############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL apeglm ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’ * installing *source* package ‘apeglm’ ... ** this is package ‘apeglm’ version ‘1.29.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppNumerical/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o In file included from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/Core:205, from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/Dense:1, from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/RcppEigenForward.h:28, from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/RcppEigen.h:25, from RcppExports.cpp:4: /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i; | ^ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b; | ^ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument ‘__m128’ [-Wignored-attributes] 49 | template<> struct is_arithmetic<__m128> { enum { value = true }; }; | ^ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes] 50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; }; | ^ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument ‘__m128d’ [-Wignored-attributes] 51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; }; | ^ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 222 | template<> struct unpacket_traits { | ^ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 228 | template<> struct unpacket_traits { | ^ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 1124 | ptranspose(PacketBlock& kernel) { | ^ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 1129 | ptranspose(PacketBlock& kernel) { | ^ In file included from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/Core:174: /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’ 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/Core:165: /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(4) float>::half’ {aka ‘__m128’} [-Wignored-attributes] /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ In file included from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/Core:271: /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet’: /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits >’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits >’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes] /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase, 0>’: /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase, 1>’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase, 3>’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase >’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase >’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase >’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase >’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ In file included from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/SparseCore:37, from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/Sparse:26, from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/RcppEigenForward.h:29: /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase >’: /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase >’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix’ /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ RcppExports.cpp:64:1: fatal error: error writing to /tmp/ccnVGngI.s: No space left on device 64 | } | ^ compilation terminated. make: *** [/home/rapidbuild/bbs-3.21-bioc-rapid/R/etc/Makeconf:202: RcppExports.o] Error 1 ERROR: compilation failed for package ‘apeglm’ * removing ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/apeglm’ * restoring previous ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/apeglm’