t = long unsigned int]’:
FeatureWeightsPosDepC.cpp:122:41:   required from here
FeatureWeightsPosDepC.cpp:59:17: error: ‘Free’ was not declared in this scope; did you mean ‘free’?
   59 |             Free(keys);
      |             ~~~~^~~~~~
      |             free
FeatureWeightsPosDepC.cpp:76:17: error: ‘Free’ was not declared in this scope; did you mean ‘free’?
   76 |             Free(keys);
      |             ~~~~^~~~~~
      |             free
FeatureWeightsPosDepC.cpp:86:9: error: ‘Free’ was not declared in this scope; did you mean ‘free’?
   86 |     Free(keys);
      |     ~~~~^~~~~~
      |     free
make: *** [/usr/lib64/R/etc/Makeconf:177: FeatureWeightsPosDepC.o] Error 1
make: *** Waiting for unfinished jobs....
ERROR: compilation failed for package ‘kebabs’
* removing ‘/build/r-kebabs/src/kebabs’
* restoring previous ‘/build/r-kebabs/src/kebabs’

[D 12-23 15:56:29.308 cmd:89] running ['sh', '-c', 'rm -f -- *.pkg.tar.xz *.pkg.tar.xz.sig *.pkg.tar.zst *.pkg.tar.zst.sig'], not using pty, showing output
[D 12-23 15:56:29.317 building:93] accept_noupdate=False, oldver=None, newver='2.10.0'
[D 12-23 15:56:29.318 cmd:89] running ['bwrap', '--unshare-all', '--ro-bind', '/', '/', '--tmpfs', '/home', '--tmpfs', '/run', '--die-with-parent', '--tmpfs', '/tmp', '--proc', '/proc', '--dev', '/dev', '--share-net', '--bind', '/home/guoyi/Packages/BioArchLinux/r-rsamtools', '/tmp/r-rsamtools', '--chdir', '/tmp/r-rsamtools', '--ro-bind', PosixPath('/home/guoyi/.lilac/gnupg'), '/home/guoyi/.gnupg', 'updpkgsums'], not using pty, showing output
==> Retrieving sources...
  -> Found Rsamtools_2.10.0.tar.gz
==> Generating checksums for source files...
[D 12-23 15:56:30.167 cmd:89] running ['recv_gpg_keys'], not using pty, showing output
[D 12-23 15:56:30.206 cmd:89] running ['bwrap', '--unshare-all', '--ro-bind', '/', '/', '--tmpfs', '/home', '--tmpfs', '/run', '--die-with-parent', '--tmpfs', '/tmp', '--proc', '/proc', '--dev', '/dev', '--share-net', '--bind', '/home/guoyi/Packages/BioArchLinux/r-rsamtools', '/tmp/r-rsamtools', '--chdir', '/tmp/r-rsamtools', '--ro-bind', PosixPath('/home/guoyi/.lilac/gnupg'), '/home/guoyi/.gnupg', 'makepkg', '-od', '--noprepare', '-A'], using pty, showing output
[D 12-23 15:56:30.206 cmd:96] pty master fd=9, slave fd=10.
�[1m�[32m==>�(B�[m�[1m Making package: r-rsamtools 2.10.0-1 (Thu 23 Dec 2021 23:56:31 CST)�(B�[m
�[1m�[33m==> WARNING:�(B�[m�[1m Skipping dependency checks.�(B�[m
�[1m�[32m==>�(B�[m�[1m Retrieving sources...�(B�[m
�[1m�[34m  ->�(B�[m�[1m Found Rsamtools_2.10.0.tar.gz�(B�[m
�[1m�[32m==>�(B�[m�[1m Validating source files with sha256sums...�(B�[m
    Rsamtools_2.10.0.tar.gz ... Passed
�[1m�[32m==>�(B�[m�[1m Extracting sources...�(B�[m
�[1m�[34m  ->�(B�[m�[1m Extracting Rsamtools_2.10.0.tar.gz with bsdtar�(B�[m
�[1m�[32m==>�(B�[m�[1m Sources are ready.�(B�[m
[I 12-23 15:56:32.109 building:117] depends: {Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-futile.logger'), pkgname='r-futile.logger'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-snow'), pkgname='r-snow'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-genomeinfodb'), pkgname='r-genomeinfodb'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-biostrings'), pkgname='r-biostrings'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-biocparallel'), pkgname='r-biocparallel'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-rcurl'), pkgname='r-rcurl'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-xvector'), pkgname='r-xvector'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-formatr'), pkgname='r-formatr'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-s4vectors'), pkgname='r-s4vectors'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-rhtslib'), pkgname='r-rhtslib'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-biocgenerics'), pkgname='r-biocgenerics'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-zlibbioc'), pkgname='r-zlibbioc'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-iranges'), pkgname='r-iranges'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-bh'), pkgname='r-bh'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-crayon'), pkgname='r-crayon'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-bitops'), pkgname='r-bitops'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-genomeinfodbdata'), pkgname='r-genomeinfodbdata'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-futile.options'), pkgname='r-futile.options'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-genomicranges'), pkgname='r-genomicranges'), Dependency(pkgdir=PosixPath('/home/guoyi/Packages/BioArchLinux/r-lambda.r'), pkgname='r-lambda.r')}, resolved: [PosixPath('/home/guoyi/Packages/BioArchLinux/r-futile.logger/r-futile.logger-1.4.3-1-any.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-snow/r-snow-0.4.4-1-any.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-genomeinfodb/r-genomeinfodb-1.30.0-1-any.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-biostrings/r-biostrings-2.62.0-1-x86_64.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-biocparallel/r-biocparallel-1.28.3-1-x86_64.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-rcurl/r-rcurl-1.98.1.5-1-x86_64.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-xvector/r-xvector-0.34.0-1-x86_64.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-formatr/r-formatr-1.11-1-any.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-s4vectors/r-s4vectors-0.32.3-1-x86_64.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-rhtslib/r-rhtslib-1.26.0-1-x86_64.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-biocgenerics/r-biocgenerics-0.40.0-1-any.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-zlibbioc/r-zlibbioc-1.40.0-1-x86_64.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-iranges/r-iranges-2.28.0-1-x86_64.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-bh/r-bh-1.78.0.0-1-any.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-crayon/r-crayon-1.4.2-1-any.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-bitops/r-bitops-1.0.7-1-x86_64.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-genomeinfodbdata/r-genomeinfodbdata-1.2.7-1-any.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-futile.options/r-futile.options-1.0.1-1-any.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-genomicranges/r-genomicranges-1.46.1-1-x86_64.pkg.tar.zst'), PosixPath('/home/guoyi/Packages/BioArchLinux/r-lambda.r/r-lambda.r-1.2.4-1-any.pkg.tar.zst')]
[I 12-23 15:56:32.110 building:192] Running build command: ['env', 'GNUPGHOME=/home/guoyi/.lilac/gnupg', 'extra-x86_64-build', '--', '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-futile.logger/r-futile.logger-1.4.3-1-any.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-snow/r-snow-0.4.4-1-any.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-genomeinfodb/r-genomeinfodb-1.30.0-1-any.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-biostrings/r-biostrings-2.62.0-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-biocparallel/r-biocparallel-1.28.3-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-rcurl/r-rcurl-1.98.1.5-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-xvector/r-xvector-0.34.0-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-formatr/r-formatr-1.11-1-any.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-s4vectors/r-s4vectors-0.32.3-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-rhtslib/r-rhtslib-1.26.0-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-biocgenerics/r-biocgenerics-0.40.0-1-any.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-zlibbioc/r-zlibbioc-1.40.0-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-iranges/r-iranges-2.28.0-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-bh/r-bh-1.78.0.0-1-any.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-crayon/r-crayon-1.4.2-1-any.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-bitops/r-bitops-1.0.7-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-genomeinfodbdata/r-genomeinfodbdata-1.2.7-1-any.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-futile.options/r-futile.options-1.0.1-1-any.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-genomicranges/r-genomicranges-1.46.1-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-lambda.r/r-lambda.r-1.2.4-1-any.pkg.tar.zst'), '-d', '/home/guoyi/go:/build/go', '-d', '/home/guoyi/.cargo:/build/.cargo', '-d', '/home/guoyi/.cache/pip:/build/.cache/pip', '-d', '/home/guoyi/.cache/go-build:/build/.cache/go-build', '-d', '/home/guoyi/.cache/archbuild-bind-cache/stack:/build/.stack', '-d', '/home/guoyi/.cache/archbuild-bind-cache:/build/.cache', '--', '--noprogressbar', '--holdver']
�[?25l:: Synchronizing package databases...
 core downloading...
 extra downloading...
 community downloading...
:: Starting full system upgrade...
 there is nothing to do
�[?25h==> Building in chroot for [extra] (x86_64)...
==> Synchronizing chroot copy [/var/lib/archbuild/extra-x86_64/root] -> [guoyi]...done
�[?25lloading packages...
resolving dependencies...
looking for conflicting packages...
warning: dependency cycle detected:
warning: harfbuzz will be installed before its freetype2 dependency

Package (52)         New Version  Net Change

extra/blas           3.10.0-1       0.33 MiB
extra/cairo          1.17.4-5       1.68 MiB
extra/fontconfig     2:2.13.94-2    1.05 MiB
extra/freetype2      2.11.1-1       1.59 MiB
extra/fribidi        1.0.11-1       0.22 MiB
extra/graphite       1:1.3.14-1     0.67 MiB
extra/harfbuzz       3.2.0-1        5.45 MiB
extra/lapack         3.10.0-1       7.18 MiB
extra/libdatrie      0.2.13-1       0.07 MiB
extra/libice         1.0.10-3       0.35 MiB
extra/libjpeg-turbo  2.1.2-1        2.02 MiB
extra/libpng         1.6.37-3       0.55 MiB
extra/libsm          1.2.3-2        0.26 MiB
extra/libthai        0.1.29-1       0.65 MiB
extra/libtiff        4.3.0-1        2.82 MiB
extra/libx11         1.7.3.1-1     10.16 MiB
extra/libxau         1.0.9-3        0.02 MiB
extra/libxcb         1.14-1         3.73 MiB
extra/libxdmcp       1.1.3-3        0.13 MiB
extra/libxext        1.3.4-3        0.30 MiB
extra/libxft         2.3.4-1        0.11 MiB
extra/libxmu         1.1.3-2        0.33 MiB
extra/libxrender     0.9.10-4       0.08 MiB
extra/libxt          1.2.1-1        2.03 MiB
core/lzo             2.10-3         0.39 MiB
extra/pango          1:1.50.3-1     2.25 MiB
extra/pixman         0.40.0-1       0.70 MiB
extra/r              4.1.2-2       79.34 MiB
extra/unzip          6.0-16         0.31 MiB
extra/xcb-proto      1.14.1-5       0.82 MiB
extra/xorgproto      2021.5-1       1.43 MiB
extra/zip            3.0-9          0.55 MiB
r-bh                 1.78.0.0-1   119.84 MiB
r-biocgenerics       0.40.0-1       0.78 MiB
r-biocparallel       1.28.3-1       1.68 MiB
r-biostrings         2.62.0-1      14.87 MiB
r-bitops             1.0.7-1        0.04 MiB
r-crayon             1.4.2-1        0.16 MiB
r-formatr            1.11-1         0.22 MiB
r-futile.logger      1.4.3-1        0.11 MiB
r-futile.options     1.0.1-1        0.02 MiB
r-genomeinfodb       1.30.0-1       4.78 MiB
r-genomeinfodbdata   1.2.7-1       10.68 MiB
r-genomicranges      1.46.1-1       3.22 MiB
r-iranges            2.28.0-1       3.22 MiB
r-lambda.r           1.2.4-1        0.11 MiB
r-rcurl              1.98.1.5-1     1.87 MiB
r-rhtslib            1.26.0-1       6.21 MiB
r-s4vectors          0.32.3-1       2.91 MiB
r-snow               0.4.4-1        0.10 MiB
r-xvector            0.34.0-1       0.97 MiB
r-zlibbioc           1.40.0-1       0.12 MiB

Total Installed Size:  299.47 MiB

:: Proceed with installation? [Y/n] y
�[?25h�[?25lchecking keyring...
checking package integrity...
loading package files...
checking for file conflicts...
:: Processing package changes...
installing blas...
installing lapack...
installing libjpeg-turbo...
Optional dependencies for libjpeg-turbo
    java-runtime>11: for TurboJPEG Java wrapper
installing libtiff...
Optional dependencies for libtiff
    freeglut: for using tiffgt
installing xcb-proto...
installing libxdmcp...
installing libxau...
installing libxcb...
installing xorgproto...
installing libx11...
installing libxext...
installing libice...
installing libsm...
installing libxt...
installing libxmu...
installing libdatrie...
installing libthai...
installing lzo...
installing libpng...
installing graphite...
installing harfbuzz...
Optional dependencies for harfbuzz
    cairo: hb-view program [pending]
    chafa: hb-view program
installing freetype2...
installing fontconfig...
Creating fontconfig configuration...
Rebuilding fontconfig cache...
installing libxrender...
installing pixman...
installing cairo...
installing libxft...
installing fribidi...
installing pango...
installing zip...
installing unzip...
installing r...
Optional dependencies for r
    tk: tcl/tk interface
    texlive-bin: latex sty files
    gcc-fortran: needed to compile some CRAN packages
    openblas: faster linear algebra
installing r-futile.options...
installing r-formatr...
Optional dependencies for r-formatr
    r-codetools
    r-knitr
    r-rmarkdown
    r-shiny
    r-testit
installing r-lambda.r...
Optional dependencies for r-lambda.r
    r-testit
installing r-futile.logger...
Optional dependencies for r-futile.logger
    r-jsonlite
    r-testthat
installing r-snow...
Optional dependencies for r-snow
    r-rlecuyer
    r-rmpi
installing r-biocgenerics...
Optional dependencies for r-biocgenerics
    r-affy
    r-affyplm
    r-annotate
    r-annotationdbi
    r-biobase
    r-biostrings [pending]
    r-delayedarray
    r-deseq2
    r-flowclust
    r-genomicranges [pending]
    r-iranges [pending]
    r-msnbase
    r-rsamtools
    r-runit
    r-s4vectors [pending]
installing r-genomeinfodbdata...
installing r-s4vectors...
Optional dependencies for r-s4vectors
    r-biocstyle
    r-data.table
    r-delayedarray
    r-genomicranges [pending]
    r-graph
    r-iranges [pending]
    r-matrix
    r-runit
    r-shortread
    r-summarizedexperiment
installing r-iranges...
Optional dependencies for r-iranges
    r-biocstyle
    r-bsgenome.celegans.ucsc.ce2
    r-genomicalignments
    r-genomicfeatures
    r-genomicranges [pending]
    r-pasillabamsubset
    r-rsamtools
    r-runit
    r-xvector [pending]
installing r-bitops...
installing r-rcurl...
Optional dependencies for r-rcurl
    r-xml
installing r-genomeinfodb...
Optional dependencies for r-genomeinfodb
    r-biocstyle
    r-bsgenome
    r-bsgenome.celegans.ucsc.ce2
    r-bsgenome.hsapiens.ncbi.grch38
    r-bsgenome.scerevisiae.ucsc.saccer2
    r-genomicalignments
    r-genomicfeatures
    r-genomicranges [pending]
    r-knitr
    r-rsamtools
    r-runit
    r-txdb.dmelanogaster.ucsc.dm3.ensgene
installing r-crayon...
Optional dependencies for r-crayon
    r-mockery
    r-rstudioapi
    r-testthat
    r-withr
installing r-zlibbioc...
installing r-xvector...
Optional dependencies for r-xvector
    r-biostrings [pending]
    r-drosophila2probe
    r-runit
installing r-biostrings...
Optional dependencies for r-biostrings
    r-affy
    r-affydata
    r-bsgenome
    r-bsgenome.celegans.ucsc.ce2
    r-bsgenome.dmelanogaster.ucsc.dm3
    r-bsgenome.hsapiens.ucsc.hg18
    r-drosophila2probe
    r-genomicfeatures
    r-hgu133aprobe
    r-hgu95av2cdf
    r-hgu95av2probe
    r-rmpi
    r-runit
installing r-bh...
installing r-biocparallel...
Optional dependencies for r-biocparallel
    r-batchjobs
    r-batchtools
    r-bbmisc
    r-biocgenerics [installed]
    r-biocstyle
    r-codetools
    r-data.table
    r-doparallel
    r-foreach
    r-genomicalignments
    r-genomicranges [pending]
    r-knitr
    r-rmpi
    r-rnaseqdata.hnrnpc.bam.chr14
    r-rsamtools
    r-runit
    r-shortread
    r-tools
    r-txdb.hsapiens.ucsc.hg19.knowngene
    r-variantannotation
installing r-rhtslib...
Optional dependencies for r-rhtslib
    r-biocstyle
    r-knitr
    r-rmarkdown
installing r-genomicranges...
Optional dependencies for r-genomicranges
    r-annotate
    r-annotationdbi
    r-annotationhub
    r-biobase
    r-biocstyle
    r-biostrings [installed]
    r-bsgenome
    r-bsgenome.hsapiens.ucsc.hg19
    r-bsgenome.mmusculus.ucsc.mm10
    r-bsgenome.scerevisiae.ucsc.saccer2
    r-deseq2
    r-dexseq
    r-digest
    r-edger
    r-genomicalignments
    r-genomicfeatures
    r-gviz
    r-hgu95av2.db
    r-hgu95av2probe
    r-kegggraph
    r-keggrest
    r-knitr
    r-matrix
    r-pasillabamsubset
    r-rmarkdown
    r-rnaseqdata.hnrnpc.bam.chr14
    r-rsamtools
    r-rtracklayer
    r-runit
    r-summarizedexperiment
    r-txdb.athaliana.biomart.plantsmart22
    r-txdb.dmelanogaster.ucsc.dm3.ensgene
    r-txdb.hsapiens.ucsc.hg19.knowngene
    r-txdb.mmusculus.ucsc.mm10.knowngene
    r-variantannotation
:: Running post-transaction hooks...
(1/2) Updating fontconfig configuration...
(2/2) Updating fontconfig cache...
�[?25h==> Making package: r-rsamtools 2.10.0-1 (Thu Dec 23 23:56:48 2021)
==> Retrieving sources...
  -> Found Rsamtools_2.10.0.tar.gz
==> Validating source files with sha256sums...
    Rsamtools_2.10.0.tar.gz ... Passed
�[1m�[32m==>�(B�[m�[1m Making package: r-rsamtools 2.10.0-1 (Thu 23 Dec 2021 03:56:51 PM GMT)�(B�[m
�[1m�[32m==>�(B�[m�[1m Checking runtime dependencies...�(B�[m
�[1m�[32m==>�(B�[m�[1m Checking buildtime dependencies...�(B�[m
�[1m�[32m==>�(B�[m�[1m Retrieving sources...�(B�[m
�[1m�[34m  ->�(B�[m�[1m Found Rsamtools_2.10.0.tar.gz�(B�[m
�[1m�[33m==> WARNING:�(B�[m�[1m Skipping all source file integrity checks.�(B�[m
�[1m�[32m==>�(B�[m�[1m Extracting sources...�(B�[m
�[1m�[34m  ->�(B�[m�[1m Extracting Rsamtools_2.10.0.tar.gz with bsdtar�(B�[m
�[1m�[32m==>�(B�[m�[1m Starting build()...�(B�[m
* installing *source* package ‘Rsamtools’ ...
** using staged installation
** libs
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c IRanges_stubs.c -o IRanges_stubs.o
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c PileupBuffer.cpp -o PileupBuffer.o
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c PosCacheColl.cpp -o PosCacheColl.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c R_init_Rsamtools.c -o R_init_Rsamtools.o
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c ResultManager.cpp -o ResultManager.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c as_bam.c -o as_bam.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c bam.c -o bam.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c bam_data.c -o bam_data.o
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from /usr/lib/R/library/Rhtslib/include/sam.h:29,
                 from Template.h:9,
                 from BamIterator.h:10,
                 from BamRangeIterator.h:7,
                 from bam_mate_iter.cpp:2:
BamRangeIterator.h: In member function ‘virtual void BamRangeIterator::finalize_inprogress(bamFile)’:
/usr/lib/R/library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
      |                                ~~~~~~~~~^~~~~~~~~~~~~~
BamRangeIterator.h:138:16: note: in expansion of macro ‘bam_seek’
  138 |         (void) bam_seek(bfile, pos, SEEK_SET);
      |                ^~~~~~~~
BamIterator.h: In constructor ‘BamIterator::BamIterator(bamFile, const bam_index_t*)’:
/usr/lib/R/library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
      |                                ~~~~~~~~~^~~~~~~~~~~~~~
BamIterator.h:87:16: note: in expansion of macro ‘bam_seek’
   87 |         (void) bam_seek(bfile, 0, 0);
      |                ^~~~~~~~
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c bam_plbuf.c -o bam_plbuf.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c bam_sort.c -o bam_sort.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c bambuffer.c -o bambuffer.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c bamfile.c -o bamfile.o
bamfile.c: In function ‘bamfile_isincomplete’:
bamfile.c:168:20: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  168 |             (void) bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c bcffile.c -o bcffile.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c encode.c -o encode.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c fafile.c -o fafile.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c idxstats.c -o idxstats.o
In file included from /usr/lib/R/library/Rhtslib/include/sam.h:29,
                 from bamfile.h:5,
                 from idxstats.c:1:
idxstats.c: In function ‘idxstats_bamfile’:
/usr/lib/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
      |                                ^~~~~~~~~~~~~~~~~~~~~~~
idxstats.c:20:12: note: in expansion of macro ‘bam_seek’
   20 |     (void) bam_seek(fp, 0, 0);
      |            ^~~~~~~~
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c io_sam.c -o io_sam.o
In file included from /usr/lib/R/library/Rhtslib/include/sam.h:29,
                 from io_sam.c:2:
io_sam.c: In function ‘_scan_bam_all’:
/usr/lib/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
      |                                ^~~~~~~~~~~~~~~~~~~~~~~
io_sam.c:304:12: note: in expansion of macro ‘bam_seek’
  304 |     (void) bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
      |            ^~~~~~~~
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c pileup.cpp -o pileup.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c pileupbam.c -o pileupbam.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c sam.c -o sam.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c sam_opts.c -o sam_opts.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c sam_utils.c -o sam_utils.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c samtools_patch.c -o samtools_patch.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c scan_bam_data.c -o scan_bam_data.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c tabixfile.c -o tabixfile.o
tabixfile.c: In function ‘index_tabix’:
tabixfile.c:190:5: warning: ‘bgzf_is_bgzf’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
  190 |     if (bgzf_is_bgzf(fn) != 1)
      |     ^~
In file included from tabixfile.c:3:
/usr/lib/R/library/Rhtslib/include/htslib/bgzf.h:243:9: note: declared here
  243 |     int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
      |         ^~~~~~~~~~~~
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c tagfilter.c -o tagfilter.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c utilities.c -o utilities.o
gcc -I"/usr/include/R/" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/R/library/Biostrings/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c zip_compression.c -o zip_compression.o
g++ -std=gnu++14 -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o Rsamtools.so Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o /usr/lib/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/usr/lib64/R/lib -lR
/usr/bin/ld: cannot find /usr/lib/R/library/Rhtslib/usrlib/libhts.a: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R//make/shlib.mk:10: Rsamtools.so] Error 1
ERROR: compilation failed for package ‘Rsamtools’
* removing ‘/build/r-rsamtools/src/Rsamtools’
* restoring previous ‘/build/r-rsamtools/src/Rsamtools’
�[1m�[31m==> ERROR:�(B�[m�[1m A failure occurred in build().�(B�[m
�[1m    Aborting...�(B�[m
==> ERROR: Build failed, check /var/lib/archbuild/extra-x86_64/guoyi/build
----In extra-x86_64----
�[1;32mClean up copy: guoyi...done�[1;0m

----In multilib-x86_64----

[I 12-23 15:57:12.533 lilac:243] build (version None) finished in 43s with result: <BuildResult.failed: CalledProcessError(255, ['env', 'GNUPGHOME=/home/guoyi/.lilac/gnupg', 'extra-x86_64-build', '--', '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-futile.logger/r-futile.logger-1.4.3-1-any.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-snow/r-snow-0.4.4-1-any.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-genomeinfodb/r-genomeinfodb-1.30.0-1-any.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-biostrings/r-biostrings-2.62.0-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-biocparallel/r-biocparallel-1.28.3-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-rcurl/r-rcurl-1.98.1.5-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-xvector/r-xvector-0.34.0-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-formatr/r-formatr-1.11-1-any.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-s4vectors/r-s4vectors-0.32.3-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-rhtslib/r-rhtslib-1.26.0-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-biocgenerics/r-biocgenerics-0.40.0-1-any.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-zlibbioc/r-zlibbioc-1.40.0-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-iranges/r-iranges-2.28.0-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-bh/r-bh-1.78.0.0-1-any.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-crayon/r-crayon-1.4.2-1-any.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-bitops/r-bitops-1.0.7-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-genomeinfodbdata/r-genomeinfodbdata-1.2.7-1-any.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-futile.options/r-futile.options-1.0.1-1-any.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-genomicranges/r-genomicranges-1.46.1-1-x86_64.pkg.tar.zst'), '-I', PosixPath('/home/guoyi/Packages/BioArchLinux/r-lambda.r/r-lambda.r-1.2.4-1-any.pkg.tar.zst'), '-d', '/home/guoyi/go:/build/go', '-d', '/home/guoyi/.cargo:/build/.cargo', '-d', '/home/guoyi/.cache/pip:/build/.cache/pip', '-d', '/home/guoyi/.cache/go-build:/build/.cache/go-build', '-d', '/home/guoyi/.cache/archbuild-bind-cache/stack:/build/.stack', '-d', '/home/guoyi/.cache/archbuild-bind-cache:/build/.cache', '--', '--noprogressbar', '--holdver'])>

splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM<unsigned int>&, const EList<ALT<unsigned int> >&)’:
splice_site.cpp:717:59: warning: ‘?:’ using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context]
  717 |             exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC);
      |                                                 ~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from edit.h:29,
                 from splice_site.cpp:20:
ds.h: In instantiation of ‘void EList<T, S>::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’:
splice_site.cpp:722:31:   required from here
ds.h:663:28: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  663 |                 std::memcpy(list_ + cur_, l, bytes);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from edit.h:30,
                 from splice_site.cpp:20:
splice_site.h:377:7: note: ‘class Exon’ declared here
  377 | class Exon {
      |       ^~~~
ERROR: compilation failed for package ‘Rhisat2’
* removing ‘/build/r-rhisat2/src/Rhisat2’
* restoring previous ‘/build/r-rhisat2/src/Rhisat2’
==> ERROR: A failure occurred in build().
    Aborting...

==> Retrieving sources...
  -> Found CGEN_3.30.0.tar.gz
==> WARNING: Skipping all source file integrity checks.
==> Extracting sources...
  -> Extracting CGEN_3.30.0.tar.gz with bsdtar
==> Starting build()...
* installing *source* package ‘CGEN’ ...
** using staged installation
** libs
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c Additive.c -o Additive.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c CML.c -o CML.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c ccl.c -o ccl.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2  -c csclust.f -o csclust.o
csclust.f:72:72:

   72 |  10      FLAG(I)=.TRUE.
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c fsclust.c -o fsclust.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c hcl.c -o hcl.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c pmatch.c -o pmatch.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c score.c -o score.o
gcc -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -lgfortran -lm -lquadmath -L/usr/lib64/R/lib -lR
/usr/bin/ld: hcl.o:(.bss+0x0): multiple definition of `h_done'; ccl.o:(.bss+0x0): first defined here
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R//make/shlib.mk:10: CGEN.so] Error 1
ERROR: compilation failed for package ‘CGEN’
* removing ‘/build/r-cgen/src/CGEN’
* restoring previous ‘/build/r-cgen/src/CGEN’

/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, -1, 1> >’
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1> >’
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7:   required from ‘class Eigen::Matrix<double, -1, 1>’
/usr/lib/R/library/RcppEigen/include/Eigen/src/QR/ColPivHouseholderQR.h:68:124:   required from ‘class Eigen::ColPivHouseholderQR<Eigen::Matrix<double, -1, -1> >’
interp.h:25:15:   required from here
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 1, -1>, 0>’:
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 1, -1>, 1>’
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 1, -1>, 3>’
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<double, 1, -1> >’
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, 1, -1> >’
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, 1, -1> >’
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7:   required from ‘class Eigen::Matrix<double, 1, -1>’
/usr/lib/R/library/RcppEigen/include/Eigen/src/QR/ColPivHouseholderQR.h:438:19:   required from ‘class Eigen::ColPivHouseholderQR<Eigen::Matrix<double, -1, -1> >’
interp.h:25:15:   required from here
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
ERROR: compilation failed for package ‘interp’
* removing ‘/build/r-interp/src/interp’
* restoring previous ‘/build/r-interp/src/interp’

** package ‘rJava’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... 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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... 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... yes
checking for sys/wait.h that is POSIX.1 compatible... 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 for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether gcc supports static inline...
yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver    : '/usr/bin/jar'
compiler    : '/usr/bin/javac'
header prep.: ''
cpp flags   : '-I/usr/lib/jvm/java-17-openjdk/include -I/usr/lib/jvm/java-17-openjdk/include/linux'
java libs   : '-L/usr/lib/jvm/java-17-openjdk/lib/server -ljvm'
checking whether Java run-time works... ./configure: line 3796: /usr/bin/java: Not a directory
no
configure: error: Java interpreter '/usr/bin/java' does not work

building pxstrec
g++ -o "pxstrec" -O3 -std=c++14 -fopenmp -Wall -DOMP -ffast-math -ftree-vectorize main_strec.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o  -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo # -lgfortran
cat man/pxstrec.1.in > man/pxstrec.1
�[1m�[32m==>�(B�[m�[1m Starting check()...�(B�[m
python3 run_tests.py
make: python3: No such file or directory
make: *** [Makefile:655: check] Error 127
�[1m�[31m==> ERROR:�(B�[m�[1m A failure occurred in check().�(B�[m
�[1m    Aborting...�(B�[m

                  -`                     root@bioarchlinux
                 .o+`                    -----------------
                `ooo/                    OS: Arch Linux [x86_64]
               `+oooo:                   Host: X10SLL-F 0123456789
              `+oooooo:                  Kernel: 5.15.43-1-lts
              -+oooooo+:                 Uptime: 28 mins
            `/:-:++oooo+:                Packages: 309 (pacman)
           `/++++/+++++++:               Shell: bash 5.1.16
          `/++++++++++++++:              Resolution: 1024x768
         `/+++ooooooooooooo/`            Terminal: /dev/pts/0
        ./ooosssso++osssssso+`           CPU: Intel Xeon E3-1230 v3 (8) @ 3.7Gz
       .oossssso-````/ossssss+`          GPU: ASPEED Technology, Inc. ASPEED Gy
      -osssssso.      :ssssssso.         Memory: 1598MiB / 15962MiB (10%)
     :osssssss/        osssso+++.        Disk (/): 52GB / 218GB (23%)
    /ossssssss/        +ssssooo/-        Locale: en_US.UTF-8
  `/ossssso+/:-        -:/+osssso+-      
 `+sso+:-`                 `.-/+oso:     ████████████████████████
`++:.                           `-/+/    ████████████████████████
.`                                 `/    

[put the output here](https://log.bioarchlinux.org/2022-04-28T16%3A00%3A12/r-bloodgen3module.log#:~:text=**%20byte%2Dcompile%20and,dyn.load%0AExecution%20halted)

==> Starting build()...
* installing *source* package ‘mfa’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG  -I'/usr/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG  -I'/usr/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c gibbs.cpp -o gibbs.o
gibbs.cpp: In function ‘double log_d_norm(double, double, double)’:
gibbs.cpp:13:31: error: ‘PI’ was not declared in this scope
   13 |   double ldn = -0.5 * log(2 * PI);
      |                               ^~
make: *** [/usr/lib64/R/etc/Makeconf:177: gibbs.o] Error 1
make: *** Waiting for unfinished jobs....
ERROR: compilation failed for package ‘mfa’
* removing ‘/build/r-mfa/src/mfa’
* restoring previous ‘/build/r-mfa/src/mfa’
==> ERROR: A failure occurred in build().
    Aborting...
==> ERROR: Build failed, check /var/lib/archbuild/BioArchLinux-x86_64/bio/build

gcc -I"/usr/include/R/" -DNDEBUG  -I'/usr/lib/R/library/RcppEigen/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c Rgin-init.c -o Rgin-init.o
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG  -I'/usr/lib/R/library/RcppEigen/include' -D_FORTIFY_SOURCE=2  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/usr/lib64/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c src/feature_selection/feature_selector.cc -o src/feature_selection/feature_selector.o
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG  -I'/usr/lib/R/library/RcppEigen/include' -D_FORTIFY_SOURCE=2  -std=c++11 -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/usr/lib64/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c src/feature_selection/scones.cc -o src/feature_selection/scones.o
In file included from ./include/gin/feature_selection/scones.h:8,
                 from src/feature_selection/feature_selector.cc:9:
./include/gin/globals.h:60:10: fatal error: Rcpp.h: No such file or directory
   60 | #include "Rcpp.h"
      |          ^~~~~~~~
compilation terminated.
In file included from ./include/gin/feature_selection/scones.h:8,
                 from src/feature_selection/scones.cc:5:
./include/gin/globals.h:60:10: fatal error: Rcpp.h: No such file or directory
   60 | #include "Rcpp.h"
      |          ^~~~~~~~
compilation terminated.
make: *** [/usr/lib64/R/etc/Makeconf:175: src/feature_selection/feature_selector.o] Error 1
make: *** Waiting for unfinished jobs....
make: *** [/usr/lib64/R/etc/Makeconf:175: src/feature_selection/scones.o] Error 1

➜  r-party git:(main) ✗ yay -S r-mass
[sudo] password for sukanka: 
resolving dependencies...
looking for conflicting packages...

Packages (1) r-mass-7.3.57-1

Total Installed Size:  1.31 MiB

:: Proceed with installation? [Y/n] 
(1/1) checking keys in keyring                                                                [######################################################] 100%
(1/1) checking package integrity                                                              [######################################################] 100%
(1/1) loading package files                                                                   [######################################################] 100%
(1/1) checking for file conflicts                                                             [######################################################] 100%
error: failed to commit transaction (conflicting files)
r-mass: /usr/lib/R/library/MASS/CITATION exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/DESCRIPTION exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/INDEX exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/Meta/Rd.rds exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/Meta/data.rds exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/Meta/features.rds exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/Meta/hsearch.rds exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/Meta/links.rds exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/Meta/nsInfo.rds exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/Meta/package.rds exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/NAMESPACE exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/NEWS exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/R/MASS exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/R/MASS.rdb exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/R/MASS.rdx exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/data/Rdata.rdb exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/data/Rdata.rds exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/data/Rdata.rdx exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/help/AnIndex exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/help/MASS.rdb exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/help/MASS.rdx exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/help/aliases.rds exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/help/paths.rds exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/html/00Index.html exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/html/R.css exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/libs/MASS.so exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/po/de/LC_MESSAGES/R-MASS.mo exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/po/en@quot/LC_MESSAGES/R-MASS.mo exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/po/fr/LC_MESSAGES/R-MASS.mo exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/po/it/LC_MESSAGES/R-MASS.mo exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/po/ko/LC_MESSAGES/R-MASS.mo exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/po/pl/LC_MESSAGES/R-MASS.mo exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/scripts/ch01.R exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/scripts/ch02.R exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/scripts/ch03.R exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/scripts/ch04.R exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/scripts/ch05.R exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/scripts/ch06.R exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/scripts/ch07.R exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/scripts/ch08.R exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/scripts/ch09.R exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/scripts/ch10.R exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/scripts/ch11.R exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/scripts/ch12.R exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/scripts/ch13.R exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/scripts/ch14.R exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/scripts/ch15.R exists in filesystem (owned by r)
r-mass: /usr/lib/R/library/MASS/scripts/ch16.R exists in filesystem (owned by r)
Errors occurred, no packages were upgraded.

* installing *source* package ‘interactiveDisplay’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Installing package into ‘/build/r-interactivedisplay/src/00LOCK-interactiveDisplay/00new’
(as ‘lib’ is unspecified)
Error in contrib.url(repos, type) : 
  trying to use CRAN without setting a mirror
Error: unable to load R code in package ‘interactiveDisplay’
Execution halted
ERROR: lazy loading failed for package ‘interactiveDisplay’
* removing ‘/build/r-interactivedisplay/src/interactiveDisplay’
* restoring previous ‘/build/r-interactivedisplay/src/interactiveDisplay’
==> ERROR: A failure occurred in build().
    Aborting...

Compile the main source files and create the MPI-parallel executable
make[1]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
make[1]: Entering directory '/build/migrate-n-mpi/src/migrate-5.0.2/src'
/bin/sh: line 1: .: showgit.sh: file not found
make[1]: Leaving directory '/build/migrate-n-mpi/src/migrate-5.0.2/src'
make[1]: Entering directory '/build/migrate-n-mpi/src/migrate-5.0.2/src'
src/sighandler.c:325:1: warning: ‘analyzer_noreturn’ attribute directive ignored [-Wattributes]
  325 | {
      | ^
src/hermite_interpoly.c:54:10: fatal error: mittag_leffler_interpol_data.h: No such file or directory
   54 | #include "mittag_leffler_interpol_data.h"
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[1]: *** [Makefile:187: hermite_interpoly.o] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: Leaving directory '/build/migrate-n-mpi/src/migrate-5.0.2/src'
make: *** [Makefile:251: mpis] Error 2

In file included from ChemmineOB.cpp:1569:
/usr/include/openbabel3/openbabel/obutil.h: In member function ‘void OpenBabel::OBStopwatch::Start()’:
/usr/include/openbabel3/openbabel/obutil.h:65:14: error: ‘clock’ was not declared in this scope
   65 |       start= clock();
      |              ^~~~~

you forget to ‘#include <cstddef>’?
class_Cache_block.h:14:23: error: expected ‘)’ before ‘size’
   14 |     Cache_block(size_t size);
      |                ~      ^~~~~
      |                       )
class_Cache_block.h:21:5: error: ‘size_t’ does not name a type
   21 |     size_t use_count() const;
      |     ^~~~~~
class_Cache_block.h:21:5: note: ‘size_t’ is defined in header ‘<cstddef>’; did you forget to ‘#include <cstddef>’?
class_Cache_block.h:23:5: error: ‘size_t’ does not name a type
   23 |     size_t get_size() const;
      |     ^~~~~~
class_Cache_block.h:23:5: note: ‘size_t’ is defined in header ‘<cstddef>’; did you forget to ‘#include <cstddef>’?
class_Cache_block.h:27:5: error: ‘size_t’ does not name a type
   27 |     size_t get_serialize_size() const;
      |     ^~~~~~
class_Cache_block.h:27:5: note: ‘size_t’ is defined in header ‘<cstddef>’; did you forget to ‘#include <cstddef>’?
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG `pkg-config fuse --cflags` -I'/usr/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c class_Memory_mapped.cpp -o class_Memory_mapped.o
g++ -std=gnu++11 -I"/usr/include/R/" -DNDEBUG `pkg-config fuse --cflags` -I'/usr/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c class_Protect_guard.cpp -o class_Protect_guard.o
class_Filesystem_file_data.cpp: In member function ‘size_t Filesystem_file_data::get_serialize_size()’:
class_Filesystem_file_data.cpp:70:26: error: ‘const class Cache_block’ has no member named ‘get_serialize_size’
   70 |         size += i.second.get_serialize_size();
      |                          ^~~~~~~~~~~~~~~~~~
class_Filesystem_file_data.cpp: In member function ‘void Filesystem_file_data::serialize(void*)’:
class_Filesystem_file_data.cpp:92:39: error: ‘const class Cache_block’ has no member named ‘get_serialize_size’
   92 |         size_t buffer_size = i.second.get_serialize_size();
      |                                       ^~~~~~~~~~~~~~~~~~
class_Filesystem_file_data.cpp: In member function ‘void Filesystem_cache_index_iterator::compute_block_info()’:
class_Filesystem_file_data.cpp:177:39: error: ‘class Cache_block’ has no member named ‘get_size’
  177 |     block_length = block_iter->second.get_size() / type_size;
      |                                       ^~~~~~~~
make: *** [/usr/lib64/R/etc/Makeconf:177: class_Filesystem_file_data.o] Error 1
make: *** Waiting for unfinished jobs....
ERROR: compilation failed for package ‘Travel’

                 from /usr/lib/R/library/bigmemory/include/bigmemory/MatrixAccessor.hpp:4,
                 from Stage_4_InteractionsSubFunctions.cpp:4:
/usr/lib/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/usr/lib/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  614 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/11.1.0/bits/locale_conv.h:41,
                 from /usr/include/c++/11.1.0/locale:43,
                 from /usr/include/c++/11.1.0/iomanip:43,
                 from /usr/lib/R/library/Rcpp/include/RcppCommon.h:53,
                 from /usr/lib/R/library/Rcpp/include/Rcpp.h:27,
                 from Stage_4_InteractionsSubFunctions.cpp:1:
/usr/include/c++/11.1.0/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
ERROR: compilation failed for package ‘MACPET’
* removing ‘/build/r-macpet/src/MACPET’
* restoring previous ‘/build/r-macpet/src/MACPET’
==> ERROR: A failure occurred in build().
    Aborting...
==> ERROR: Build failed, check /var/lib/archbuild/extra-x86_64/bio/build

Error: package or namespace load failed for ‘Rsamtools’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/build/r-rsamtools/src/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so':
  /build/r-rsamtools/src/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so: undefined symbol: hts_open_format
Error: loading failed
Execution halted
ERROR: loading failed

put the output here

* installing *source* package ‘affyPara’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Warning message:
no DISPLAY variable so Tk is not available 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: no DISPLAY variable so Tk is not available
Error: package or namespace load failed for ‘affyPara’:
 .onLoad failed in loadNamespace() for 'affyPara', details:
  call: assign(".affyParaInternalEnv", .affyParaInternalEnv, envir = topenv(parent.frame()))
  error: cannot add binding of '.affyParaInternalEnv' to the base environment
Error: loading failed
Execution halted
ERROR: loading failed

➜  ~ yay -S bioarchlinux-keyring
[sudo] sukanka 的密码：
对不起，请重试。
[sudo] sukanka 的密码：
警告：bioarchlinux-keyring-20220422-2 已经为最新 -- 重新安装
正在解析依赖关系...
正在查找软件包冲突...

软件包 (1) bioarchlinux-keyring-20220422-2

全部安装大小：  0.00 MiB
净更新大小：    0.00 MiB

:: 进行安装吗？ [Y/n] 
(1/1) 正在检查密钥环里的密钥                                                                               [################################################################] 100%
(1/1) 正在检查软件包完整性                                                                                 [################################################################] 100%
错误：bioarchlinux-keyring: 来自 "Guoyi Zhang <[email protected]>" 的签名是未知信任的
:: 文件 /var/cache/pacman/pkg/bioarchlinux-keyring-20220422-2-any.pkg.tar.zst 已损坏 (无效或已损坏的软件包 (PGP 签名)).
打算删除吗？ [Y/n] 

➜  ~ yay -S bioarchlinux-keyring
正在解析依赖关系...
正在查找软件包冲突...

软件包 (1) bioarchlinux-keyring-20220422-2

下载大小：      0.00 MiB
全部安装大小：  0.00 MiB

:: 进行安装吗？ [Y/n] 
:: 正在获取软件包......
 bioarchlinux-keyring-20220422-2-any                                                                                    4.5 KiB  11.7 KiB/s 00:00 [#########################################################################################] 100%
(1/1) 正在检查密钥环里的密钥                                                                                                                      [#########################################################################################] 100%
(1/1) 正在检查软件包完整性                                                                                                                        [#########################################################################################] 100%
(1/1) 正在加载软件包文件                                                                                                                          [#########################################################################################] 100%
(1/1) 正在检查文件冲突                                                                                                                            [#########################################################################################] 100%
(1/1) 正在检查可用存储空间                                                                                                                        [#########################################################################################] 100%
:: 正在处理软件包的变化...
(1/1) 正在安装 bioarchlinux-keyring                                                                                                               [#########################################################################################] 100%
pub   rsa3072 2021-08-09 [SC]
      0E0F97FB6684B82146D326AEB1F96021DB62254D
uid             [ 未知 ] Guoyi Zhang <[email protected]>
sub   rsa3072 2021-08-09 [E]

➜  ~ yay -S r-stringi                                             
警告：r-stringi-1.7.6-9 已经为最新 -- 重新安装
正在解析依赖关系...
正在查找软件包冲突...

软件包 (1) r-stringi-1.7.6-9

下载大小：      0.78 MiB
全部安装大小：  1.32 MiB
净更新大小：    0.00 MiB

:: 进行安装吗？ [Y/n] 
:: 正在获取软件包......
r-stringi-1.7.6-9-x86_64                                                      800.1 KiB  1865 KiB/s 00:00 [################################################################] 100%
(1/1) 正在检查密钥环里的密钥                                                                               [################################################################] 100%
(1/1) 正在检查软件包完整性                                                                                 [################################################################] 100%
错误：r-stringi: 来自 "Guoyi Zhang <[email protected]>" 的签名是未知信任的
:: 文件 /var/cache/pacman/pkg/r-stringi-1.7.6-9-x86_64.pkg.tar.zst 已损坏 (无效或已损坏的软件包 (PGP 签名)).
打算删除吗？ [Y/n] 

* installing *source* package ‘tenXplore’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: class "RESTfulSummarizedExperiment" is not exported by 'namespace:restfulSE'
Execution halted
ERROR: lazy loading failed for package ‘tenXplore’
* removing ‘/build/r-tenxplore/src/tenXplore’
* restoring previous ‘/build/r-tenxplore/src/tenXplore’

 g++ -DHAVE_CONFIG_H -I. -I. -D_FORTIFY_SOURCE=2 -w -g -O2 -DCOINUTILS_BUILD -c CoinSnapshot.cpp  -fPIC -DPIC -o CoinSnapshot.o
/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I`echo .`   -D_FORTIFY_SOURCE=2  -w -g -O2   -DCOINUTILS_BUILD -c -o CoinWarmStartBasis.lo CoinWarmStartBasis.cpp
 g++ -DHAVE_CONFIG_H -I. -I. -D_FORTIFY_SOURCE=2 -w -g -O2 -DCOINUTILS_BUILD -c CoinWarmStartBasis.cpp  -fPIC -DPIC -o CoinWarmStartBasis.o
/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I`echo .`   -D_FORTIFY_SOURCE=2  -w -g -O2   -DCOINUTILS_BUILD -c -o CoinWarmStartVector.lo CoinWarmStartVector.cpp
 g++ -DHAVE_CONFIG_H -I. -I. -D_FORTIFY_SOURCE=2 -w -g -O2 -DCOINUTILS_BUILD -c CoinWarmStartVector.cpp  -fPIC -DPIC -o CoinWarmStartVector.o
/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I`echo .`   -D_FORTIFY_SOURCE=2  -w -g -O2   -DCOINUTILS_BUILD -c -o CoinWarmStartDual.lo CoinWarmStartDual.cpp
 g++ -DHAVE_CONFIG_H -I. -I. -D_FORTIFY_SOURCE=2 -w -g -O2 -DCOINUTILS_BUILD -c CoinWarmStartDual.cpp  -fPIC -DPIC -o CoinWarmStartDual.o
/bin/sh ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I`echo .`   -D_FORTIFY_SOURCE=2  -w -g -O2   -DCOINUTILS_BUILD -c -o CoinWarmStartPrimalDual.lo CoinWarmStartPrimalDual.cpp
 g++ -DHAVE_CONFIG_H -I. -I. -D_FORTIFY_SOURCE=2 -w -g -O2 -DCOINUTILS_BUILD -c CoinWarmStartPrimalDual.cpp  -fPIC -DPIC -o CoinWarmStartPrimalDual.o
/bin/sh ../../libtool --tag=CXX --mode=link g++  -w -g -O2   -DCOINUTILS_BUILD  -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o libCoinUtils.la -rpath /tmp/Rtmprhkc3h/R.INSTALL409469cff59/lpsymphony/src/SYMPHONY/lib -no-undefined -version-info 13:6:10 CoinAlloc.lo CoinBuild.lo CoinDenseVector.lo CoinError.lo CoinFactorization1.lo CoinFactorization2.lo CoinFactorization3.lo CoinFactorization4.lo CoinSimpFactorization.lo CoinDenseFactorization.lo CoinOslFactorization.lo CoinOslFactorization2.lo CoinOslFactorization3.lo CoinFileIO.lo CoinFinite.lo CoinIndexedVector.lo CoinLpIO.lo CoinMessage.lo CoinMessageHandler.lo CoinModel.lo CoinStructuredModel.lo CoinModelUseful.lo CoinModelUseful2.lo CoinMpsIO.lo CoinPackedMatrix.lo CoinPackedVector.lo CoinPackedVectorBase.lo CoinParam.lo CoinParamUtils.lo CoinPostsolveMatrix.lo CoinPrePostsolveMatrix.lo CoinPresolveDoubleton.lo CoinPresolveDual.lo CoinPresolveDupcol.lo CoinPresolveEmpty.lo CoinPresolveFixed.lo CoinPresolveForcing.lo CoinPresolveHelperFunctions.lo CoinPresolveImpliedFree.lo CoinPresolveIsolated.lo CoinPresolveMatrix.lo CoinPresolvePsdebug.lo CoinPresolveMonitor.lo CoinPresolveSingleton.lo CoinPresolveSubst.lo CoinPresolveTighten.lo CoinPresolveTripleton.lo CoinPresolveUseless.lo CoinPresolveZeros.lo CoinRational.lo CoinSearchTree.lo CoinShallowPackedVector.lo CoinSnapshot.lo CoinWarmStartBasis.lo CoinWarmStartVector.lo CoinWarmStartDual.lo CoinWarmStartPrimalDual.lo -lm  
mkdir .libs
ar cru .libs/libCoinUtils.a  CoinAlloc.o CoinBuild.o CoinDenseVector.o CoinError.o CoinFactorization1.o CoinFactorization2.o CoinFactorization3.o CoinFactorization4.o CoinSimpFactorization.o CoinDenseFactorization.o CoinOslFactorization.o CoinOslFactorization2.o CoinOslFactorization3.o CoinFileIO.o CoinFinite.o CoinIndexedVector.o CoinLpIO.o CoinMessage.o CoinMessageHandler.o CoinModel.o CoinStructuredModel.o CoinModelUseful.o CoinModelUseful2.o CoinMpsIO.o CoinPackedMatrix.o CoinPackedVector.o CoinPackedVectorBase.o CoinParam.o CoinParamUtils.o CoinPostsolveMatrix.o CoinPrePostsolveMatrix.o CoinPresolveDoubleton.o CoinPresolveDual.o CoinPresolveDupcol.o CoinPresolveEmpty.o CoinPresolveFixed.o CoinPresolveForcing.o CoinPresolveHelperFunctions.o CoinPresolveImpliedFree.o CoinPresolveIsolated.o CoinPresolveMatrix.o CoinPresolvePsdebug.o CoinPresolveMonitor.o CoinPresolveSingleton.o CoinPresolveSubst.o CoinPresolveTighten.o CoinPresolveTripleton.o CoinPresolveUseless.o CoinPresolveZeros.o CoinRational.o CoinSearchTree.o CoinShallowPackedVector.o CoinSnapshot.o CoinWarmStartBasis.o CoinWarmStartVector.o CoinWarmStartDual.o CoinWarmStartPrimalDual.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib .libs/libCoinUtils.a
creating libCoinUtils.la
(cd .libs && rm -f libCoinUtils.la && ln -s ../libCoinUtils.la libCoinUtils.la)
make[4]: Leaving directory '/tmp/Rtmprhkc3h/R.INSTALL409469cff59/lpsymphony/src/SYMPHONY/CoinUtils/src'
make[3]: Leaving directory '/tmp/Rtmprhkc3h/R.INSTALL409469cff59/lpsymphony/src/SYMPHONY/CoinUtils/src'
make[3]: Entering directory '/tmp/Rtmprhkc3h/R.INSTALL409469cff59/lpsymphony/src/SYMPHONY/CoinUtils'
make[3]: Nothing to be done for 'all-am'.
make[3]: Leaving directory '/tmp/Rtmprhkc3h/R.INSTALL409469cff59/lpsymphony/src/SYMPHONY/CoinUtils'
make[2]: Leaving directory '/tmp/Rtmprhkc3h/R.INSTALL409469cff59/lpsymphony/src/SYMPHONY/CoinUtils'
Making all in Osi
make[2]: Entering directory '/tmp/Rtmprhkc3h/R.INSTALL409469cff59/lpsymphony/src/SYMPHONY/Osi'
Making all in src/Osi
make[3]: Entering directory '/tmp/Rtmprhkc3h/R.INSTALL409469cff59/lpsymphony/src/SYMPHONY/Osi/src/Osi'
make  all-am
make[4]: Entering directory '/tmp/Rtmprhkc3h/R.INSTALL409469cff59/lpsymphony/src/SYMPHONY/Osi/src/Osi'
/bin/sh ../../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I`echo .`  -I/tmp/RtmprwBDNn/Rbuild12daa92b38f71c/lpsymphony/src/SYMPHONY/include/coin  -D_FORTIFY_SOURCE=2  -w -g -O2   -DOSI_BUILD -c -o OsiAuxInfo.lo OsiAuxInfo.cpp
 g++ -DHAVE_CONFIG_H -I. -I. -I/tmp/RtmprwBDNn/Rbuild12daa92b38f71c/lpsymphony/src/SYMPHONY/include/coin -D_FORTIFY_SOURCE=2 -w -g -O2 -DOSI_BUILD -c OsiAuxInfo.cpp  -fPIC -DPIC -o OsiAuxInfo.o
OsiAuxInfo.cpp:10:10: fatal error: CoinPragma.hpp: No such file or directory
   10 | #include "CoinPragma.hpp"
      |          ^~~~~~~~~~~~~~~~
compilation terminated.
make[4]: *** [Makefile:535: OsiAuxInfo.lo] Error 1
make[4]: Leaving directory '/tmp/Rtmprhkc3h/R.INSTALL409469cff59/lpsymphony/src/SYMPHONY/Osi/src/Osi'
make[3]: *** [Makefile:407: all] Error 2
make[3]: Leaving directory '/tmp/Rtmprhkc3h/R.INSTALL409469cff59/lpsymphony/src/SYMPHONY/Osi/src/Osi'
make[2]: *** [Makefile:532: all-recursive] Error 1
make[2]: Leaving directory '/tmp/Rtmprhkc3h/R.INSTALL409469cff59/lpsymphony/src/SYMPHONY/Osi'
make[1]: *** [Makefile:324: all-recursive] Error 1
make[1]: Leaving directory '/tmp/Rtmprhkc3h/R.INSTALL409469cff59/lpsymphony/src/SYMPHONY'
make: *** [Makevars:13: SYMPHONY.ts] Error 2
ERROR: compilation failed for package ‘lpsymphony’

==> Starting build()...
* installing *source* package ‘gpart’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG  -I'/usr/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG  -I'/usr/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c gpart_cpp.cpp -o gpart_cpp.o
gpart_cpp.cpp: In function ‘uint32_t cubic_real_roots(double, double, double, Rcpp::NumericVector)’:
gpart_cpp.cpp:622:42: error: ‘PI’ was not declared in this scope
  622 |     solutions[1] = sq * cos(dxx + (2.0 * PI / 3.0)) - adiv3;
      |                                          ^~
make: *** [/usr/lib64/R/etc/Makeconf:177: gpart_cpp.o] Error 1
make: *** Waiting for unfinished jobs....
ERROR: compilation failed for package ‘gpart’
* removing ‘/build/r-gpart/src/gpart’
* restoring previous ‘/build/r-gpart/src/gpart’
==> ERROR: A failure occurred in build().
    Aborting...

g++ -std=gnu++14 -I"/usr/include/R/" -DNDEBUG  -I'/usr/lib/R/library/Rcpp/include' -I'/usr/lib/R/library/BH/include' -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -flto=auto  -c Tests/Core/test-SquareLattice.cpp -o Tests/Core/test-SquareLattice.o
In file included from /usr/include/signal.h:328,
                 from Tests/catch.h:6450,
                 from test-runner.cpp:2:
Tests/catch.h:6473:33: error: size of array ‘altStackMem’ is not an integral constant-expression
 6473 |         static char altStackMem[SIGSTKSZ];
      |                                 ^~~~~~~~
Tests/catch.h:6524:45: error: size of array ‘altStackMem’ is not an integral constant-expression
 6524 |     char FatalConditionHandler::altStackMem[SIGSTKSZ] = {};
      |                                             ^~~~~~~~
make: *** [/usr/lib64/R/etc/Makeconf:177: test-runner.o] Error 1
ERROR: compilation failed for package ‘CancerInSilico’
* removing ‘/build/r-cancerinsilico/src/CancerInSilico’
* restoring previous ‘/build/r-cancerinsilico/src/CancerInSilico’

fastBMA.hpp:1408:211: error: ‘max_iter’ was not declared in this scope
 1408 |                 Result r2 = boost::math::tools::brent_find_minima(BMAoptimizeFunction<T>(ATA,nVars,nRows,nCols,pord,ATb,sst,btb,postProbs,parents,&npostProbs,logpriors,twoLogOR), (T) 1, (T)nRows, optimizeBits, max_iter);
      |                                                                                                                                                                                                                   ^~~~~~~~
make: *** [/usr/lib64/R/etc/Makeconf:177: fastBMAR.o] Error 1
ERROR: compilation failed for package ‘networkBMA’
* removing ‘/build/r-networkbma/src/networkBMA’
* restoring previous ‘/build/r-networkbma/src/networkBMA’
==> ERROR: A failure occurred in build().
    Aborting...
==> ERROR: Build failed, check /var/lib/archbuild/extra-x86_64/bio/build

  -> Extracting VegaMC_3.32.0.tar.gz with bsdtar
==> Starting build()...
* installing *source* package ‘VegaMC’ ...
** using staged installation
** libs
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c run_vegaMC.c -o run_vegaMC.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c sort_data.c -o sort_data.o
gcc -I"/usr/include/R/" -DNDEBUG   -D_FORTIFY_SOURCE=2   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt  -c vegaMC.c -o vegaMC.o
gcc -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o VegaMC.so run_vegaMC.o sort_data.o vegaMC.o -L/usr/lib64/R/lib -lR
/usr/bin/ld: sort_data.o:(.bss+0x20): multiple definition of `dataset'; run_vegaMC.o:(.bss+0xf8): first defined here
/usr/bin/ld: sort_data.o:(.bss+0x18): multiple definition of `output_file_name'; run_vegaMC.o:(.bss+0xf0): first defined here
/usr/bin/ld: vegaMC.o:(.bss+0xa0): multiple definition of `beta'; run_vegaMC.o:(.bss+0xec): first defined here
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R//make/shlib.mk:10: VegaMC.so] Error 1
ERROR: compilation failed for package ‘VegaMC’
* removing ‘/build/r-vegamc/src/VegaMC’
* restoring previous ‘/build/r-vegamc/src/VegaMC’
==> ERROR: A failure occurred in build().
    Aborting..

put the output here

put the output here

      | 
lto-wrapper: fatal error: write: No space left on device
compilation terminated.
/usr/bin/ld: error: lto-wrapper failed
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/iqtree2.dir/build.make:136: iqtree2] Error 1
make[1]: *** [CMakeFiles/Makefile2:535: CMakeFiles/iqtree2.dir/all] Error 2
make: *** [Makefile:156: all] Error 2

❯ LANG=en.US_UTF-8 pacman -Si tracer
Repository      : community
Name            : tracer
Version         : 0.7.8-2
Description     : OTracer finds outdated running applications in your system
Architecture    : any
URL             : http://tracer-package.com/
Licenses        : GPL
Groups          : None
Provides        : None
Depends On      : python  python-distro  python-psutil  python-six  dbus-python  pyalpm
Optional Deps   : None
Conflicts With  : None
Replaces        : None
Download Size   : 80.29 KiB
Installed Size  : 359.32 KiB
Packager        : Felix Yan <[email protected]>
Build Date      : Fri Dec 3 08:27:58 2021
Validated By    : MD5 Sum  SHA-256 Sum  Signature

Repository      : bioarchlinux
Name            : tracer
Version         : 1.7.2-4
Description     : Posterior summarisation in Bayesian phylogenetics.
                  https://doi.org/10.1093/sysbio/syy032
Architecture    : x86_64
URL             : https://github.com/beast-dev/tracer
Licenses        : unknown
Groups          : None
Provides        : None
Depends On      : java-runtime
Optional Deps   : None
Conflicts With  : None
Replaces        : None
Download Size   : 4.16 MiB
Installed Size  : 4.63 MiB
Packager        : starsareintherose (on behalf of starsareintherose)
                  <[email protected]>
Build Date      : Sun Jan 16 12:03:41 2022
Validated By    : MD5 Sum  SHA-256 Sum  Signature

* installing *source* package ‘puma’ ...
** using staged installation
** libs
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -flto  -c PMmultimgmos.c -o PMmultimgmos.o
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -flto  -c cregistration.c -o cregistration.o
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -flto  -c donlp2.c -o donlp2.o
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -flto  -c gme.c -o gme.o
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -flto  -c ipplr_c.c -o ipplr_c.o
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -flto  -c multimgmos.c -o multimgmos.o
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -flto  -c newx.c -o newx.o
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -flto  -c pplr_c.c -o pplr_c.o
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -flto  -c pumaclust_c.c -o pumaclust_c.o
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -flto  -c pumaclustii_c.c -o pumaclustii_c.o
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include   -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -flto  -c user_eval.c -o user_eval.o
gcc -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -flto -o puma.so PMmultimgmos.o cregistration.o donlp2.o gme.o ipplr_c.o multimgmos.o newx.o pplr_c.o pumaclust_c.o pumaclustii_c.o user_eval.o -L/usr/lib64/R/lib -lR
user_eval.c:69:13: error: variable ‘eval_extern’ redeclared as function
   69 |     void    eval_extern(IINTEGER mode);
      |             ^
donlp2.c:182:18: note: previously declared here
  182 | func_void_mode_t eval_extern;
      |                  ^
lto1: fatal error: errors during merging of translation units
compilation terminated.
lto-wrapper: fatal error: gcc returned 1 exit status
compilation terminated.
/usr/bin/ld: error: lto-wrapper failed
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R//make/shlib.mk:10: puma.so] Error 1
ERROR: compilation failed for package ‘puma’