| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-08 11:35 -0500 (Thu, 08 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4815 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 1500/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| openCyto 2.23.0 (landing page) Mike Jiang
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the openCyto package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/openCyto.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: 2.23.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL openCyto |
| StartedAt: 2026-01-07 15:16:12 -0500 (Wed, 07 Jan 2026) |
| EndedAt: 2026-01-07 15:16:15 -0500 (Wed, 07 Jan 2026) |
| EllapsedTime: 2.3 seconds |
| RetCode: 1 |
| Status: ERROR |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL openCyto
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘openCyto’ ...
** this is package ‘openCyto’ version ‘2.23.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/cpp11/include' -I'/home/biocbuild/bbs-3.23-bioc/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 /home/biocbuild/bbs-3.23-bioc/R/site-library/cpp11/include/cpp11.hpp:7,
from Cdqrls.cpp:5:
/home/biocbuild/bbs-3.23-bioc/R/site-library/cpp11/include/cpp11/data_frame.hpp: In static member function ‘static R_xlen_t cpp11::data_frame::calc_nrow(SEXP)’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/cpp11/include/cpp11/data_frame.hpp:29:16: error: ‘R_nrow’ was not declared in this scope; did you mean ‘nrow’?
29 | return R_nrow(x);
| ^~~~~~
| nrow
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/biocbuild/bbs-3.23-bioc/R/etc/Makeconf:209: Cdqrls.o] Error 1
ERROR: compilation failed for package ‘openCyto’
* removing ‘/home/biocbuild/bbs-3.23-bioc/R/site-library/openCyto’
* restoring previous ‘/home/biocbuild/bbs-3.23-bioc/R/site-library/openCyto’