| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:37 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 569/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| destiny 3.22.0 (landing page) Philipp Angerer
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the destiny package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/destiny.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: destiny |
| Version: 3.22.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:destiny.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings destiny_3.22.0.tar.gz |
| StartedAt: 2025-10-15 22:36:05 -0400 (Wed, 15 Oct 2025) |
| EndedAt: 2025-10-15 22:46:56 -0400 (Wed, 15 Oct 2025) |
| EllapsedTime: 650.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: destiny.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:destiny.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings destiny_3.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/destiny.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘destiny/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘destiny’ version ‘3.22.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.lintr
.vscode
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘destiny’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* 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:
‘rgl’ ‘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 ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) Gene-Relevance.Rd:94: Escaped LaTeX specials: \_
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'DiffusionMap-class.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'ExpressionSet-helpers.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'dm_predict.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'find_sigmas.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'guo.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
Non-topic package-anchored link(s) in Rd file 'projection_dist.Rd':
‘[Biobase:class.ExpressionSet]{ExpressionSet}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in Rd file 'coercions.Rd':
‘fortify.DiffusionMap’ ‘fortify.DPT’
S3 methods shown with full name in Rd file 'plot.DPT.Rd':
‘plot.DPT’
S3 methods shown with full name in Rd file 'plot.DiffusionMap.Rd':
‘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 $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Gene-Relevance-plotting 5.114 0.064 5.179
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
y[1]: "element_blank"
── Failure ('test_ggplot.r:39:2'): ggplot plots have the ticks/boxes they should have ──
class(p3$theme$panel.border)[[1L]] not identical to "element_blank".
1/1 mismatches
x[1]: "ggplot2::element_blank"
y[1]: "element_blank"
── Failure ('test_ggplot.r:40:2'): ggplot plots have the ticks/boxes they should have ──
class(p4$theme$panel.border)[[1L]] not identical to "element_rect".
1/1 mismatches
x[1]: "ggplot2::element_rect"
y[1]: "element_rect"
[ FAIL 8 | WARN 1 | SKIP 1 | PASS 59 ]
Error: Test failures
Execution halted
* 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 ERROR, 7 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/destiny.Rcheck/00check.log’
for details.
destiny.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL destiny
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘destiny’ ...
** this is package ‘destiny’ version ‘3.22.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.21-bioc/R/library/grDevices/include' -I/usr/local/include -ggdb -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/Core:205,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/RcppEigenForward.h:28,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/Core:174:
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/Core:165:
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/Core:271:
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<float, 4, 1>’
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<float> >’
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion<float>’
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<double, 4, 1>’
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<double> >’
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion<double>’
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here
/home/biocbuild/bbs-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/SparseCore:37,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/Sparse:26,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/RcppEigenForward.h:29:
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix<double, 0, int>’
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:917:27: 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-3.21-bioc/R/site-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:778:26: 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-3.21-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]’
RcppExports.cpp:27:48: required from here
/home/biocbuild/bbs-3.21-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++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.21-bioc/R/library/grDevices/include' -I/usr/local/include -ggdb -fpic -g -O2 -Wall -Werror=format-security -c censoring.cpp -o censoring.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/Core:205,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/Dense:1,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/RcppEigenForward.h:28,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/RcppEigen.h:25,
from censoring.cpp:7:
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/Core:174:
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/Core:165:
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/Core:271:
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<float, 4, 1>’
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<float> >’
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion<float>’
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from ‘class Eigen::Matrix<double, 4, 1>’
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from ‘class Eigen::QuaternionBase<Eigen::Quaternion<double> >’
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from ‘class Eigen::Quaternion<double>’
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here
/home/biocbuild/bbs-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/SparseCore:37,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/Eigen/Sparse:26,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/RcppEigenForward.h:29:
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from ‘class Eigen::SparseMatrix<double, 0, int>’
/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:917:27: 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-3.21-bioc/R/site-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-3.21-bioc/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:778:26: 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-3.21-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]’
censoring.cpp:103:17: required from here
/home/biocbuild/bbs-3.21-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++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppEigen/include' -I'/home/biocbuild/bbs-3.21-bioc/R/library/grDevices/include' -I/usr/local/include -ggdb -fpic -g -O2 -Wall -Werror=format-security -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o destiny.so RcppExports.o censoring.o utils.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-destiny/00new/destiny/libs
** R
** data
** demo
** 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 (destiny)
destiny.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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.
> library(testthat)
> library(destiny)
>
> test_check('destiny')
[ FAIL 8 | WARN 1 | SKIP 1 | PASS 59 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• Not yet stable (1): 'test_gr.r:23:2'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_ggplot.r:31:2'): ggplot plots have the ticks/boxes they should have ──
class(p1$theme$axis.ticks)[[1L]] not identical to "element_blank".
1/1 mismatches
x[1]: "ggplot2::element_blank"
y[1]: "element_blank"
── Failure ('test_ggplot.r:32:2'): ggplot plots have the ticks/boxes they should have ──
class(p2$theme$axis.ticks)[[1L]] not identical to "element_line".
1/1 mismatches
x[1]: "ggplot2::element_line"
y[1]: "element_line"
── Failure ('test_ggplot.r:33:2'): ggplot plots have the ticks/boxes they should have ──
class(p3$theme$axis.ticks)[[1L]] not identical to "element_blank".
1/1 mismatches
x[1]: "ggplot2::element_blank"
y[1]: "element_blank"
── Failure ('test_ggplot.r:34:2'): ggplot plots have the ticks/boxes they should have ──
class(p4$theme$axis.ticks)[[1L]] not identical to "element_blank".
1/1 mismatches
x[1]: "ggplot2::element_blank"
y[1]: "element_blank"
── Failure ('test_ggplot.r:37:2'): ggplot plots have the ticks/boxes they should have ──
class(p1$theme$panel.border)[[1L]] not identical to "element_blank".
1/1 mismatches
x[1]: "ggplot2::element_blank"
y[1]: "element_blank"
── Failure ('test_ggplot.r:38:2'): ggplot plots have the ticks/boxes they should have ──
class(p2$theme$panel.border)[[1L]] not identical to "element_blank".
1/1 mismatches
x[1]: "ggplot2::element_blank"
y[1]: "element_blank"
── Failure ('test_ggplot.r:39:2'): ggplot plots have the ticks/boxes they should have ──
class(p3$theme$panel.border)[[1L]] not identical to "element_blank".
1/1 mismatches
x[1]: "ggplot2::element_blank"
y[1]: "element_blank"
── Failure ('test_ggplot.r:40:2'): ggplot plots have the ticks/boxes they should have ──
class(p4$theme$panel.border)[[1L]] not identical to "element_rect".
1/1 mismatches
x[1]: "ggplot2::element_rect"
y[1]: "element_rect"
[ FAIL 8 | WARN 1 | SKIP 1 | PASS 59 ]
Error: Test failures
Execution halted
destiny.Rcheck/destiny-Ex.timings
| name | user | system | elapsed | |
| DPT-matrix-methods | 1.354 | 0.021 | 1.375 | |
| DPT-methods | 1.234 | 0.051 | 1.285 | |
| DPT | 0.713 | 0.042 | 0.755 | |
| DiffusionMap-accessors | 0.987 | 0.053 | 1.040 | |
| DiffusionMap-class | 2.648 | 0.004 | 2.654 | |
| DiffusionMap-methods | 0.297 | 0.011 | 0.308 | |
| ExpressionSet-helpers | 0.086 | 0.001 | 0.087 | |
| Gene-Relevance-methods | 1.171 | 0.002 | 1.173 | |
| Gene-Relevance-plotting | 5.114 | 0.064 | 5.179 | |
| Gene-Relevance | 2.093 | 0.025 | 2.118 | |
| Sigmas-class | 0.100 | 0.003 | 0.104 | |
| coercions | 0.334 | 0.015 | 0.349 | |
| colorlegend | 0.012 | 0.001 | 0.012 | |
| cube_helix | 0.007 | 0.000 | 0.006 | |
| destiny-generics | 0.366 | 0.062 | 0.429 | |
| destiny | 4.76 | 0.11 | 4.87 | |
| dm_predict | 0.360 | 0.009 | 0.369 | |
| eig_decomp | 0.000 | 0.001 | 0.002 | |
| extractions | 0.622 | 0.020 | 0.642 | |
| find_dm_k | 0.011 | 0.000 | 0.011 | |
| find_sigmas | 0.396 | 0.002 | 0.399 | |
| find_tips | 0.335 | 0.003 | 0.339 | |
| l_which | 0 | 0 | 0 | |
| plot.DPT | 2.045 | 0.036 | 2.081 | |
| plot.DiffusionMap | 0.432 | 0.006 | 0.438 | |
| plot.Sigmas | 0.111 | 0.009 | 0.120 | |
| projection_dist | 0.180 | 0.001 | 0.182 | |
| random_root | 0.313 | 0.001 | 0.315 | |