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### Running command:
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###   /home/hpages/bbs-3.18-bioc/R/bin/R CMD INSTALL nem
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* installing to library ‘/home/hpages/bbs-3.18-bioc-testing/Rlibs’
* installing *source* package ‘nem’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0’
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c MCMC.c -o MCMC.o
MCMC.c: In function ‘network_likelihood’:
MCMC.c:116:62: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  116 |                                         if(egene_prior[i][s] > 0 & s < nsgenes){
      |                                            ~~~~~~~~~~~~~~~~~~^~~
MCMC.c:125:62: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  125 |                                         if(egene_prior[i][s] > 0 & s == nsgenes){ // virtual "null" S-gene (not connected to any other S-gene, never perturbed) ==> automatic E-gene selection
      |                                            ~~~~~~~~~~~~~~~~~~^~~
MCMC.c: In function ‘MCMCrun’:
MCMC.c:403:10: warning: unused variable ‘stored2’ [-Wunused-variable]
  403 |     long stored2 = 0;
      |          ^~~~~~~
MCMC.c:402:10: warning: unused variable ‘stored’ [-Wunused-variable]
  402 |     long stored = 0;
      |          ^~~~~~
MCMC.c:359:35: warning: unused variable ‘mutinf’ [-Wunused-variable]
  359 |     double loglikMean, loglikSum, mutinf, delta, logPrior_cur_scale;
      |                                   ^~~~~~
MCMC.c: In function ‘network_likelihood’:
MCMC.c:155:34: warning: ‘max_loglik0_idx’ may be used uninitialized [-Wmaybe-uninitialized]
  155 |                 loglik += loglik0[max_loglik0_idx] + log(1 + loglik_tmp); // the "1" is there, because exp(loglik0[max_loglik0_idx] - loglik0[max_loglik0_idx]) = 1, which is omitted in the loop above
      |                                  ^
MCMC.c:108:13: note: ‘max_loglik0_idx’ was declared here
  108 |         int max_loglik0_idx;
      |             ^~~~~~~~~~~~~~~
MCMC.c: In function ‘MCMCrun’:
MCMC.c:455:19: warning: ‘delta_poss_operations’ may be used uninitialized [-Wmaybe-uninitialized]
  455 |         hfactor = updateFactor(likLogOld, logPriorOld, logPriorScale, likelihood, logPrior_cur, logPrior_cur_scale, n_neighbors, n_neighbors + delta_poss_operations);
      |                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MCMC.c:420:9: note: ‘delta_poss_operations’ was declared here
  420 |     int delta_poss_operations;
      |         ^~~~~~~~~~~~~~~~~~~~~
MCMC.c:455:19: warning: ‘logPrior_cur’ may be used uninitialized [-Wmaybe-uninitialized]
  455 |         hfactor = updateFactor(likLogOld, logPriorOld, logPriorScale, likelihood, logPrior_cur, logPrior_cur_scale, n_neighbors, n_neighbors + delta_poss_operations);
      |                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MCMC.c:407:24: note: ‘logPrior_cur’ was declared here
  407 |     double likelihood, logPrior_cur, priorScale_new;
      |                        ^~~~~~~~~~~~
MCMC.c:455:19: warning: ‘likelihood’ may be used uninitialized [-Wmaybe-uninitialized]
  455 |         hfactor = updateFactor(likLogOld, logPriorOld, logPriorScale, likelihood, logPrior_cur, logPrior_cur_scale, n_neighbors, n_neighbors + delta_poss_operations);
      |                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MCMC.c:407:12: note: ‘likelihood’ was declared here
  407 |     double likelihood, logPrior_cur, priorScale_new;
      |            ^~~~~~~~~~
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c netlearn.c -o netlearn.o
netlearn.c: In function ‘learn_network’:
netlearn.c:168:16: warning: unused variable ‘lik_switch’ [-Wunused-variable]
  168 |         double lik_switch;
      |                ^~~~~~~~~~
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c wrapper.c -o wrapper.o
wrapper.c: In function ‘MCMCrunWrapper’:
wrapper.c:107:27: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  107 |     int useMCMC = (sample > 0 & burnin > 0);
      |                    ~~~~~~~^~~
gcc -shared -L/usr/local/lib -o nem.so MCMC.o netlearn.o wrapper.o
installing to /home/hpages/bbs-3.18-bioc-testing/Rlibs/00LOCK-nem/00new/nem/libs
** R
** data
** 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
Warning: Package 'nem' is deprecated and will be removed from Bioconductor
  version 3.12
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'nem' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (nem)