| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-27 11:32 -0400 (Mon, 27 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4980 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 116/2417 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| atacInferCnv 0.99.7 (landing page) Konstantin Okonechnikov
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| See other builds for atacInferCnv in R Universe. | ||||||||||||||
|
To the developers/maintainers of the atacInferCnv package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/atacInferCnv.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: atacInferCnv |
| Version: 0.99.7 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:atacInferCnv.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings atacInferCnv_0.99.7.tar.gz |
| StartedAt: 2026-04-26 21:27:51 -0400 (Sun, 26 Apr 2026) |
| EndedAt: 2026-04-26 21:39:14 -0400 (Sun, 26 Apr 2026) |
| EllapsedTime: 682.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: atacInferCnv.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:atacInferCnv.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings atacInferCnv_0.99.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/atacInferCnv.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-27 01:27:52 UTC
* checking for file ‘atacInferCnv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘atacInferCnv’ version ‘0.99.7’
* 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 ‘atacInferCnv’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotCnvBlocks: no visible binding for global variable ‘x’
plotCnvBlocks: no visible binding for global variable ‘value’
Undefined global functions or variables:
value x
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotCnvBlocks 50.342 1.639 51.947
runAtacInferCnv 41.006 0.719 41.712
prepareAtacInferCnvInput 15.553 0.789 16.344
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/atacInferCnv.Rcheck/00check.log’
for details.
atacInferCnv.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL atacInferCnv
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘atacInferCnv’ ...
** this is package ‘atacInferCnv’ version ‘0.99.7’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/Core:205,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/RcppEigenForward.h:28,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes]
46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i;
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes]
47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b;
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument ‘__m128’ [-Wignored-attributes]
49 | template<> struct is_arithmetic<__m128> { enum { value = true }; };
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes]
50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; };
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument ‘__m128d’ [-Wignored-attributes]
51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; };
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes]
222 | template<> struct unpacket_traits<Packet4f> {
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes]
228 | template<> struct unpacket_traits<Packet2d> {
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes]
1124 | ptranspose(PacketBlock<Packet4f,4>& kernel) {
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes]
1129 | ptranspose(PacketBlock<Packet2d,2>& kernel) {
| ^
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/Core:174:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes]
16 | struct conj_helper<PACKET_REAL, PACKET_CPLX, false, false> { \
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes]
29 | struct conj_helper<PACKET_CPLX, PACKET_REAL, false, false> { \
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes]
16 | struct conj_helper<PACKET_REAL, PACKET_CPLX, false, false> { \
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes]
29 | struct conj_helper<PACKET_CPLX, PACKET_REAL, false, false> { \
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/Core:165:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<float, 4>’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits<Eigen::Matrix<float, 4, 1> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits<Eigen::Quaternion<float> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__m128’} [-Wignored-attributes]
190 | bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__m128’} [-Wignored-attributes]
190 | bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__m128’} [-Wignored-attributes]
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(4) float>::half’ {aka ‘__m128’} [-Wignored-attributes]
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__m128’} [-Wignored-attributes]
208 | typedef typename find_best_packet_helper<Size,typename packet_traits<T>::type>::type type;
| ^~~~
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/Core:271:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 0>’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 1>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Matrix<float, 4, 1> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Matrix<float, 4, 1> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<float, 4, 1> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<float, 4, 1>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<float> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion<float>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__m128’} [-Wignored-attributes]
56 | >::type PacketReturnType;
| ^~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<double, 4>’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits<Eigen::Matrix<double, 4, 1> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits<Eigen::Quaternion<double> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
190 | bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
190 | bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes]
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
208 | typedef typename find_best_packet_helper<Size,typename packet_traits<T>::type>::type type;
| ^~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 0>’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 1>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Matrix<double, 4, 1> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, 4, 1> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, 4, 1> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<double, 4, 1>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<double> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion<double>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
56 | >::type PacketReturnType;
| ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/SparseCore:37,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/Sparse:26,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/RcppEigenForward.h:29:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase<Eigen::SparseMatrix<double, 0, int> >’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 0, int> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix<double, 0, int>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
47 | >::type PacketReturnType;
| ^~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::SparseMatrix<double, 0, int>, 0>’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80: required from ‘struct Eigen::internal::evaluator<Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 0, int> > >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from ‘struct Eigen::internal::evaluator<Eigen::SparseMatrix<double, 0, int> >’
/home/biocbuild/bbs-3.23-bioc/R/site-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-3.23-bioc/R/site-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 DstXprType::Scalar = double; typename SrcXprType::Scalar = double]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:49: 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 = assign_op<double, double>]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:917:27: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:713:13: required from ‘Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::SparseMatrix(const Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>&) [with _Scalar = double; int _Options = 0; _StorageIndex = int]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/RcppEigenWrap.h:387:24: required from ‘Eigen::SparseMatrix<Scalar> Rcpp::traits::Exporter<Eigen::SparseMatrix<Scalar> >::get() [with T = double]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp/as.h:88:32: required from ‘T Rcpp::internal::as(SEXP, Rcpp::traits::r_type_generic_tag) [with T = Eigen::SparseMatrix<double, 0, int>; SEXP = SEXPREC*]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp/as.h:151:31: required from ‘T Rcpp::as(SEXP) [with T = Eigen::SparseMatrix<double, 0, int>; SEXP = SEXPREC*]’
/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp/InputParameter.h:72:59: required from ‘Rcpp::ConstReferenceInputParameter<T>::ConstReferenceInputParameter(SEXP) [with T = Eigen::SparseMatrix<double, 0, int>; SEXP = SEXPREC*]’
RcppExports.cpp:23:110: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
56 | >::type PacketReturnType;
| ^~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c aggregate_bins.cpp -o aggregate_bins.o
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/Core:205,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/RcppEigenForward.h:28,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/RcppEigen.h:25,
from aggregate_bins.cpp:1:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes]
46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i;
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes]
47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b;
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument ‘__m128’ [-Wignored-attributes]
49 | template<> struct is_arithmetic<__m128> { enum { value = true }; };
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument ‘__m128i’ [-Wignored-attributes]
50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; };
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument ‘__m128d’ [-Wignored-attributes]
51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; };
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes]
222 | template<> struct unpacket_traits<Packet4f> {
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes]
228 | template<> struct unpacket_traits<Packet2d> {
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes]
1124 | ptranspose(PacketBlock<Packet4f,4>& kernel) {
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes]
1129 | ptranspose(PacketBlock<Packet2d,2>& kernel) {
| ^
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/Core:174:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes]
16 | struct conj_helper<PACKET_REAL, PACKET_CPLX, false, false> { \
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f’ {aka ‘__m128’} [-Wignored-attributes]
29 | struct conj_helper<PACKET_CPLX, PACKET_REAL, false, false> { \
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes]
16 | struct conj_helper<PACKET_REAL, PACKET_CPLX, false, false> { \
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d’ {aka ‘__m128d’} [-Wignored-attributes]
29 | struct conj_helper<PACKET_CPLX, PACKET_REAL, false, false> { \
| ^
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro ‘EIGEN_MAKE_CONJ_HELPER_CPLX_REAL’
298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/Core:165:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<float, 4>’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits<Eigen::Matrix<float, 4, 1> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits<Eigen::Quaternion<float> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__m128’} [-Wignored-attributes]
190 | bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__m128’} [-Wignored-attributes]
190 | bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__m128’} [-Wignored-attributes]
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(4) float>::half’ {aka ‘__m128’} [-Wignored-attributes]
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__m128’} [-Wignored-attributes]
208 | typedef typename find_best_packet_helper<Size,typename packet_traits<T>::type>::type type;
| ^~~~
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/Core:271:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 0>’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 1>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<float, 4, 1>, 3>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Matrix<float, 4, 1> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Matrix<float, 4, 1> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<float, 4, 1> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<float, 4, 1>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<float> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion<float>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<float>::type’ {aka ‘__m128’} [-Wignored-attributes]
56 | >::type PacketReturnType;
| ^~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of ‘struct Eigen::internal::find_best_packet<double, 4>’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from ‘struct Eigen::internal::traits<Eigen::Matrix<double, 4, 1> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from ‘struct Eigen::internal::traits<Eigen::Quaternion<double> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
190 | bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
190 | bool Stop = Size==Dynamic || (Size%unpacket_traits<PacketType>::size)==0 || is_same<PacketType,typename unpacket_traits<PacketType>::half>::value>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument ‘Eigen::internal::unpacket_traits<__vector(2) double>::half’ {aka ‘__m128d’} [-Wignored-attributes]
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
208 | typedef typename find_best_packet_helper<Size,typename packet_traits<T>::type>::type type;
| ^~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 0>’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 1>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from ‘class Eigen::DenseCoeffsBase<Eigen::Matrix<double, 4, 1>, 3>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from ‘class Eigen::DenseBase<Eigen::Matrix<double, 4, 1> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from ‘class Eigen::MatrixBase<Eigen::Matrix<double, 4, 1> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from ‘class Eigen::PlainObjectBase<Eigen::Matrix<double, 4, 1> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<double, 4, 1>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<double> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion<double>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
56 | >::type PacketReturnType;
| ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/SparseCore:37,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/Sparse:26,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/RcppEigenForward.h:29:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of ‘class Eigen::SparseMatrixBase<Eigen::SparseMatrix<double, 0, int> >’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from ‘class Eigen::SparseCompressedBase<Eigen::SparseMatrix<double, 0, int> >’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix<double, 0, int>’
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__m128d’} [-Wignored-attributes]
47 | >::type PacketReturnType;
| ^~~~~~~~~~~~~~~~
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o atacInferCnv.so RcppExports.o aggregate_bins.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-atacInferCnv/00new/atacInferCnv/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 (atacInferCnv)
atacInferCnv.Rcheck/tests/testthat.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(atacInferCnv)
>
> test_check("atacInferCnv")
Loading input...
Loading input...
Loading input...
Input is a file, assuming peaks matrix...
Loading input...
Input is a file, assuming peaks matrix...
Loading input...
Input is a file, assuming peaks matrix...
Using target annotation column: cnvBlock
C1 C2 Normal 167 116 17
Loading input...
Using existing input object
Loading input...
Input is a file, assuming peaks matrix...
Using target annotation column: cnvBlock
Using external control (assigned as ExtControl)
Loading input...
Input is a file, assuming peaks matrix...
Using target annotation column: cnvBlock
C1 C2 Normal 16 10 4
Creating result directory: /tmp/Rtmpr3K7dH/file321005e01526a
Prepare input data...
Adjust for custom annotation
Save signal...
Write configuration...
Loading input...
C1 C2 Normal 16 10 4
Creating result directory: /tmp/Rtmpr3K7dH/file321007286046b
Save signal...
Write configuration...
Prepared input.
Loading InferCNV configuration from: infercnv_config.yml
Processing sample_infercnv
Input: sample_raw_counts.txt.gz
Annotation: sample_cnv_ann.txt
Normal clusters: Normal
Cut off: 0.1
Num tumor clusters: 1
Assign custom reference: sample_cnv_ref.txt
INFO [2026-04-26 21:35:46] Parsing matrix: sample_raw_counts.txt.gz
INFO [2026-04-26 21:35:47] Parsing gene order file: sample_cnv_ref.txt
INFO [2026-04-26 21:35:47] Parsing cell annotations file: sample_cnv_ann.txt
INFO [2026-04-26 21:35:47] ::order_reduce:Start.
INFO [2026-04-26 21:35:47] .order_reduce(): expr and order match.
INFO [2026-04-26 21:35:47] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 80677,30 Total=241851 Min=0 Max=90.
INFO [2026-04-26 21:35:47] num genes removed taking into account provided gene ordering list: 41 = 0.050819936289153% removed.
INFO [2026-04-26 21:35:47] -filtering out cells < 100 or > Inf, removing 0 % of cells
WARN [2026-04-26 21:35:47] Please use "options(scipen = 100)" before running infercnv if you are using the analysis_mode="subclusters" option or you may encounter an error while the hclust is being generated.
INFO [2026-04-26 21:35:47] validating infercnv_obj
INFO [2026-04-26 21:35:47] ::process_data:Start
INFO [2026-04-26 21:35:47] Creating output path sample_infercnv
INFO [2026-04-26 21:35:47] Checking for saved results.
INFO [2026-04-26 21:35:47]
STEP 1: incoming data
INFO [2026-04-26 21:35:48]
STEP 02: Removing lowly expressed genes
INFO [2026-04-26 21:35:48] ::above_min_mean_expr_cutoff:Start
INFO [2026-04-26 21:35:48] Removing 58582 genes from matrix as below mean expr threshold: 0.1
INFO [2026-04-26 21:35:48] validating infercnv_obj
INFO [2026-04-26 21:35:48] There are 22054 genes and 30 cells remaining in the expr matrix.
INFO [2026-04-26 21:35:48] Removed 9102 genes having fewer than 3 min cells per gene = 41.2714 % genes removed here
INFO [2026-04-26 21:35:48] validating infercnv_obj
INFO [2026-04-26 21:35:49]
STEP 03: normalization by sequencing depth
INFO [2026-04-26 21:35:49] normalizing counts matrix by depth
INFO [2026-04-26 21:35:49] Computed total sum normalization factor as median libsize: 3623.500000
INFO [2026-04-26 21:35:49]
STEP 04: log transformation of data
INFO [2026-04-26 21:35:49] transforming log2xplus1()
INFO [2026-04-26 21:35:50]
STEP 08: removing average of reference data (before smoothing)
INFO [2026-04-26 21:35:50] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2026-04-26 21:35:50] subtracting mean(normal) per gene per cell across all data
INFO [2026-04-26 21:35:54] -subtracting expr per gene, use_bounds=TRUE
INFO [2026-04-26 21:35:56]
STEP 09: apply max centered expression threshold: 3
INFO [2026-04-26 21:35:56] ::process_data:setting max centered expr, threshold set to: +/-: 3
INFO [2026-04-26 21:35:57]
STEP 10: Smoothing data per cell by chromosome
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 1
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 2
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 3
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 4
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 5
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 6
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 7
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 8
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 9
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 10
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 11
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 12
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 13
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 14
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 15
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 16
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 17
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 18
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 19
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 20
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 21
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: 22
INFO [2026-04-26 21:35:57] smooth_by_chromosome: chr: X
INFO [2026-04-26 21:35:59]
STEP 11: re-centering data across chromosome after smoothing
INFO [2026-04-26 21:35:59] ::center_smooth across chromosomes per cell
INFO [2026-04-26 21:36:00]
STEP 12: removing average of reference data (after smoothing)
INFO [2026-04-26 21:36:00] ::subtract_ref_expr_from_obs:Start inv_log=FALSE, use_bounds=TRUE
INFO [2026-04-26 21:36:00] subtracting mean(normal) per gene per cell across all data
INFO [2026-04-26 21:36:05] -subtracting expr per gene, use_bounds=TRUE
INFO [2026-04-26 21:36:06]
STEP 14: invert log2(FC) to FC
INFO [2026-04-26 21:36:06] invert_log2(), computing 2^x
INFO [2026-04-26 21:36:08]
STEP 15: computing tumor subclusters via leiden
INFO [2026-04-26 21:36:08] define_signif_tumor_subclusters(p_val=0.1
INFO [2026-04-26 21:36:08] define_signif_tumor_subclusters(), tumor: C1
INFO [2026-04-26 21:36:08] Less cells in group C1 than k_nn setting. Keeping as a single subcluster.
INFO [2026-04-26 21:36:08] define_signif_tumor_subclusters(), tumor: C2
INFO [2026-04-26 21:36:08] Less cells in group C2 than k_nn setting. Keeping as a single subcluster.
INFO [2026-04-26 21:36:08] define_signif_tumor_subclusters(), tumor: Normal
INFO [2026-04-26 21:36:08] Less cells in group Normal than k_nn setting. Keeping as a single subcluster.
INFO [2026-04-26 21:36:09] ::plot_cnv:Start
INFO [2026-04-26 21:36:09] ::plot_cnv:Current data dimensions (r,c)=12952,30 Total=389496.513662872 Min=0.790258757829601 Max=1.61478114475046.
INFO [2026-04-26 21:36:09] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2026-04-26 21:36:09] plot_cnv(): auto thresholding at: (0.861114 , 1.143707)
INFO [2026-04-26 21:36:09] plot_cnv_observation:Start
INFO [2026-04-26 21:36:09] Observation data size: Cells= 26 Genes= 12952
INFO [2026-04-26 21:36:09] clustering observations via method: ward.D
INFO [2026-04-26 21:36:09] Number of cells in group(1) is 16
INFO [2026-04-26 21:36:09] group size being clustered: 16,12952
INFO [2026-04-26 21:36:09] Number of cells in group(2) is 10
INFO [2026-04-26 21:36:09] group size being clustered: 10,12952
INFO [2026-04-26 21:36:09] plot_cnv_observation:Writing observation groupings/color.
INFO [2026-04-26 21:36:09] plot_cnv_observation:Done writing observation groupings/color.
INFO [2026-04-26 21:36:09] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2026-04-26 21:36:09] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2026-04-26 21:36:09] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2026-04-26 21:36:09] Quantiles of plotted data range: 0.86111376099084,0.96527385916358,0.998865481750607,1.03584507397658,1.14370667169843
INFO [2026-04-26 21:36:09] plot_cnv_references:Start
INFO [2026-04-26 21:36:09] Reference data size: Cells= 4 Genes= 12952
INFO [2026-04-26 21:36:09] plot_cnv_references:Number reference groups= 1
INFO [2026-04-26 21:36:09] plot_cnv_references:Plotting heatmap.
INFO [2026-04-26 21:36:09] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2026-04-26 21:36:09] Quantiles of plotted data range: 0.872622511719713,0.978122386705928,0.998865481750801,1.02033117977316,1.14370667169843
INFO [2026-04-26 21:36:11] ::plot_cnv:Start
INFO [2026-04-26 21:36:11] ::plot_cnv:Current data dimensions (r,c)=12952,30 Total=389496.513662872 Min=0.790258757829601 Max=1.61478114475046.
INFO [2026-04-26 21:36:11] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2026-04-26 21:36:11] plot_cnv(): auto thresholding at: (0.861114 , 1.143707)
INFO [2026-04-26 21:36:11] plot_cnv_observation:Start
INFO [2026-04-26 21:36:11] Observation data size: Cells= 26 Genes= 12952
INFO [2026-04-26 21:36:11] plot_cnv_observation:Writing observation groupings/color.
INFO [2026-04-26 21:36:11] plot_cnv_observation:Done writing observation groupings/color.
INFO [2026-04-26 21:36:11] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2026-04-26 21:36:11] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2026-04-26 21:36:11] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2026-04-26 21:36:11] Quantiles of plotted data range: 0.86111376099084,0.96527385916358,0.998865481750607,1.03584507397658,1.14370667169843
INFO [2026-04-26 21:36:11] plot_cnv_references:Start
INFO [2026-04-26 21:36:11] Reference data size: Cells= 4 Genes= 12952
INFO [2026-04-26 21:36:11] plot_cnv_references:Number reference groups= 1
INFO [2026-04-26 21:36:11] plot_cnv_references:Plotting heatmap.
INFO [2026-04-26 21:36:11] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2026-04-26 21:36:11] Quantiles of plotted data range: 0.872622511719713,0.978122386705928,0.998865481750801,1.02033117977316,1.14370667169843
INFO [2026-04-26 21:36:11]
STEP 22: Denoising
INFO [2026-04-26 21:36:11] ::process_data:Remove noise, noise threshold defined via ref mean sd_amplifier: 1.5
INFO [2026-04-26 21:36:11] denoising using mean(normal) +- sd_amplifier * sd(normal) per gene per cell across all data
INFO [2026-04-26 21:36:11] :: **** clear_noise_via_ref_quantiles **** : removing noise between bounds: 0.949958858030604 - 1.05119143943608
INFO [2026-04-26 21:36:14] ::plot_cnv:Start
INFO [2026-04-26 21:36:14] ::plot_cnv:Current data dimensions (r,c)=12952,30 Total=390011.121721246 Min=0.790258757829601 Max=1.61478114475046.
INFO [2026-04-26 21:36:14] ::plot_cnv:Depending on the size of the matrix this may take a moment.
INFO [2026-04-26 21:36:14] plot_cnv(): auto thresholding at: (0.856293 , 1.143707)
INFO [2026-04-26 21:36:14] plot_cnv_observation:Start
INFO [2026-04-26 21:36:14] Observation data size: Cells= 26 Genes= 12952
INFO [2026-04-26 21:36:14] plot_cnv_observation:Writing observation groupings/color.
INFO [2026-04-26 21:36:14] plot_cnv_observation:Done writing observation groupings/color.
INFO [2026-04-26 21:36:14] plot_cnv_observation:Writing observation heatmap thresholds.
INFO [2026-04-26 21:36:14] plot_cnv_observation:Done writing observation heatmap thresholds.
INFO [2026-04-26 21:36:14] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2026-04-26 21:36:14] Quantiles of plotted data range: 0.856293328301567,1.00057514873334,1.00057514873334,1.00057514873334,1.14370667169843
INFO [2026-04-26 21:36:14] plot_cnv_references:Start
INFO [2026-04-26 21:36:14] Reference data size: Cells= 4 Genes= 12952
INFO [2026-04-26 21:36:14] plot_cnv_references:Number reference groups= 1
INFO [2026-04-26 21:36:14] plot_cnv_references:Plotting heatmap.
INFO [2026-04-26 21:36:14] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000
INFO [2026-04-26 21:36:14] Quantiles of plotted data range: 0.872622511719713,1.00057514873334,1.00057514873334,1.00057514873334,1.14370667169843
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
>
> proc.time()
user system elapsed
107.499 5.396 112.896
atacInferCnv.Rcheck/atacInferCnv-Ex.timings
| name | user | system | elapsed | |
| plotCnvBlocks | 50.342 | 1.639 | 51.947 | |
| prepareAtacInferCnvInput | 15.553 | 0.789 | 16.344 | |
| runAtacInferCnv | 41.006 | 0.719 | 41.712 | |