Multiple platform build/check report for BioC 3.20 - INSTALL results for ternarynet on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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 nebbiolo2

To the developers/maintainers of the ternarynet package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org: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.

raw results

Summary

Package: ternarynet

Version: 1.50.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ternarynet

StartedAt: 2024-12-19 15:15:02 -0500 (Thu, 19 Dec 2024)

EndedAt: 2024-12-19 15:15:10 -0500 (Thu, 19 Dec 2024)

EllapsedTime: 8.3 seconds

RetCode: 0

Status: OK

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ternarynet
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘ternarynet’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c array.c -o array.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -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/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c gn_Rwrap.c -o gn_Rwrap.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -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:24:9: warning: variable ‘perturbationType’ set but not used [-Wunused-but-set-variable]
   24 |     int perturbationType, scoreType, backupStage, maxStage, maxTransition;
      |         ^~~~~~~~~~~~~~~~
tnetfit.cc:24:27: warning: variable ‘scoreType’ set but not used [-Wunused-but-set-variable]
   24 |     int perturbationType, scoreType, backupStage, maxStage, maxTransition;
      |                           ^~~~~~~~~
tnetfit.cc:24:38: warning: variable ‘backupStage’ set but not used [-Wunused-but-set-variable]
   24 |     int perturbationType, scoreType, backupStage, maxStage, maxTransition;
      |                                      ^~~~~~~~~~~
tnetfit.cc:73:39: warning: unused variable ‘tempi’ [-Wunused-variable]
   73 |     int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition;
      |                                       ^~~~~
tnetfit.cc:207:25: warning: ‘sigma0’ may be used uninitialized [-Wmaybe-uninitialized]
  207 |             convergence = (muci-muci_old)/sigma0;
      |             ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
tnetfit.cc:98:12: note: ‘sigma0’ was declared here
   98 |     double sigma0, sigmaci, sigmaRaw, muci, muci_old, convergence;
      |            ^~~~~~
tnetfit.cc:202:43: warning: ‘sigmaci’ may be used uninitialized [-Wmaybe-uninitialized]
  202 |           sigmaci = rho*sigmaRaw + (1-rho)*sigmaci;
      |                                    ~~~~~~~^~~~~~~~
tnetfit.cc:98:20: note: ‘sigmaci’ was declared here
   98 |     double sigma0, sigmaci, sigmaRaw, muci, muci_old, convergence;
      |                    ^~~~~~~
tnetfit.cc:207:32: warning: ‘muci_old’ may be used uninitialized [-Wmaybe-uninitialized]
  207 |             convergence = (muci-muci_old)/sigma0;
      |                           ~~~~~^~~~~~~~~~
tnetfit.cc:98:45: note: ‘muci_old’ was declared here
   98 |     double sigma0, sigmaci, sigmaRaw, muci, muci_old, convergence;
      |                                             ^~~~~~~~
tnetfit.cc:311:19: warning: ‘newScore’ may be used uninitialized [-Wmaybe-uninitialized]
  311 |     SET_VECTOR_ELT(Routput, 10, ScalarReal(newScore));
      |     ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tnetfit.cc:77:12: note: ‘newScore’ was declared here
   77 |     double newScore, oldScore, difference, minScore = 999999999;
      |            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c tnetfuncs.cc -o tnetfuncs.o
tnetfuncs.cc: In function ‘double AttractorDistanceForced(int, int, int, int, double, int*, int*, int*, const double*, const int*)’:
tnetfuncs.cc:427:5: warning: unused variable ‘tableWidth’ [-Wunused-variable]
  427 | int tableWidth = powi(nOutcomes,maxDegree);
      |     ^~~~~~~~~~
tnetfuncs.cc:435:5: warning: unused variable ‘ipause’ [-Wunused-variable]
  435 | int ipause;
      |     ^~~~~~
tnetfuncs.cc: In function ‘double initialTemp(double, int, int, int, int, int, double, double, double, int, const double*, int*, int*, int*, const double*, const int*)’:
tnetfuncs.cc:517:13: warning: unused variable ‘ipause’ [-Wunused-variable]
  517 |         int ipause;
      |             ^~~~~~
tnetfuncs.cc:521:21: warning: unused variable ‘i’ [-Wunused-variable]
  521 |         int m1, m2, i;
      |                     ^
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c tnetpost.cc -o tnetpost.o
tnetpost.cc: In function ‘SEXPREC* tnetpost(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
tnetpost.cc:25:9: warning: unused variable ‘ipause’ [-Wunused-variable]
   25 |     int ipause;
      |         ^~~~~~
tnetpost.cc:27:9: warning: unused variable ‘m0fit’ [-Wunused-variable]
   27 |     int m0fit;
      |         ^~~~~
tnetpost.cc:28:32: warning: variable ‘minScore’ set but not used [-Wunused-but-set-variable]
   28 |     double newScore, oldScore, minScore, finalScore;
      |                                ^~~~~~~~
tnetpost.cc:28:42: warning: unused variable ‘finalScore’ [-Wunused-variable]
   28 |     double newScore, oldScore, minScore, finalScore;
      |                                          ^~~~~~~~~~
tnetpost.cc:30:9: warning: unused variable ‘l0’ [-Wunused-variable]
   30 |     int l0, stage_count, tempi, jtrans, nTransition;
      |         ^~
tnetpost.cc:30:13: warning: unused variable ‘stage_count’ [-Wunused-variable]
   30 |     int l0, stage_count, tempi, jtrans, nTransition;
      |             ^~~~~~~~~~~
tnetpost.cc:30:26: warning: unused variable ‘tempi’ [-Wunused-variable]
   30 |     int l0, stage_count, tempi, jtrans, nTransition;
      |                          ^~~~~
tnetpost.cc:30:33: warning: unused variable ‘jtrans’ [-Wunused-variable]
   30 |     int l0, stage_count, tempi, jtrans, nTransition;
      |                                 ^~~~~~
tnetpost.cc:30:41: warning: unused variable ‘nTransition’ [-Wunused-variable]
   30 |     int l0, stage_count, tempi, jtrans, nTransition;
      |                                         ^~~~~~~~~~~
tnetpost.cc:36:21: warning: variable ‘xSeedFit’ set but not used [-Wunused-but-set-variable]
   36 |     int m0, mdelta, xSeedFit;
      |                     ^~~~~~~~
tnetpost.cc:38:9: warning: variable ‘perturbationType’ set but not used [-Wunused-but-set-variable]
   38 |     int perturbationType, scoreType, backupStage;
      |         ^~~~~~~~~~~~~~~~
tnetpost.cc:38:27: warning: variable ‘scoreType’ set but not used [-Wunused-but-set-variable]
   38 |     int perturbationType, scoreType, backupStage;
      |                           ^~~~~~~~~
tnetpost.cc:38:38: warning: variable ‘backupStage’ set but not used [-Wunused-but-set-variable]
   38 |     int perturbationType, scoreType, backupStage;
      |                                      ^~~~~~~~~~~
tnetpost.cc:39:9: warning: variable ‘maxStage’ set but not used [-Wunused-but-set-variable]
   39 |     int maxStage, maxTransition;
      |         ^~~~~~~~
tnetpost.cc:39:19: warning: variable ‘maxTransition’ set but not used [-Wunused-but-set-variable]
   39 |     int maxStage, maxTransition;
      |                   ^~~~~~~~~~~~~
tnetpost.cc:40:12: warning: variable ‘epsilon’ set but not used [-Wunused-but-set-variable]
   40 |     double epsilon, chi0, delta, rho;
      |            ^~~~~~~
tnetpost.cc:40:21: warning: variable ‘chi0’ set but not used [-Wunused-but-set-variable]
   40 |     double epsilon, chi0, delta, rho;
      |                     ^~~~
tnetpost.cc:40:27: warning: variable ‘delta’ set but not used [-Wunused-but-set-variable]
   40 |     double epsilon, chi0, delta, rho;
      |                           ^~~~~
tnetpost.cc:40:34: warning: variable ‘rho’ set but not used [-Wunused-but-set-variable]
   40 |     double epsilon, chi0, delta, rho;
      |                                  ^~~
In file included from tnetpost.cc:14:
/home/biocbuild/bbs-3.20-bioc/R/include/Rmath.h:210:25: warning: variable ‘Rf_beta’ set but not used [-Wunused-but-set-variable]
  210 | #define beta            Rf_beta
      |                         ^~~~~~~
tnetpost.cc:41:9: note: in expansion of macro ‘beta’
   41 |     int beta;
      |         ^~~~
tnetpost.cc:44:9: warning: variable ‘ne’ set but not used [-Wunused-but-set-variable]
   44 |     int ne, maxDegree;
      |         ^~
tnetpost.cc:150:10: warning: variable ‘minDump’ set but not used [-Wunused-but-set-variable]
  150 |     bool minDump = true;
      |          ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c util.c -o util.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o ternarynet.so array.o gn.o gn_Rwrap.o init.o tnetfit.o tnetfuncs.o tnetpost.o util.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-ternarynet/00new/ternarynet/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ternarynet)