Mike Jiang
| Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/openCyto |
| git_branch: devel |
| git_last_commit: 35cdc28 |
| git_last_commit_date: 2025-04-15 10:27:07 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-15 12:07 -0400 (Fri, 15 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4554 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| 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 1482/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| openCyto 2.21.0 (landing page) Mike Jiang
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 2.21.0 |
| Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL openCyto |
| StartedAt: 2025-08-14 16:04:09 -0400 (Thu, 14 Aug 2025) |
| EndedAt: 2025-08-14 16:06:05 -0400 (Thu, 14 Aug 2025) |
| EllapsedTime: 116.0 seconds |
| RetCode: 0 |
| Status: OK |
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###
### Running command:
###
### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL openCyto
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'openCyto' ...
** this is package 'openCyto' version '2.21.0'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
using C++17
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/cpp11/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/BH/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Cdqrls.cpp -o Cdqrls.o
Cdqrls.cpp: In function 'SEXPREC* Cdqrls(SEXP, SEXP, SEXP)':
Cdqrls.cpp:43:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
43 | for (R_xlen_t i = 0 ; i < XLENGTH(x) ; i++)
| ^~~
Cdqrls.cpp:46:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
46 | rptr = REAL(y);
| ^~~~
Cdqrls.cpp:47:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
47 | for (R_xlen_t i = 0 ; i < XLENGTH(y) ; i++)
| ^~~
Cdqrls.cpp:50:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
50 | const char *ansNms[] = {"qr", "coefficients", "residuals", "effects",
| ^~~~~
Cdqrls.cpp:72:7: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
72 | for(int i = 0; i < p; i++)
| ^~~
Cdqrls.cpp:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
74 | SET_VECTOR_ELT(ans, 8, Rf_ScalarLogical(pivoted));
| ^~~~~~~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/cpp11/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/BH/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Hungarian.cpp -o Hungarian.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/cpp11/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/BH/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/cpp11/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/BH/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c lm_wfit.cpp -o lm_wfit.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/cpp11/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/BH/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c misc.cpp -o misc.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/cpp11/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/BH/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rlm.cpp -o rlm.o
In file included from F:/biocbuild/bbs-3.22-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from F:/biocbuild/bbs-3.22-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from F:/biocbuild/bbs-3.22-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from F:/biocbuild/bbs-3.22-bioc/R/library/BH/include/boost/accumulators/statistics/median.hpp:11,
from rlm.cpp:5:
F:/biocbuild/bbs-3.22-bioc/R/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 | );
| ~
F:/biocbuild/bbs-3.22-bioc/R/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 | );
| ~
| -
F:/biocbuild/bbs-3.22-bioc/R/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 | );
| ~
F:/biocbuild/bbs-3.22-bioc/R/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:52:10: warning: 'scale' may be used uninitialized [-Wmaybe-uninitialized]
52 | double scale;
| ^~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/cpp11/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/BH/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c solve_LSAP.cpp -o solve_LSAP.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/cpp11/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/BH/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c unlockNamespace.cpp -o unlockNamespace.o
g++ -shared -s -static-libgcc -o openCyto.dll tmp.def Cdqrls.o Hungarian.o cpp11.o lm_wfit.o misc.o rlm.o solve_LSAP.o unlockNamespace.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-openCyto/00new/openCyto/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (openCyto)