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This page was generated on 2022-01-15 11:06:52 -0500 (Sat, 15 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4160
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4055
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3997
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4114
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 nebbiolo1


To the developers/maintainers of the ternarynet package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1935/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ternarynet 1.39.0  (landing page)
McCall N. Matthew
Snapshot Date: 2022-01-14 13:55:18 -0500 (Fri, 14 Jan 2022)
git_url: https://git.bioconductor.org/packages/ternarynet
git_branch: master
git_last_commit: 5e7b0fe
git_last_commit_date: 2021-10-26 12:02:04 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'BiocParallel' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ternarynet
Version: 1.39.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL ternarynet
StartedAt: 2022-01-14 15:07:48 -0500 (Fri, 14 Jan 2022)
EndedAt: 2022-01-14 15:07:57 -0500 (Fri, 14 Jan 2022)
EllapsedTime: 9.5 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL ternarynet
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘ternarynet’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c array.c -o array.o
gcc -I"/home/biocbuild/bbs-3.15-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-3.15-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-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-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:311:19: warning: ‘newScore’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  311 |     SET_VECTOR_ELT(Routput, 10, ScalarReal(newScore));
      |     ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tnetfit.cc:207:25: warning: ‘muci_old’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  207 |      convergence = (muci-muci_old)/sigma0;
      |                    ~~~~~^~~~~~~~~~
tnetfit.cc:202:36: warning: ‘sigmaci’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  202 |    sigmaci = rho*sigmaRaw + (1-rho)*sigmaci;
      |                             ~~~~~~~^~~~~~~~
tnetfit.cc:207:18: warning: ‘sigma0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  207 |      convergence = (muci-muci_old)/sigma0;
      |      ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-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:517:6: warning: unused variable ‘ipause’ [-Wunused-variable]
  517 |  int ipause;
      |      ^~~~~~
tnetfuncs.cc:521:16: warning: unused variable ‘i’ [-Wunused-variable]
  521 |    int m1, m2, i;
      |                ^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-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-3.15-bioc/R/include/Rmath.h:209:15: warning: variable ‘Rf_beta’ set but not used [-Wunused-but-set-variable]
  209 | #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-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c util.c -o util.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-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-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/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)