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This page was generated on 2023-03-27 05:50:44 -0000 (Mon, 27 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" 6083
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INSTALL results for SingleR on kunpeng1


To the developers/maintainers of the SingleR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SingleR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1908/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SingleR 2.1.0  (landing page)
Aaron Lun
Snapshot Date: 2023-03-24 01:40:07 -0000 (Fri, 24 Mar 2023)
git_url: https://git.bioconductor.org/packages/SingleR
git_branch: devel
git_last_commit: 61f5032
git_last_commit_date: 2022-11-01 15:20:26 -0000 (Tue, 01 Nov 2022)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    TIMEOUT  skipped

Summary

Package: SingleR
Version: 2.1.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SingleR
StartedAt: 2023-03-24 04:50:33 -0000 (Fri, 24 Mar 2023)
EndedAt: 2023-03-24 04:53:05 -0000 (Fri, 24 Mar 2023)
EllapsedTime: 151.6 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SingleR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘SingleR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/  -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/  -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -c find_classic_markers.cpp -o find_classic_markers.o
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/DenseMatrix.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.h:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/utils.hpp:15,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/raticate.hpp:5,
                 from utils.h:13,
                 from find_classic_markers.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp: In instantiation of ‘std::pair<double, double> tatami::Matrix<T, IDX>::dimension_preference() const [with T = double; IDX = int]’:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39:   required from here
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  105 |     virtual std::pair<double, double> dimension_preference () const {
      |                                       ^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/  -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -c integrate_build.cpp -o integrate_build.o
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/DenseMatrix.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.h:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/utils.hpp:15,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/raticate.hpp:5,
                 from utils.h:13,
                 from integrate_build.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp: In instantiation of ‘std::pair<double, double> tatami::Matrix<T, IDX>::dimension_preference() const [with T = double; IDX = int]’:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39:   required from here
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  105 |     virtual std::pair<double, double> dimension_preference () const {
      |                                       ^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/  -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -c integrate_run.cpp -o integrate_run.o
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/DenseMatrix.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.h:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/utils.hpp:15,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/raticate.hpp:5,
                 from utils.h:13,
                 from integrate_run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp: In instantiation of ‘std::pair<double, double> tatami::Matrix<T, IDX>::dimension_preference() const [with T = double; IDX = int]’:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39:   required from here
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  105 |     virtual std::pair<double, double> dimension_preference () const {
      |                                       ^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/  -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -c prebuild.cpp -o prebuild.o
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/DenseMatrix.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.h:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/utils.hpp:15,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/raticate.hpp:5,
                 from utils.h:13,
                 from prebuild.cpp:4:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp: In instantiation of ‘std::pair<double, double> tatami::Matrix<T, IDX>::dimension_preference() const [with T = double; IDX = int]’:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39:   required from here
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  105 |     virtual std::pair<double, double> dimension_preference () const {
      |                                       ^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I../inst/include/  -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -c run.cpp -o run.o
In file included from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/DenseMatrix.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.h:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/tatami.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/utils.hpp:15,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
                 from /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/raticate/raticate.hpp:5,
                 from utils.h:13,
                 from run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp: In instantiation of ‘std::pair<double, double> tatami::Matrix<T, IDX>::dimension_preference() const [with T = double; IDX = int]’:
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39:   required from here
/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/beachmat/include/tatami/base/Matrix.hpp:105:39: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  105 |     virtual std::pair<double, double> dimension_preference () const {
      |                                       ^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib -o SingleR.so RcppExports.o find_classic_markers.o integrate_build.o integrate_run.o prebuild.o run.o
installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-SingleR/00new/SingleR/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 (SingleR)