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This page was generated on 2024-11-21 09:25 -0500 (Thu, 21 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-11-14 r87333) -- "Unsuffered Consequences" 858
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Package 150/215HostnameOS / ArchINSTALLBUILDCHECK
openCyto 2.19.0  (landing page)
Mike Jiang
Snapshot Date: 2024-11-21 06:00 -0500 (Thu, 21 Nov 2024)
git_url: https://git.bioconductor.org/packages/openCyto
git_branch: devel
git_last_commit: d3a4d87
git_last_commit_date: 2024-10-29 09:48:49 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  

INSTALL results for openCyto on teran2

To the developers/maintainers of the openCyto package:
- 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.

raw results


Summary

Package: openCyto
Version: 2.19.0
Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL openCyto
StartedAt: 2024-11-21 06:17:03 -0500 (Thu, 21 Nov 2024)
EndedAt: 2024-11-21 06:17:26 -0500 (Thu, 21 Nov 2024)
EllapsedTime: 23.4 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL openCyto
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘openCyto’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++17
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c Hungarian.cpp -o Hungarian.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c cpp11.cpp -o cpp11.o
In file included from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include/cpp11.hpp:3,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include/cpp11/declarations.hpp:13,
                 from cpp11.cpp:5:
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include/cpp11/R.hpp:11: warning: "R_NO_REMAP" redefined
   11 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c misc.cpp -o misc.o
In file included from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include/cpp11.hpp:3,
                 from misc.cpp:1:
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include/cpp11/R.hpp:11: warning: "R_NO_REMAP" redefined
   11 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c rlm.cpp -o rlm.o
In file included from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include/cpp11.hpp:3,
                 from rlm.cpp:4:
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include/cpp11/R.hpp:11: warning: "R_NO_REMAP" redefined
   11 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
In file included from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include/boost/accumulators/statistics/median.hpp:11,
                 from rlm.cpp:8:
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
rlm.cpp: In function ‘cpp11::list rlm_cpp(cpp11::doubles_matrix<>, cpp11::doubles, int)’:
rlm.cpp:55:10: warning: ‘scale’ may be used uninitialized [-Wmaybe-uninitialized]
   55 |   double scale;
      |          ^~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c solve_LSAP.cpp -o solve_LSAP.o
In file included from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include/cpp11.hpp:3,
                 from solve_LSAP.cpp:3:
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include/cpp11/R.hpp:11: warning: "R_NO_REMAP" redefined
   11 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -DR_NO_REMAP -c unlockNamespace.cpp -o unlockNamespace.o
In file included from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include/cpp11.hpp:3,
                 from unlockNamespace.cpp:1:
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cpp11/include/cpp11/R.hpp:11: warning: "R_NO_REMAP" redefined
   11 | #define R_NO_REMAP
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17 -shared -L/usr/local/lib -o openCyto.so Hungarian.o cpp11.o misc.o rlm.o solve_LSAP.o unlockNamespace.o
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-openCyto/00new/openCyto/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 (openCyto)