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This page was generated on 2023-05-10 10:04:41 -0000 (Wed, 10 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" 6211
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INSTALL results for SingleR on kunpeng1


To the developers/maintainers of the SingleR package:
- 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 Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1903/2194HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SingleR 2.3.0  (landing page)
Aaron Lun
Snapshot Date: 2023-05-08 19:11:19 -0000 (Mon, 08 May 2023)
git_url: https://git.bioconductor.org/packages/SingleR
git_branch: devel
git_last_commit: 53b9991
git_last_commit_date: 2023-04-25 15:12:06 -0000 (Tue, 25 Apr 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    WARNINGS  

Summary

Package: SingleR
Version: 2.3.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SingleR
StartedAt: 2023-05-08 22:12:08 -0000 (Mon, 08 May 2023)
EndedAt: 2023-05-08 22:14:43 -0000 (Mon, 08 May 2023)
EllapsedTime: 155.1 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)