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This page was generated on 2026-04-04 16:08 -0400 (Sat, 04 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.3 LTS)x86_644.6.0 alpha (2026-03-30 r89742) 920
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Package 159/230HostnameOS / ArchINSTALLBUILDCHECK
openCyto 2.23.1  (landing page)
Mike Jiang
Snapshot Date: 2026-04-04 12:00 -0400 (Sat, 04 Apr 2026)
git_url: https://git.bioconductor.org/packages/openCyto
git_branch: devel
git_last_commit: 6c42736
git_last_commit_date: 2026-03-12 16:32:43 -0400 (Thu, 12 Mar 2026)
teran2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR    ERROR  skipped


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: 2.23.1
Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL openCyto
StartedAt: 2026-04-04 12:24:59 -0400 (Sat, 04 Apr 2026)
EndedAt: 2026-04-04 12:25:00 -0400 (Sat, 04 Apr 2026)
EllapsedTime: 1.0 seconds
RetCode: 1
Status:   ERROR  

Command output

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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL openCyto
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘openCyto’ ...
** this is package ‘openCyto’ version ‘2.23.1’
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c Cdqrls.cpp -o Cdqrls.o
In file included from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/cpp11/include/cpp11.hpp:3,
                 from Cdqrls.cpp:5:
/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/cpp11/include/cpp11/R.hpp: In function ‘SEXPREC* cpp11::detail::r_ns_env(const char*)’:
/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/cpp11/include/cpp11/R.hpp:128:10: error: ‘R_getRegisteredNamespace’ was not declared in this scope
  128 |   return R_getRegisteredNamespace(name);
      |          ^~~~~~~~~~~~~~~~~~~~~~~~
Cdqrls.cpp: In function ‘SEXPREC* Cdqrls(SEXP, SEXP, SEXP)’:
Cdqrls.cpp:38:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   38 |   for (R_xlen_t i = 0 ; i < XLENGTH(x) ; i++)
      |   ^~~
Cdqrls.cpp:41:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   41 |     rptr = REAL(y);
      |     ^~~~
Cdqrls.cpp:42:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   42 |     for (R_xlen_t i = 0 ; i < XLENGTH(y) ; i++)
      |     ^~~
Cdqrls.cpp:45:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   45 |       const char *ansNms[] = {"qr", "coefficients", "residuals", "effects",
      |       ^~~~~
Cdqrls.cpp:67:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
   67 |       for(int i = 0; i < p; i++)
      |       ^~~
Cdqrls.cpp:69:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
   69 |         SET_VECTOR_ELT(ans, 8, Rf_ScalarLogical(pivoted));
      |         ^~~~~~~~~~~~~~
make: *** [/home/rapidbuild/bbs-3.23-bioc-rapid/R/etc/Makeconf:197: Cdqrls.o] Error 1
ERROR: compilation failed for package ‘openCyto’
* removing ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/openCyto’
* restoring previous ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/openCyto’