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This page was generated on 2026-04-04 16:08 -0400 (Sat, 04 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.6.0 alpha (2026-03-30 r89742) | 920 |
| 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 159/230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| openCyto 2.23.1 (landing page) Mike Jiang
| teran2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||
|
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. |
| 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 |
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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’