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INSTALL report for nem on tokay1

This page was generated on 2018-04-12 13:18:26 -0400 (Thu, 12 Apr 2018).

Package 933/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nem 2.52.0
Holger Froehlich
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/nem
Branch: RELEASE_3_6
Last Commit: d2507a6
Last Changed Date: 2017-10-30 12:39:18 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: nem
Version: 2.52.0
Command: rm -rf nem.buildbin-libdir && mkdir nem.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/nem_2.52.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=nem.buildbin-libdir --merge-multiarch nem_2.52.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL nem_2.52.0.zip && rm nem_2.52.0.tar.gz nem_2.52.0.zip
StartedAt: 2018-04-11 18:39:08 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 18:40:32 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 84.2 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   rm -rf nem.buildbin-libdir && mkdir nem.buildbin-libdir  && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/nem_2.52.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=nem.buildbin-libdir --merge-multiarch nem_2.52.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL nem_2.52.0.zip  && rm nem_2.52.0.tar.gz nem_2.52.0.zip
###
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100 4182k  100 4182k    0     0  67.2M      0 --:--:-- --:--:-- --:--:-- 71.6M

install for i386

* installing *source* package 'nem' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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]
                                         if(egene_prior[i][s] > 0 & s < nsgenes){
                                                              ^
MCMC.c:125:27: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
      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]
     long stored2 = 0;
          ^
MCMC.c:402:10: warning: unused variable 'stored' [-Wunused-variable]
     long stored = 0;
          ^
MCMC.c:359:35: warning: unused variable 'mutinf' [-Wunused-variable]
     double loglikMean, loglikSum, mutinf, delta, logPrior_cur_scale;  
                                   ^
MCMC.c: In function 'network_likelihood':
MCMC.c:108:6: warning: 'max_loglik0_idx' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int max_loglik0_idx;
      ^
MCMC.c: In function 'MCMCrun':
MCMC.c:455:12: warning: 'delta_poss_operations' may be used uninitialized in this function [-Wmaybe-uninitialized]
  hfactor = updateFactor(likLogOld, logPriorOld, logPriorScale, likelihood, logPrior_cur, logPrior_cur_scale, n_neighbors, n_neighbors + delta_poss_operations);
            ^
MCMC.c:28:48: warning: 'logPrior_cur' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return((likLogNew - likLogOld) + (logPriorNew - logPriorOld) + (logPriorScaleNew - logPriorScaleOld) + (log((double)oldNeighborhood) - log((double)newNeighborhood)));   // hastings ratio ### Modified to handle Prior information  
                                                ^
MCMC.c:407:24: note: 'logPrior_cur' was declared here
     double likelihood, logPrior_cur, priorScale_new;    
                        ^
MCMC.c:28:20: warning: 'likelihood' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return((likLogNew - likLogOld) + (logPriorNew - logPriorOld) + (logPriorScaleNew - logPriorScaleOld) + (log((double)oldNeighborhood) - log((double)newNeighborhood)));   // hastings ratio ### Modified to handle Prior information  
                    ^
MCMC.c:407:12: note: 'likelihood' was declared here
     double likelihood, logPrior_cur, priorScale_new;    
            ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c netlearn.c -o netlearn.o
netlearn.c: In function 'learn_network':
netlearn.c:168:9: warning: unused variable 'lik_switch' [-Wunused-variable]
  double lik_switch;
         ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c wrapper.c -o wrapper.o
wrapper.c: In function 'MCMCrunWrapper':
wrapper.c:107:27: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
     int useMCMC = (sample > 0 & burnin > 0);
                           ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o nem.dll tmp.def MCMC.o netlearn.o wrapper.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/nem.buildbin-libdir/nem/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'nem'
    finding HTML links ... done
    BFSlevel                                html  
    BoutrosRNAi2002                         html  
    Ivanova2006RNAiTimeSeries               html  
    NiederbergerMediator2012                html  
    SCCgraph                                html  
    SahinRNAi2008                           html  
    closest.transitive.greedy               html  
    enumerate.models                        html  
    generateNetwork                         html  
    getDensityMatrix                        html  
    infer.edge.type                         html  
    internal                                html  
    local.model.prior                       html  
    nem                                     html  
    nem.bootstrap                           html  
    nem.calcSignificance                    html  
    nem.consensus                           html  
    nem.cont.preprocess                     html  
    nem.discretize                          html  
    nem.jackknife                           html  
    nemModelSelection                       html  
    network.AIC                             html  
    plot.nem                                html  
    plotEffects                             html  
    prior.EgeneAttach.EB                    html  
    prune.graph                             html  
    quicknem                                html  
    selectEGenes                            html  
    set.default.parameters                  html  
    sim.intervention                        html  
    subsets                                 html  
    transitive.closure                      html  
    transitive.projections                  html  
    transitive.reduction                    html  
** building package indices
** installing vignettes
   'nem.Rnw' using 'latin1' 
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'nem' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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]
                                         if(egene_prior[i][s] > 0 & s < nsgenes){
                                                              ^
MCMC.c:125:27: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
      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]
     long stored2 = 0;
          ^
MCMC.c:402:10: warning: unused variable 'stored' [-Wunused-variable]
     long stored = 0;
          ^
MCMC.c:359:35: warning: unused variable 'mutinf' [-Wunused-variable]
     double loglikMean, loglikSum, mutinf, delta, logPrior_cur_scale;  
                                   ^
MCMC.c: In function 'network_likelihood':
MCMC.c:108:6: warning: 'max_loglik0_idx' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int max_loglik0_idx;
      ^
MCMC.c: In function 'MCMCrun':
MCMC.c:455:12: warning: 'delta_poss_operations' may be used uninitialized in this function [-Wmaybe-uninitialized]
  hfactor = updateFactor(likLogOld, logPriorOld, logPriorScale, likelihood, logPrior_cur, logPrior_cur_scale, n_neighbors, n_neighbors + delta_poss_operations);
            ^
MCMC.c:455:10: warning: 'logPrior_cur' may be used uninitialized in this function [-Wmaybe-uninitialized]
  hfactor = updateFactor(likLogOld, logPriorOld, logPriorScale, likelihood, logPrior_cur, logPrior_cur_scale, n_neighbors, n_neighbors + delta_poss_operations);
          ^
MCMC.c:455:10: warning: 'likelihood' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c netlearn.c -o netlearn.o
netlearn.c: In function 'learn_network':
netlearn.c:168:9: warning: unused variable 'lik_switch' [-Wunused-variable]
  double lik_switch;
         ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c wrapper.c -o wrapper.o
wrapper.c: In function 'MCMCrunWrapper':
wrapper.c:107:27: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
     int useMCMC = (sample > 0 & burnin > 0);
                           ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o nem.dll tmp.def MCMC.o netlearn.o wrapper.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/nem.buildbin-libdir/nem/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'nem' as nem_2.52.0.zip
* DONE (nem)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'nem' successfully unpacked and MD5 sums checked
In R CMD INSTALL