############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings EnrichmentBrowser_2.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/EnrichmentBrowser.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK * this is package ‘EnrichmentBrowser’ version ‘2.36.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘EnrichmentBrowser’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: 'pathview:::parseKGML2Graph2' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .getGOFromBiomart: no visible binding for global variable ‘go_linkage_type’ Undefined global functions or variables: go_linkage_type * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘EnrichmentBrowser-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: ebrowser > ### Title: Seamless navigation through enrichment analysis results > ### Aliases: ebrowser > > ### ** Examples > > > # expression data from file > exprs.file <- system.file("extdata/exprs.tab", package="EnrichmentBrowser") > cdat.file <- system.file("extdata/colData.tab", package="EnrichmentBrowser") > rdat.file <- system.file("extdata/rowData.tab", package="EnrichmentBrowser") > > # getting all human KEGG gene sets > # hsa.gs <- getGenesets(org="hsa", db="kegg") > gs.file <- system.file("extdata/hsa_kegg_gs.gmt", package="EnrichmentBrowser") > hsa.gs <- getGenesets(gs.file) > > # output destination > out.dir <- configEBrowser("OUTDIR.DEFAULT") > > # set-based enrichment analysis > ebrowser( meth="ora", perm=0, + exprs=exprs.file, cdat=cdat.file, rdat=rdat.file, + gs=hsa.gs, org="hsa", nr.show=3, + out.dir=out.dir, report.name="oraReport") Read expression data ... Normalize ... Excluding 211 genes not satisfying min.cpm threshold Corresponding software package not found: EDASeq Make sure that you have it installed. Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14) Installing package(s) 'BiocVersion', 'EDASeq' also installing the dependencies 'deldir', 'RcppEigen', 'jpeg', 'interp', 'pwalign', 'latticeExtra', 'ShortRead', 'aroma.light' trying URL 'https://cloud.r-project.org/src/contrib/deldir_2.0-4.tar.gz' Content type 'application/x-gzip' length 103621 bytes (101 KB) ================================================== downloaded 101 KB trying URL 'https://cloud.r-project.org/src/contrib/RcppEigen_0.3.4.0.2.tar.gz' Content type 'application/x-gzip' length 1761745 bytes (1.7 MB) ================================================== downloaded 1.7 MB trying URL 'https://cloud.r-project.org/src/contrib/jpeg_0.1-10.tar.gz' Content type 'application/x-gzip' length 18667 bytes (18 KB) ================================================== downloaded 18 KB trying URL 'https://cloud.r-project.org/src/contrib/interp_1.1-6.tar.gz' Content type 'application/x-gzip' length 1112116 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/pwalign_1.2.0.tar.gz' Content type 'application/x-gzip' length 355962 bytes (347 KB) ================================================== downloaded 347 KB trying URL 'https://cloud.r-project.org/src/contrib/latticeExtra_0.6-30.tar.gz' Content type 'application/x-gzip' length 1292936 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/ShortRead_1.64.0.tar.gz' Content type 'application/x-gzip' length 5321116 bytes (5.1 MB) ================================================== downloaded 5.1 MB trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/aroma.light_3.36.0.tar.gz' Content type 'application/x-gzip' length 393732 bytes (384 KB) ================================================== downloaded 384 KB trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/BiocVersion_3.20.0.tar.gz' Content type 'application/x-gzip' length 983 bytes ================================================== downloaded 983 bytes trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/EDASeq_2.40.0.tar.gz' Content type 'application/x-gzip' length 1191585 bytes (1.1 MB) ================================================== downloaded 1.1 MB * installing *source* package ‘deldir’ ... ** package ‘deldir’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ using Fortran compiler: ‘GNU Fortran (GCC) 10.3.1’ gfortran -fPIC -g -O2 -Wall -c acchk.f90 -o acchk.o gfortran -fPIC -g -O2 -Wall -c addpt.f90 -o addpt.o gfortran -fPIC -g -O2 -Wall -c adjchk.f90 -o adjchk.o gfortran -fPIC -g -O2 -Wall -c binsrt.f90 -o binsrt.o gfortran -fPIC -g -O2 -Wall -c circen.f90 -o circen.o gfortran -fPIC -g -O2 -Wall -c cross.f90 -o cross.o cross.f90:101:23: 101 | cprd = (a*d - b*c)/smin | ^ Warning: ‘smin’ may be used uninitialized in this function [-Wmaybe-uninitialized] gfortran -fPIC -g -O2 -Wall -c delet.f90 -o delet.o gfortran -fPIC -g -O2 -Wall -c delet1.f90 -o delet1.o gfortran -fPIC -g -O2 -Wall -c delout.f90 -o delout.o gfortran -fPIC -g -O2 -Wall -c delseg.f90 -o delseg.o gfortran -fPIC -g -O2 -Wall -c dirout.f90 -o dirout.o gfortran -fPIC -g -O2 -Wall -c dirseg.f90 -o dirseg.o gfortran -fPIC -g -O2 -Wall -c dldins.f90 -o dldins.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o gfortran -fPIC -g -O2 -Wall -c initad.f90 -o initad.o gfortran -fPIC -g -O2 -Wall -c insrt.f90 -o insrt.o gfortran -fPIC -g -O2 -Wall -c insrt1.f90 -o insrt1.o gfortran -fPIC -g -O2 -Wall -c intri.f90 -o intri.o gfortran -fPIC -g -O2 -Wall -c locn.f90 -o locn.o gfortran -fPIC -g -O2 -Wall -c master.f90 -o master.o gfortran -fPIC -g -O2 -Wall -c mnnd.f90 -o mnnd.o gfortran -fPIC -g -O2 -Wall -c pred.f90 -o pred.o gfortran -fPIC -g -O2 -Wall -c qtest.f90 -o qtest.o gfortran -fPIC -g -O2 -Wall -c qtest1.f90 -o qtest1.o gfortran -fPIC -g -O2 -Wall -c stoke.f90 -o stoke.o gfortran -fPIC -g -O2 -Wall -c succ.f90 -o succ.o gfortran -fPIC -g -O2 -Wall -c swap.f90 -o swap.o gfortran -fPIC -g -O2 -Wall -c testeq.f90 -o testeq.o gfortran -fPIC -g -O2 -Wall -c triar.f90 -o triar.o gfortran -fPIC -g -O2 -Wall -c trifnd.f90 -o trifnd.o gcc -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o deldir.so acchk.o addpt.o adjchk.o binsrt.o circen.o cross.o delet.o delet1.o delout.o delseg.o dirout.o dirseg.o dldins.o init.o initad.o insrt.o insrt1.o intri.o locn.o master.o mnnd.o pred.o qtest.o qtest1.o stoke.o succ.o swap.o testeq.o triar.o trifnd.o -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/00LOCK-deldir/00new/deldir/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (deldir) * installing *source* package ‘RcppEigen’ ... ** package ‘RcppEigen’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Rcpp/include' -I/usr/local/include -I../inst/include -fPIC -g -O2 -Wall -c RcppEigen.cpp -o RcppEigen.o In file included from ../inst/include/Eigen/Core:214, from ../inst/include/Eigen/Dense:1, from ../inst/include/RcppEigenForward.h:28, from ../inst/include/RcppEigen.h:25, from RcppEigen.cpp:22: ../inst/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::pload(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': ../inst/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/Eigen/Core:172: ../inst/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ ../inst/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::ploadu(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': ../inst/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Rcpp/include' -I/usr/local/include -I../inst/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o In file included from ../inst/include/Eigen/Core:214, from ../inst/include/Eigen/Dense:1, from ../inst/include/RcppEigenForward.h:28, from ../inst/include/RcppEigen.h:25, from RcppExports.cpp:4: ../inst/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::pload(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': ../inst/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/Eigen/Core:172: ../inst/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ ../inst/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::ploadu(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': ../inst/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Rcpp/include' -I/usr/local/include -I../inst/include -fPIC -g -O2 -Wall -c fastLm.cpp -o fastLm.o In file included from ../inst/include/Eigen/Core:214, from ../inst/include/Eigen/Dense:1, from ../inst/include/RcppEigenForward.h:28, from ../inst/include/RcppEigen.h:25, from fastLm.h:25, from fastLm.cpp:23: ../inst/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::pload(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': ../inst/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/Eigen/Core:172: ../inst/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ ../inst/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::ploadu(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': ../inst/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../inst/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/Eigen/Core:337: ../inst/include/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function 'static void Eigen::internal::selfadjoint_product_impl::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Block, -1, 1, false>; Lhs = Eigen::Block, -1, -1, false>; int LhsMode = 17; Rhs = Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Block, -1, 1, true>, -1, 1, false> >]': ../inst/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:229:7: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 227 | internal::selfadjoint_matrix_vector_product::Flags&RowMajorBit) ? RowMajor : ColMajor, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 228 | int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 229 | ( | ^ 230 | lhs.rows(), // size | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 231 | &lhs.coeffRef(0,0), lhs.outerStride(), // lhs info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 232 | actualRhsPtr, // rhs info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 | actualDestPtr, // result info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 | actualAlpha // scale factor | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 | ); | ~ ../inst/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:41:6: note: by argument 4 of type 'const double*' to 'static void Eigen::internal::selfadjoint_matrix_vector_product::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = double; Index = long int; int StorageOrder = 0; int UpLo = 1; bool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]' declared here 41 | void selfadjoint_matrix_vector_product::run( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/Eigen/Core:341: ../inst/include/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': ../inst/include/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ ../inst/include/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o RcppEigen.so RcppEigen.o RcppExports.o fastLm.o -lopenblas -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/00LOCK-RcppEigen/00new/RcppEigen/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RcppEigen) * installing *source* package ‘jpeg’ ... ** package ‘jpeg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c read.c -o read.o In file included from read.c:1: rjcommon.h:11:10: fatal error: jpeglib.h: No such file or directory 11 | #include | ^~~~~~~~~~~ compilation terminated. make: *** [/home/biocbuild/R/R-4.4.1/etc/Makeconf:195: read.o] Error 1 ERROR: compilation failed for package ‘jpeg’ * removing ‘/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/jpeg’ installation of package 'jpeg' had non-zero exit status * installing *source* package ‘pwalign’ ... ** package ‘pwalign’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/S4Vectors/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/IRanges/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/XVector/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/S4Vectors/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/IRanges/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/XVector/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/S4Vectors/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/IRanges/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/XVector/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -c R_init_pairwiseAlignment.c -o R_init_pairwiseAlignment.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/S4Vectors/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/IRanges/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/XVector/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/S4Vectors/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/IRanges/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/XVector/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/S4Vectors/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/IRanges/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/XVector/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/S4Vectors/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/IRanges/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/XVector/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -c align_utils.c -o align_utils.o align_utils.c: In function 'PairwiseAlignmentsSingleSubject_align_aligned': align_utils.c:234:78: warning: 'indelStartPattern' may be used uninitialized [-Wmaybe-uninitialized] 234 | if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ align_utils.c:223:21: note: 'indelStartPattern' was declared here 223 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject; | ^~~~~~~~~~~~~~~~~ align_utils.c:240:55: warning: 'indelWidthPattern' may be used uninitialized [-Wmaybe-uninitialized] 240 | for (k = 0; k < indelWidthPattern; k++) { | ~~^~~~~~~~~~~~~~~~~~~ align_utils.c:223:40: note: 'indelWidthPattern' was declared here 223 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject; | ^~~~~~~~~~~~~~~~~ align_utils.c:233:63: warning: 'indelStartSubject' may be used uninitialized [-Wmaybe-uninitialized] 233 | if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) { | ~~~^~~~~~~~~~~~~~~~~~~~ align_utils.c:223:59: note: 'indelStartSubject' was declared here 223 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject; | ^~~~~~~~~~~~~~~~~ align_utils.c:252:42: warning: 'indelWidthSubject' may be used uninitialized [-Wmaybe-uninitialized] 252 | jPattern += indelWidthSubject; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ align_utils.c:223:78: note: 'indelWidthSubject' was declared here 223 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject; | ^~~~~~~~~~~~~~~~~ gcc -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o pwalign.so Biostrings_stubs.o IRanges_stubs.o R_init_pairwiseAlignment.o S4Vectors_stubs.o XVector_stubs.o align_pairwiseAlignment.o align_utils.o -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/00LOCK-pwalign/00new/pwalign/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘insertion’ in package ‘pwalign’ Creating a new generic function for ‘deletion’ in package ‘pwalign’ Creating a new generic function for ‘unaligned’ in package ‘pwalign’ Creating a new generic function for ‘aligned’ in package ‘pwalign’ Creating a new generic function for ‘indel’ in package ‘pwalign’ Creating a new generic function for ‘nindel’ in package ‘pwalign’ Creating a new generic function for ‘PairwiseAlignments’ in package ‘pwalign’ Creating a new generic function for ‘alignedPattern’ in package ‘pwalign’ Creating a new generic function for ‘alignedSubject’ in package ‘pwalign’ Creating a new generic function for ‘PairwiseAlignmentsSingleSubject’ in package ‘pwalign’ Creating a new generic function for ‘nedit’ in package ‘pwalign’ Creating a new generic function for ‘mismatchTable’ in package ‘pwalign’ Creating a new generic function for ‘mismatchSummary’ in package ‘pwalign’ Creating a new generic function for ‘compareStrings’ in package ‘pwalign’ Creating a new generic function for ‘pid’ in package ‘pwalign’ Creating a new generic function for ‘pairwiseAlignment’ in package ‘pwalign’ Creating a new generic function for ‘stringDist’ in package ‘pwalign’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (pwalign) * installing *source* package ‘aroma.light’ ... ** package ‘aroma.light’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (aroma.light) * installing *source* package ‘BiocVersion’ ... ** using staged installation ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocVersion) * installing *source* package ‘interp’ ... ** package ‘interp’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ using Fortran compiler: ‘GNU Fortran (GCC) 10.3.1’ using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Rcpp/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c BiLin.cpp -o BiLin.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Rcpp/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o In file included from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Core:214, from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Dense:1, from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/RcppEigenForward.h:28, from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/RcppEigen.h:25, from RcppExports.cpp:4: /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::pload(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Core:172: /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::ploadu(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Rcpp/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c aSpline.cpp -o aSpline.o In file included from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Core:214, from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Dense:1, from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/RcppEigenForward.h:28, from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/RcppEigen.h:25, from interp.h:7, from aSpline.cpp:7: /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::pload(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Core:172: /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::ploadu(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ gfortran -fPIC -g -O2 -Wall -c bilinear.f -o bilinear.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Rcpp/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c circum.cpp -o circum.o In file included from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Core:214, from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Dense:1, from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/RcppEigenForward.h:28, from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/RcppEigen.h:25, from interp.h:7, from circum.cpp:3: /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::pload(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Core:172: /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::ploadu(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Rcpp/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c common.cpp -o common.o In file included from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Core:214, from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Dense:1, from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/RcppEigenForward.h:28, from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/RcppEigen.h:25, from interp.h:7, from common.cpp:1: /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::pload(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Core:172: /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::ploadu(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Rcpp/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c convexHull.cpp -o convexHull.o convexHull.cpp: In function 'Rcpp::List ConvexHull(Rcpp::NumericVector, Rcpp::NumericVector)': convexHull.cpp:122:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 122 | for(int i=0; i::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Core:172: /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::ploadu(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Rcpp/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c partDeriv.cpp -o partDeriv.o In file included from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Core:214, from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Dense:1, from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/RcppEigenForward.h:28, from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/RcppEigen.h:25, from interp.h:7, from partDeriv.cpp:2: /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::pload(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Core:172: /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::ploadu(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Core:337: /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function 'static void Eigen::internal::selfadjoint_product_impl::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Block, -1, 1, false>; Lhs = Eigen::Block, -1, -1, false>; int LhsMode = 17; Rhs = Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Block, -1, 1, true>, -1, 1, false> >]': /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:229:7: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 227 | internal::selfadjoint_matrix_vector_product::Flags&RowMajorBit) ? RowMajor : ColMajor, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 228 | int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 229 | ( | ^ 230 | lhs.rows(), // size | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 231 | &lhs.coeffRef(0,0), lhs.outerStride(), // lhs info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 232 | actualRhsPtr, // rhs info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 | actualDestPtr, // result info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 | actualAlpha // scale factor | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 | ); | ~ /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:41:6: note: by argument 4 of type 'const double*' to 'static void Eigen::internal::selfadjoint_matrix_vector_product::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = double; Index = long int; int StorageOrder = 0; int UpLo = 1; bool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]' declared here 41 | void selfadjoint_matrix_vector_product::run( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Core:341: /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const double*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Core:295: In constructor 'Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const T0&, const T1&) [with T0 = int; T1 = int; _Scalar = double; int _Rows = -1; int _Cols = -1; int _Options = 0; int _MaxRows = -1; int _MaxCols = -1]', inlined from 'PDEst pD(Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, NN, double, double, Rcpp::CharacterVector, Rcpp::NumericVector, std::string, int)' at partDeriv.cpp:299:18: /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/Matrix.h:340:35: warning: 'p' may be used uninitialized [-Wmaybe-uninitialized] 340 | Base::template _init2(x, y); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ partDeriv.cpp: In function 'PDEst pD(Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, NN, double, double, Rcpp::CharacterVector, Rcpp::NumericVector, std::string, int)': partDeriv.cpp:289:7: note: 'p' declared here 289 | int p; | ^ In constructor 'Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const T&) [with T = int; _Scalar = double; int _Rows = -1; int _Cols = 1; int _Options = 0; int _MaxRows = -1; int _MaxCols = 1]', inlined from 'PDEst pDsmooth(Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, NN, double, double, Rcpp::CharacterVector, Rcpp::NumericVector, std::string, int, int, bool)' at partDeriv.cpp:632:22: /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/Matrix.h:332:31: warning: 'p' may be used uninitialized [-Wmaybe-uninitialized] 332 | Base::template _init1(x); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ partDeriv.cpp: In function 'PDEst pDsmooth(Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, NN, double, double, Rcpp::CharacterVector, Rcpp::NumericVector, std::string, int, int, bool)': partDeriv.cpp:529:7: note: 'p' was declared here 529 | int p; | ^ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Rcpp/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c s_hull_pro.cpp -o s_hull_pro.o s_hull_pro.cpp: In function 'int s_hull_pro(std::vector&, std::vector&, int)': s_hull_pro.cpp:638:25: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and '__gnu_cxx::__alloc_traits, int>::value_type' {aka 'int'} [-Wsign-compare] 638 | if(triads.size()>=tridx[p]+1){ | ~~~~~~~~~~~~~^~~~~~~~~~~~ s_hull_pro.cpp:712:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 712 | if(nits>2*(2*pts.size()-ch_size-2)){ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/Rcpp/include' -I'/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include' -I/usr/local/include -fPIC -g -O2 -Wall -c shullDeltri.cpp -o shullDeltri.o In file included from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Core:214, from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Dense:1, from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/RcppEigenForward.h:28, from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/RcppEigen.h:25, from interp.h:7, from shullDeltri.cpp:2: /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::pload(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1671 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/Core:172: /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function 'Packet Eigen::internal::ploadu(const typename unpacket_traits::type*) [with Packet = eigen_packet_wrapper; typename unpacket_traits::type = signed char]': /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: 'void* memcpy(void*, const void*, size_t)' copying an object of non-trivial type 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} from an array of 'const int8_t' {aka 'const signed char'} [-Wclass-memaccess] 1716 | memcpy(&res, from, sizeof(Packet4c)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: 'Eigen::internal::Packet4c' {aka 'struct Eigen::internal::eigen_packet_wrapper'} declared here 159 | struct eigen_packet_wrapper | ^~~~~~~~~~~~~~~~~~~~ In file included from interp.h:4: In copy constructor 'Shx::Shx(const Shx&)', inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Shx; _Args = {const Shx&}; _Tp = Shx]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/new_allocator.h:191:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Shx; _Args = {const Shx&}; _Tp = Shx]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/alloc_traits.h:534:17, inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Shx; _Alloc = std::allocator]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_vector.h:1288:30, inlined from 'Triang shDt(std::vector, std::vector, double, double, int)' at shullDeltri.cpp:312:20: s_hull_pro.h:79:63: warning: 'pt.Shx::tr' may be used uninitialized [-Wmaybe-uninitialized] 79 | Shx(const Shx &p) : id(p.id), trid(p.trid), r(p.r), c(p.c), tr(p.tr), tc(p.tc), ro(p.ro) {}; | ^~~~~~~~ shullDeltri.cpp: In function 'Triang shDt(std::vector, std::vector, double, double, int)': shullDeltri.cpp:308:11: note: 'pt.Shx::tr' was declared here 308 | Shx pt; | ^~ In copy constructor 'Shx::Shx(const Shx&)', inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = Shx; _Args = {const Shx&}; _Tp = Shx]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/new_allocator.h:191:4, inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = Shx; _Args = {const Shx&}; _Tp = Shx]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/alloc_traits.h:534:17, inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Shx; _Alloc = std::allocator]' at /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_vector.h:1288:30, inlined from 'Triang shDt(std::vector, std::vector, double, double, int)' at shullDeltri.cpp:312:20: s_hull_pro.h:79:73: warning: 'pt.Shx::tc' may be used uninitialized [-Wmaybe-uninitialized] 79 | Shx(const Shx &p) : id(p.id), trid(p.trid), r(p.r), c(p.c), tr(p.tr), tc(p.tc), ro(p.ro) {}; | ^~~~~~~~ shullDeltri.cpp: In function 'Triang shDt(std::vector, std::vector, double, double, int)': shullDeltri.cpp:308:11: note: 'pt.Shx::tc' was declared here 308 | Shx pt; | ^~ g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o interp.so BiLin.o RcppExports.o aSpline.o bilinear.o circum.o common.o convexHull.o init.o interp.o partDeriv.o s_hull_pro.o shullDeltri.o -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/00LOCK-interp/00new/interp/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (interp) ERROR: dependency ‘jpeg’ is not available for package ‘latticeExtra’ * removing ‘/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/latticeExtra’ installation of package 'latticeExtra' had non-zero exit status ERROR: dependency ‘latticeExtra’ is not available for package ‘ShortRead’ * removing ‘/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/ShortRead’ installation of package 'ShortRead' had non-zero exit status ERROR: dependency ‘ShortRead’ is not available for package ‘EDASeq’ * removing ‘/home/biocbuild/tmp/RtmpoZAfYD/RLIBS_7dc9d41c9858b/EDASeq’ installation of package 'EDASeq' had non-zero exit status The downloaded source packages are in '/home/biocbuild/tmp/RtmpAWjdT2/downloaded_packages' Error in betweenLaneNormalization(assay(se), which = norm.method) : could not find function "betweenLaneNormalization" Calls: ebrowser -> normalize Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/EnrichmentBrowser.Rcheck/00check.log’ for details.