Multiple platform build/check report for BioC 3.21 - INSTALL results for ternarynet on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4752
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4464
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4415
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4370
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4279
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*

INSTALL results for ternarynet on kunpeng2

To the developers/maintainers of the ternarynet package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/ternarynet.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: ternarynet

Version: 1.51.0

Command: /home/biocbuild/R/R/bin/R CMD INSTALL ternarynet

StartedAt: 2024-12-11 19:41:37 -0000 (Wed, 11 Dec 2024)

EndedAt: 2024-12-11 19:41:39 -0000 (Wed, 11 Dec 2024)

EllapsedTime: 2.6 seconds

RetCode: 1

Status: ERROR

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ternarynet
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘ternarynet’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)’
using C++ compiler: ‘g++ (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c array.c -o array.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c gn.c -o gn.o
gn.c: In function ‘score’:
gn.c:486: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  486 | #pragma omp parallel for
      | 
gn.c:493: warning: ignoring ‘#pragma omp atomic’ [-Wunknown-pragmas]
  493 | #pragma omp atomic
      | 
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c gn_Rwrap.c -o gn_Rwrap.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c init.c -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c tnetfit.cc -o tnetfit.o
tnetfit.cc: In function ‘SEXPREC* tnetfit(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
tnetfit.cc:35:32: error: ‘coerceVector’ was not declared in this scope; did you mean ‘Rf_coerceVector’?
   35 |     perturbationType = INTEGER(coerceVector(RperturbationType, INTSXP))[0];
      |                                ^~~~~~~~~~~~
      |                                Rf_coerceVector
In file included from /home/biocbuild/R/R/include/Rdefines.h:41,
                 from tnetfit.cc:12:
tnetfit.cc:220:23: error: ‘allocVector’ was not declared in this scope; did you mean ‘Rf_allocVector’?
  220 |     PROTECT(Routput = allocVector(VECSXP, 14));
      |                       ^~~~~~~~~~~
/home/biocbuild/R/R/include/Rinternals.h:388:31: note: in definition of macro ‘PROTECT’
  388 | #define PROTECT(s) Rf_protect(s)
      |                               ^
tnetfit.cc:311:33: error: ‘ScalarReal’ was not declared in this scope; did you mean ‘Rf_ScalarReal’?
  311 |     SET_VECTOR_ELT(Routput, 10, ScalarReal(newScore));
      |                                 ^~~~~~~~~~
      |                                 Rf_ScalarReal
tnetfit.cc:315:33: error: ‘ScalarInteger’ was not declared in this scope; did you mean ‘Rf_ScalarInteger’?
  315 |     SET_VECTOR_ELT(Routput, 12, ScalarInteger(stage_count));
      |                                 ^~~~~~~~~~~~~
      |                                 Rf_ScalarInteger
tnetfit.cc:320:29: error: ‘mkChar’ was not declared in this scope
  320 |     SET_STRING_ELT(Rnames,0,mkChar("degreeObj"));
      |                             ^~~~~~
tnetfit.cc:334:5: error: ‘setAttrib’ was not declared in this scope; did you mean ‘Rf_setAttrib’?
  334 |     setAttrib(Routput, R_NamesSymbol, Rnames);
      |     ^~~~~~~~~
      |     Rf_setAttrib
tnetfit.cc:73:39: warning: unused variable ‘tempi’ [-Wunused-variable]
   73 |     int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition;
      |                                       ^~~~~
make: *** [/home/biocbuild/R/R/etc/Makeconf:202: tnetfit.o] Error 1
ERROR: compilation failed for package ‘ternarynet’
* removing ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/ternarynet’