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CHECK report for destiny on malbec1

This page was generated on 2020-04-15 12:10:20 -0400 (Wed, 15 Apr 2020).

Package 446/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
destiny 3.0.1
Philipp Angerer
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/destiny
Branch: RELEASE_3_10
Last Commit: 1348b8f
Last Changed Date: 2020-01-16 06:24:52 -0400 (Thu, 16 Jan 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: destiny
Version: 3.0.1
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:destiny.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings destiny_3.0.1.tar.gz
StartedAt: 2020-04-15 03:10:58 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 03:15:56 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 297.2 seconds
RetCode: 0
Status:  OK 
CheckDir: destiny.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:destiny.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings destiny_3.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/destiny.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘destiny/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘destiny’ version ‘3.0.1’
* 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 ‘destiny’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘tidyr’ ‘SingleCellExperiment’
A package should be listed in only one of these fields.
'LinkingTo' for ‘grDevices’ is unused as it has no 'include' directory
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.DPT plot.DiffusionMap
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get_pca: no visible binding for global variable ‘pcs’
plot.DiffusionMap: no visible binding for global variable ‘hcl.colors’
plot_differential_map: no visible binding for global variable
  ‘hcl.colors’
plot_gradient_map: no visible binding for global variable ‘hcl.colors’
plot_differential_map,DiffusionMap-missing: no visible binding for
  global variable ‘hcl.colors’
plot_differential_map,GeneRelevance-missing: no visible binding for
  global variable ‘hcl.colors’
plot_differential_map,matrix-matrix: no visible binding for global
  variable ‘hcl.colors’
Undefined global functions or variables:
  hcl.colors pcs
Consider adding
  importFrom("grDevices", "hcl.colors")
to your NAMESPACE file.
* 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 ... NOTE
S3 methods shown with full name in documentation object 'plot.DPT':
  ‘plot.DPT’

S3 methods shown with full name in documentation object 'plot.DiffusionMap':
  ‘plot.DiffusionMap’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
Gene-Relevance-plotting 9.572  0.016   9.919
destiny                 9.100  0.020   9.192
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/destiny.Rcheck/00check.log’
for details.

Installation output

destiny.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL destiny
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘destiny’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/grDevices/include" -I/usr/local/include -ggdb -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Core:392:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:60:39: warning: ignoring attributes on template argument ‘__m128 {aka __vector(4) float}’ [-Wignored-attributes]
 template<> struct is_arithmetic<__m128>  { enum { value = true }; };
                                       ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:61:40: warning: ignoring attributes on template argument ‘__m128i {aka __vector(2) long long int}’ [-Wignored-attributes]
 template<> struct is_arithmetic<__m128i> { enum { value = true }; };
                                        ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:62:40: warning: ignoring attributes on template argument ‘__m128d {aka __vector(2) double}’ [-Wignored-attributes]
 template<> struct is_arithmetic<__m128d> { enum { value = true }; };
                                        ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:161:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 template<> struct unpacket_traits<Packet4f> { typedef float  type; enum {size=4, alignment=Aligned16}; typedef Packet4f half; };
                                           ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:162:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 template<> struct unpacket_traits<Packet2d> { typedef double type; enum {size=2, alignment=Aligned16}; typedef Packet2d half; };
                                           ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:163:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i {aka __vector(2) long long int}’ [-Wignored-attributes]
 template<> struct unpacket_traits<Packet4i> { typedef int    type; enum {size=4, alignment=Aligned16}; typedef Packet4i half; };
                                           ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:718:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 struct palign_impl<Offset,Packet4f>
                                   ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:741:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i {aka __vector(2) long long int}’ [-Wignored-attributes]
 struct palign_impl<Offset,Packet4i>
                                   ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:764:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 struct palign_impl<Offset,Packet2d>
                                   ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:778:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 ptranspose(PacketBlock<Packet4f,4>& kernel) {
                                  ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:783:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 ptranspose(PacketBlock<Packet2d,2>& kernel) {
                                  ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:790:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i {aka __vector(2) long long int}’ [-Wignored-attributes]
 ptranspose(PacketBlock<Packet4i,4>& kernel) {
                                  ^
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Core:374:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:15:70: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
   template<> struct conj_helper<PACKET_REAL, PACKET_CPLX, false,false> {                                          \
                                                                      ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:232:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
 EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:22:70: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
   template<> struct conj_helper<PACKET_CPLX, PACKET_REAL, false,false> {                                          \
                                                                      ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:232:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
 EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:15:70: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
   template<> struct conj_helper<PACKET_REAL, PACKET_CPLX, false,false> {                                          \
                                                                      ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:417:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
 EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:22:70: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
   template<> struct conj_helper<PACKET_CPLX, PACKET_REAL, false,false> {                                          \
                                                                      ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:417:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
 EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Core:367:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<float, 4>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57:   required from ‘struct Eigen::internal::traits<Eigen::Matrix<float, 4, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:224:7:   required from ‘struct Eigen::internal::traits<Eigen::Quaternion<float> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:24:46:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type {aka __vector(4) float}’ [-Wignored-attributes]
          bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
                                       ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type {aka __vector(4) float}’ [-Wignored-attributes]
          bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type {aka __vector(4) float}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(4) float>::half {aka __vector(4) float}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:188:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type {aka __vector(4) float}’ [-Wignored-attributes]
   typedef typename find_best_packet_helper<Size,typename packet_traits<T>::type>::type type;
                                                                                        ^~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Core:434:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 0>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<float, 4, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<float, 4, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<float, 4, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7:   required from ‘class Eigen::Matrix<float, 4, 1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50:   required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<float> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:232:7:   required from ‘class Eigen::Quaternion<float>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:27:3:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type {aka __vector(4) float}’ [-Wignored-attributes]
                      >::type PacketReturnType;
                              ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Core:367:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<double, 4>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57:   required from ‘struct Eigen::internal::traits<Eigen::Matrix<double, 4, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:224:7:   required from ‘struct Eigen::internal::traits<Eigen::Quaternion<double> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:88:47:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
          bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
                                       ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
          bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half {aka __vector(2) double}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:188:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
   typedef typename find_best_packet_helper<Size,typename packet_traits<T>::type>::type type;
                                                                                        ^~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Core:434:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 0>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<double, 4, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, 4, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, 4, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7:   required from ‘class Eigen::Matrix<double, 4, 1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50:   required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<double> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:232:7:   required from ‘class Eigen::Quaternion<double>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:92:3:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
                      >::type PacketReturnType;
                              ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/SparseCore:37:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Sparse:26,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenForward.h:31,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase<Eigen::SparseMatrix<double, 0, int> >’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7:   required from ‘class Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 0, int> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7:   required from ‘class Eigen::SparseMatrix<double, 0, int>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
                      >::type PacketReturnType;
                              ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Core:367:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<int, -1>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57:   required from ‘struct Eigen::internal::traits<Eigen::Matrix<int, -1, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<int, -1, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7:   required from ‘class Eigen::Matrix<int, -1, 1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h:168:29:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
          bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
                                       ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
          bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) long long int>::half {aka __vector(2) long long int}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:188:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
   typedef typename find_best_packet_helper<Size,typename packet_traits<T>::type>::type type;
                                                                                        ^~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Core:434:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, 1>, 0>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, 1>, 1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, 1>, 3>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<int, -1, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<int, -1, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<int, -1, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7:   required from ‘class Eigen::Matrix<int, -1, 1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h:168:29:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
                      >::type PacketReturnType;
                              ^~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> >, 0>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> >, 1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> >, 3>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> > >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> > >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Transpose.h:115:37:   required from ‘class Eigen::TransposeImpl<Eigen::Matrix<int, -1, 1>, Eigen::Dense>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Transpose.h:52:37:   required from ‘class Eigen::Transpose<Eigen::Matrix<int, -1, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h:178:72:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, -1>, 0>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, -1>, 1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, -1>, 3>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<int, -1, -1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<int, -1, -1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<int, -1, -1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7:   required from ‘class Eigen::Matrix<int, -1, -1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h:179:36:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::SparseMatrix<double, 0, int>, 0>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:298:80:   required from ‘struct Eigen::internal::evaluator<Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 0, int> > >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1390:8:   required from ‘struct Eigen::internal::evaluator<Eigen::SparseMatrix<double, 0, int> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:77:20:   required from ‘void Eigen::internal::assign_sparse_to_sparse(DstXprType&, const SrcXprType&) [with DstXprType = Eigen::SparseMatrix<double, 0, int>; SrcXprType = Eigen::SparseMatrix<double, 0, int>]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:132:28:   required from ‘static void Eigen::internal::Assignment<DstXprType, SrcXprType, Functor, Eigen::internal::Sparse2Sparse>::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op<typename DstXprType::Scalar, typename SrcXprType::Scalar>&) [with DstXprType = Eigen::SparseMatrix<double, 0, int>; SrcXprType = Eigen::SparseMatrix<double, 0, int>; Functor = Eigen::internal::assign_op<double, double>; typename SrcXprType::Scalar = double; typename DstXprType::Scalar = double]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836:49:   required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::SparseMatrix<double, 0, int>; Src = Eigen::SparseMatrix<double, 0, int>; Func = Eigen::internal::assign_op<double, double>]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:842:27:   required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&) [with Dst = Eigen::SparseMatrix<double, 0, int>; Src = Eigen::SparseMatrix<double, 0, int>]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:45:37:   required from ‘Derived& Eigen::SparseMatrixBase<Derived>::operator=(const Derived&) [with Derived = Eigen::SparseMatrix<double, 0, int>]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:773:26:   required from ‘Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>& Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>&) [with _Scalar = double; int _Options = 0; _StorageIndex = int]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:708:13:   required from ‘Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::SparseMatrix(const Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>&) [with _Scalar = double; int _Options = 0; _StorageIndex = int]’
RcppExports.cpp:22:127:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> >, 0>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:478:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> >, 2>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> > >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> > >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/MapBase.h:37:34:   required from ‘class Eigen::MapBase<Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> >, 0>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Map.h:94:79:   required from ‘class Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:65:29:   [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenWrap.h:149:39:   required from ‘SEXPREC* Rcpp::RcppEigen::eigen_wrap(const T&) [with T = Eigen::SparseMatrix<double, 0, int>; SEXP = SEXPREC*]’
/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:776:49:   required from ‘SEXPREC* Rcpp::internal::wrap_dispatch_eigen(const T&, Rcpp::traits::true_type) [with T = Eigen::SparseMatrix<double, 0, int>; SEXP = SEXPREC*; Rcpp::traits::true_type = Rcpp::traits::integral_constant<bool, true>]’
/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:787:39:   required from ‘SEXPREC* Rcpp::internal::wrap_dispatch_unknown_importable(const T&, Rcpp::traits::false_type) [with T = Eigen::SparseMatrix<double, 0, int>; SEXP = SEXPREC*; Rcpp::traits::false_type = Rcpp::traits::integral_constant<bool, false>]’
/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:807:52:   required from ‘SEXPREC* Rcpp::internal::wrap_dispatch(const T&, Rcpp::traits::wrap_type_unknown_tag) [with T = Eigen::SparseMatrix<double, 0, int>; SEXP = SEXPREC*]’
/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include/Rcpp/internal/wrap_end.h:30:38:   required from ‘SEXPREC* Rcpp::wrap(const T&) [with T = Eigen::SparseMatrix<double, 0, int>; SEXP = SEXPREC*]’
RcppExports.cpp:22:128:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘Eigen::Index Eigen::internal::first_default_aligned(const Eigen::DenseBase<Derived>&) [with Derived = Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> >; Eigen::Index = long int]’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Redux.h:225:63:   required from ‘static Eigen::internal::redux_impl<Func, Derived, 3, 0>::Scalar Eigen::internal::redux_impl<Func, Derived, 3, 0>::run(const Derived&, const Func&) [with Func = Eigen::internal::scalar_sum_op<int, int>; Derived = Eigen::internal::redux_evaluator<Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> > >; Eigen::internal::redux_impl<Func, Derived, 3, 0>::Scalar = int]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Redux.h:418:56:   required from ‘typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::redux(const Func&) const [with BinaryOp = Eigen::internal::scalar_sum_op<int, int>; Derived = Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> >; typename Eigen::internal::traits<T>::Scalar = int]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Redux.h:453:73:   required from ‘typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::sum() const [with Derived = Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> >; typename Eigen::internal::traits<T>::Scalar = int]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:65:36:   required from ‘Eigen::Index Eigen::SparseCompressedBase<Derived>::nonZeros() const [with Derived = Eigen::SparseMatrix<double, 0, int>; Eigen::Index = long int]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenWrap.h:119:26:   [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenWrap.h:149:39:   required from ‘SEXPREC* Rcpp::RcppEigen::eigen_wrap(const T&) [with T = Eigen::SparseMatrix<double, 0, int>; SEXP = SEXPREC*]’
/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:776:49:   required from ‘SEXPREC* Rcpp::internal::wrap_dispatch_eigen(const T&, Rcpp::traits::true_type) [with T = Eigen::SparseMatrix<double, 0, int>; SEXP = SEXPREC*; Rcpp::traits::true_type = Rcpp::traits::integral_constant<bool, true>]’
/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:787:39:   required from ‘SEXPREC* Rcpp::internal::wrap_dispatch_unknown_importable(const T&, Rcpp::traits::false_type) [with T = Eigen::SparseMatrix<double, 0, int>; SEXP = SEXPREC*; Rcpp::traits::false_type = Rcpp::traits::integral_constant<bool, false>]’
/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include/Rcpp/internal/wrap.h:807:52:   required from ‘SEXPREC* Rcpp::internal::wrap_dispatch(const T&, Rcpp::traits::wrap_type_unknown_tag) [with T = Eigen::SparseMatrix<double, 0, int>; SEXP = SEXPREC*]’
/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include/Rcpp/internal/wrap_end.h:30:38:   required from ‘SEXPREC* Rcpp::wrap(const T&) [with T = Eigen::SparseMatrix<double, 0, int>; SEXP = SEXPREC*]’
RcppExports.cpp:22:128:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:650:34: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
   return internal::first_aligned<int(unpacket_traits<DefaultPacketType>::alignment),Derived>(m);
                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/grDevices/include" -I/usr/local/include -ggdb -fpic  -g -O2  -Wall -c censoring.cpp -o censoring.o
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Core:392:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from censoring.cpp:7:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:60:39: warning: ignoring attributes on template argument ‘__m128 {aka __vector(4) float}’ [-Wignored-attributes]
 template<> struct is_arithmetic<__m128>  { enum { value = true }; };
                                       ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:61:40: warning: ignoring attributes on template argument ‘__m128i {aka __vector(2) long long int}’ [-Wignored-attributes]
 template<> struct is_arithmetic<__m128i> { enum { value = true }; };
                                        ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:62:40: warning: ignoring attributes on template argument ‘__m128d {aka __vector(2) double}’ [-Wignored-attributes]
 template<> struct is_arithmetic<__m128d> { enum { value = true }; };
                                        ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:161:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 template<> struct unpacket_traits<Packet4f> { typedef float  type; enum {size=4, alignment=Aligned16}; typedef Packet4f half; };
                                           ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:162:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 template<> struct unpacket_traits<Packet2d> { typedef double type; enum {size=2, alignment=Aligned16}; typedef Packet2d half; };
                                           ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:163:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i {aka __vector(2) long long int}’ [-Wignored-attributes]
 template<> struct unpacket_traits<Packet4i> { typedef int    type; enum {size=4, alignment=Aligned16}; typedef Packet4i half; };
                                           ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:718:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 struct palign_impl<Offset,Packet4f>
                                   ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:741:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i {aka __vector(2) long long int}’ [-Wignored-attributes]
 struct palign_impl<Offset,Packet4i>
                                   ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:764:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 struct palign_impl<Offset,Packet2d>
                                   ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:778:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 ptranspose(PacketBlock<Packet4f,4>& kernel) {
                                  ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:783:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 ptranspose(PacketBlock<Packet2d,2>& kernel) {
                                  ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:790:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i {aka __vector(2) long long int}’ [-Wignored-attributes]
 ptranspose(PacketBlock<Packet4i,4>& kernel) {
                                  ^
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Core:374:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from censoring.cpp:7:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:15:70: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
   template<> struct conj_helper<PACKET_REAL, PACKET_CPLX, false,false> {                                          \
                                                                      ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:232:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
 EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
 ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:22:70: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
   template<> struct conj_helper<PACKET_CPLX, PACKET_REAL, false,false> {                                          \
                                                                      ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:232:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
 EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
 ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:15:70: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
   template<> struct conj_helper<PACKET_REAL, PACKET_CPLX, false,false> {                                          \
                                                                      ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:417:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
 EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
 ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:22:70: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
   template<> struct conj_helper<PACKET_CPLX, PACKET_REAL, false,false> {                                          \
                                                                      ^
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:417:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
 EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
 ^
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Core:367:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from censoring.cpp:7:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<float, 4>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57:   required from ‘struct Eigen::internal::traits<Eigen::Matrix<float, 4, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:224:7:   required from ‘struct Eigen::internal::traits<Eigen::Quaternion<float> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:24:46:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type {aka __vector(4) float}’ [-Wignored-attributes]
          bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
                                       ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type {aka __vector(4) float}’ [-Wignored-attributes]
          bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type {aka __vector(4) float}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(4) float>::half {aka __vector(4) float}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:188:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type {aka __vector(4) float}’ [-Wignored-attributes]
   typedef typename find_best_packet_helper<Size,typename packet_traits<T>::type>::type type;
                                                                                        ^~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Core:434:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from censoring.cpp:7:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 0>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<float, 4, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<float, 4, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<float, 4, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7:   required from ‘class Eigen::Matrix<float, 4, 1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50:   required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<float> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:232:7:   required from ‘class Eigen::Quaternion<float>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:27:3:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type {aka __vector(4) float}’ [-Wignored-attributes]
                      >::type PacketReturnType;
                              ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Core:367:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from censoring.cpp:7:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<double, 4>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57:   required from ‘struct Eigen::internal::traits<Eigen::Matrix<double, 4, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:224:7:   required from ‘struct Eigen::internal::traits<Eigen::Quaternion<double> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:88:47:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
          bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
                                       ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
          bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half {aka __vector(2) double}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:188:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
   typedef typename find_best_packet_helper<Size,typename packet_traits<T>::type>::type type;
                                                                                        ^~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Core:434:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from censoring.cpp:7:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 0>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<double, 4, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, 4, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, 4, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7:   required from ‘class Eigen::Matrix<double, 4, 1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50:   required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<double> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:232:7:   required from ‘class Eigen::Quaternion<double>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SSE.h:92:3:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
                      >::type PacketReturnType;
                              ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/SparseCore:37:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Sparse:26,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenForward.h:31,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from censoring.cpp:7:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase<Eigen::SparseMatrix<double, 0, int> >’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7:   required from ‘class Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 0, int> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7:   required from ‘class Eigen::SparseMatrix<double, 0, int>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
                      >::type PacketReturnType;
                              ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Core:367:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from censoring.cpp:7:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<int, -1>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57:   required from ‘struct Eigen::internal::traits<Eigen::Matrix<int, -1, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<int, -1, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7:   required from ‘class Eigen::Matrix<int, -1, 1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h:168:29:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
          bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
                                       ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
          bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:170:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) long long int>::half {aka __vector(2) long long int}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:188:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
   typedef typename find_best_packet_helper<Size,typename packet_traits<T>::type>::type type;
                                                                                        ^~~~
In file included from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Core:434:0,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from censoring.cpp:7:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, 1>, 0>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, 1>, 1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, 1>, 3>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<int, -1, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<int, -1, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<int, -1, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7:   required from ‘class Eigen::Matrix<int, -1, 1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h:168:29:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
                      >::type PacketReturnType;
                              ^~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> >, 0>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> >, 1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> >, 3>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> > >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Transpose<Eigen::Matrix<int, -1, 1> > >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Transpose.h:115:37:   required from ‘class Eigen::TransposeImpl<Eigen::Matrix<int, -1, 1>, Eigen::Dense>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Transpose.h:52:37:   required from ‘class Eigen::Transpose<Eigen::Matrix<int, -1, 1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h:178:72:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, -1>, 0>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:300:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, -1>, 1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:551:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<int, -1, -1>, 3>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Matrix<int, -1, -1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Matrix<int, -1, -1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7:   required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<int, -1, -1> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7:   required from ‘class Eigen::Matrix<int, -1, -1>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h:179:36:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> >, 0>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:478:7:   required from ‘class Eigen::DenseCoeffsBase<Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> >, 2>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:   required from ‘class Eigen::DenseBase<Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> > >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:   required from ‘class Eigen::MatrixBase<Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> > >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/MapBase.h:37:34:   required from ‘class Eigen::MapBase<Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> >, 0>’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Map.h:94:79:   required from ‘class Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:65:29:   required from ‘Eigen::Index Eigen::SparseCompressedBase<Derived>::nonZeros() const [with Derived = Eigen::SparseMatrix<double, 0, int>; Eigen::Index = long int]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:163:21:   required from ‘Eigen::SparseCompressedBase<Derived>::InnerIterator::InnerIterator(const Eigen::SparseCompressedBase<Derived>&, Eigen::Index) [with Derived = Eigen::SparseMatrix<double, 0, int>; Eigen::Index = long int]’
censoring.cpp:116:46:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘Eigen::Index Eigen::internal::first_default_aligned(const Eigen::DenseBase<Derived>&) [with Derived = Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> >; Eigen::Index = long int]’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Redux.h:225:63:   required from ‘static Eigen::internal::redux_impl<Func, Derived, 3, 0>::Scalar Eigen::internal::redux_impl<Func, Derived, 3, 0>::run(const Derived&, const Func&) [with Func = Eigen::internal::scalar_sum_op<int, int>; Derived = Eigen::internal::redux_evaluator<Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> > >; Eigen::internal::redux_impl<Func, Derived, 3, 0>::Scalar = int]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Redux.h:418:56:   required from ‘typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::redux(const Func&) const [with BinaryOp = Eigen::internal::scalar_sum_op<int, int>; Derived = Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> >; typename Eigen::internal::traits<T>::Scalar = int]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/Redux.h:453:73:   required from ‘typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::sum() const [with Derived = Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> >; typename Eigen::internal::traits<T>::Scalar = int]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:65:36:   required from ‘Eigen::Index Eigen::SparseCompressedBase<Derived>::nonZeros() const [with Derived = Eigen::SparseMatrix<double, 0, int>; Eigen::Index = long int]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:163:21:   required from ‘Eigen::SparseCompressedBase<Derived>::InnerIterator::InnerIterator(const Eigen::SparseCompressedBase<Derived>&, Eigen::Index) [with Derived = Eigen::SparseMatrix<double, 0, int>; Eigen::Index = long int]’
censoring.cpp:116:46:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:650:34: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<int>::type {aka __vector(2) long long int}’ [-Wignored-attributes]
   return internal::first_aligned<int(unpacket_traits<DefaultPacketType>::alignment),Derived>(m);
                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::SparseMatrix<double, 0, int>, 0>’:
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:298:80:   required from ‘struct Eigen::internal::evaluator<Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 0, int> > >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1390:8:   required from ‘struct Eigen::internal::evaluator<Eigen::SparseMatrix<double, 0, int> >’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:77:20:   required from ‘void Eigen::internal::assign_sparse_to_sparse(DstXprType&, const SrcXprType&) [with DstXprType = Eigen::SparseMatrix<double, 0, int>; SrcXprType = Eigen::SparseMatrix<double, 0, int>]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:132:28:   required from ‘static void Eigen::internal::Assignment<DstXprType, SrcXprType, Functor, Eigen::internal::Sparse2Sparse>::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op<typename DstXprType::Scalar, typename SrcXprType::Scalar>&) [with DstXprType = Eigen::SparseMatrix<double, 0, int>; SrcXprType = Eigen::SparseMatrix<double, 0, int>; Functor = Eigen::internal::assign_op<double, double>; typename SrcXprType::Scalar = double; typename DstXprType::Scalar = double]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836:49:   required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::SparseMatrix<double, 0, int>; Src = Eigen::SparseMatrix<double, 0, int>; Func = Eigen::internal::assign_op<double, double>]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:842:27:   required from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&) [with Dst = Eigen::SparseMatrix<double, 0, int>; Src = Eigen::SparseMatrix<double, 0, int>]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:45:37:   required from ‘Derived& Eigen::SparseMatrixBase<Derived>::operator=(const Derived&) [with Derived = Eigen::SparseMatrix<double, 0, int>]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:773:26:   required from ‘Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>& Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>&) [with _Scalar = double; int _Options = 0; _StorageIndex = int]’
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:708:13:   required from ‘Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::SparseMatrix(const Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>&) [with _Scalar = double; int _Options = 0; _StorageIndex = int]’
censoring.cpp:105:17:   required from here
/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type {aka __vector(2) double}’ [-Wignored-attributes]
                      >::type PacketReturnType;
                              ^~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/grDevices/include" -I/usr/local/include -ggdb -fpic  -g -O2  -Wall -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o destiny.so RcppExports.o censoring.o utils.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-destiny/00new/destiny/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
From .checkSubclasses(): subclass "dgTMatrix" of class "dsparseMatrix" is not local and is not updated for new inheritance information currently; 
[where=<environment: 0x556e3f980a90>, where2=<environment: namespace:destiny>]
From .checkSubclasses(): subclass "dtTMatrix" of class "dsparseMatrix" is not local and is not updated for new inheritance information currently; 
[where=<environment: 0x556e3f980a90>, where2=<environment: namespace:destiny>]
From .checkSubclasses(): subclass "dsTMatrix" of class "dsparseMatrix" is not local and is not updated for new inheritance information currently; 
[where=<environment: 0x556e3f980a90>, where2=<environment: namespace:destiny>]
From .checkSubclasses(): subclass "dgCMatrix" of class "dsparseMatrix" is not local and is not updated for new inheritance information currently; 
[where=<environment: 0x556e3f980a90>, where2=<environment: namespace:destiny>]
From .checkSubclasses(): subclass "dtCMatrix" of class "dsparseMatrix" is not local and is not updated for new inheritance information currently; 
[where=<environment: 0x556e3f980a90>, where2=<environment: namespace:destiny>]
From .checkSubclasses(): subclass "dsCMatrix" of class "dsparseMatrix" is not local and is not updated for new inheritance information currently; 
[where=<environment: 0x556e3f980a90>, where2=<environment: namespace:destiny>]
From .checkSubclasses(): subclass "dgRMatrix" of class "dsparseMatrix" is not local and is not updated for new inheritance information currently; 
[where=<environment: 0x556e3f980a90>, where2=<environment: namespace:destiny>]
From .checkSubclasses(): subclass "dtRMatrix" of class "dsparseMatrix" is not local and is not updated for new inheritance information currently; 
[where=<environment: 0x556e3f980a90>, where2=<environment: namespace:destiny>]
From .checkSubclasses(): subclass "dsRMatrix" of class "dsparseMatrix" is not local and is not updated for new inheritance information currently; 
[where=<environment: 0x556e3f980a90>, where2=<environment: namespace:destiny>]
** 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 (destiny)

Tests output

destiny.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(destiny)
> 
> test_check('destiny')
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 67 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 19.008   0.628  29.322

Example timings

destiny.Rcheck/destiny-Ex.timings

nameusersystemelapsed
DPT-matrix-methods2.3120.0082.431
DPT-methods2.4040.0362.484
DPT2.0280.0082.047
DiffusionMap-accessors0.9120.0400.953
DiffusionMap-class3.8840.0283.948
DiffusionMap-methods0.7480.0200.774
ExpressionSet-helpers0.1640.0000.165
Gene-Relevance-methods2.0200.0042.035
Gene-Relevance-plotting9.5720.0169.919
Gene-Relevance4.5960.0244.670
Sigmas-class0.1680.0040.175
coercions0.8960.0240.921
colorlegend0.0200.0000.017
cube_helix0.0080.0000.009
destiny-deprecated0.0000.0040.000
destiny-generics0.9160.0480.966
destiny9.1000.0209.192
dm_predict0.6840.0000.683
eig_decomp0.0000.0000.002
extractions2.0040.0082.027
find_dm_k0.0040.0000.005
find_sigmas0.9240.0000.923
find_tips0.8680.0000.872
l_which000
plot.DPT3.1000.0003.109
plot.DiffusionMap1.0760.0321.106
plot.Sigmas0.9120.0000.921
projection_dist0.4080.0000.408
random_root0.8240.0000.828