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###
### 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
###
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* 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'
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trying URL 'https://cloud.r-project.org/src/contrib/RcppEigen_0.3.4.0.2.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/jpeg_0.1-10.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/interp_1.1-6.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/pwalign_1.2.0.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/latticeExtra_0.6-30.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/ShortRead_1.64.0.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/aroma.light_3.36.0.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/BiocVersion_3.20.0.tar.gz'
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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)
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* 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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<Lhs, LhsMode, false, Rhs, 0, true>::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Block<Eigen::Matrix<double, -1, 1>, -1, 1, false>; Lhs = Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>; int LhsMode = 17; Rhs = 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::Block<Eigen::Block<Eigen::Matrix<double, -1, -1>, -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<Scalar, Index, (internal::traits<ActualLhsTypeCleaned>::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<Scalar, Index, StorageOrder, UpLo, ConjugateLhs, ConjugateRhs, Version>::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<Scalar,Index,StorageOrder,UpLo,ConjugateLhs,ConjugateRhs,Version>::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<Mode, 1>::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose<const 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<const Eigen::Block<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose<Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1, 1, -1, -1>, 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 |       <Index,Mode,
      |       ~~~~~~~~~~~~
  329 |        LhsScalar, LhsBlasTraits::NeedToConjugate,
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  330 |        RhsScalar, RhsBlasTraits::NeedToConjugate,
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  331 |        RowMajor>
      |        ~~~~~~~~~
  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<Index, Mode, LhsScalar, ConjLhs, RhsScalar, ConjRhs, 1, Version>::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<Index,Mode,LhsScalar,ConjLhs,RhsScalar,ConjRhs,RowMajor,Version>
      |                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 <jpeglib.h>
      |          ^~~~~~~~~~~
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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<Point2D>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  122 |     for(int i=0; i<hull.size();i++){
      |                  ~^~~~~~~~~~~~
gcc -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 init.c -o init.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 interp.cpp -o interp.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 interp.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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<Lhs, LhsMode, false, Rhs, 0, true>::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Block<Eigen::Matrix<double, -1, 1>, -1, 1, false>; Lhs = Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>; int LhsMode = 17; Rhs = 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::Block<Eigen::Block<Eigen::Matrix<double, -1, -1>, -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<Scalar, Index, (internal::traits<ActualLhsTypeCleaned>::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<Scalar, Index, StorageOrder, UpLo, ConjugateLhs, ConjugateRhs, Version>::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<Scalar,Index,StorageOrder,UpLo,ConjugateLhs,ConjugateRhs,Version>::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<Mode, 1>::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose<const 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<const Eigen::Block<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose<Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1, 1, -1, -1>, 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 |       <Index,Mode,
      |       ~~~~~~~~~~~~
  329 |        LhsScalar, LhsBlasTraits::NeedToConjugate,
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  330 |        RhsScalar, RhsBlasTraits::NeedToConjugate,
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  331 |        RowMajor>
      |        ~~~~~~~~~
  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<Index, Mode, LhsScalar, ConjLhs, RhsScalar, ConjRhs, 1, Version>::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<Index,Mode,LhsScalar,ConjLhs,RhsScalar,ConjRhs,RowMajor,Version>
      |                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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<T0,T1>(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<T>(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<Shx>&, std::vector<Triad>&, int)':
s_hull_pro.cpp:638:25: warning: comparison of integer expressions of different signedness: 'std::vector<Triad>::size_type' {aka 'long unsigned int'} and '__gnu_cxx::__alloc_traits<std::allocator<int>, 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<Shx>::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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::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<int, 2>'} 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<int, 2>'} 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<std::allocator<_Tp1> >::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<Shx>]' 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<double>, std::vector<double>, 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<double>, std::vector<double>, 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<std::allocator<_Tp1> >::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<Shx>]' 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<double>, std::vector<double>, 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<double>, std::vector<double>, 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.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL EnrichmentBrowser
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘EnrichmentBrowser’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (EnrichmentBrowser)