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BioC 3.4: INSTALL report for nem on moscato1

This page was generated on 2016-09-21 03:41:53 -0700 (Wed, 21 Sep 2016).

Package 809/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nem 2.47.0
Holger Froehlich
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/nem
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: nem
Version: 2.47.0
Command: rm -rf nem.buildbin-libdir && mkdir nem.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/nem_2.47.0.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=nem.buildbin-libdir --merge-multiarch nem_2.47.0.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL nem_2.47.0.zip && rm nem_2.47.0.tar.gz nem_2.47.0.zip
StartedAt: 2016-09-19 21:10:53 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 21:11:27 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 34.6 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 http://zin1/BBS/3.4/bioc/src/contrib/nem_2.47.0.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=nem.buildbin-libdir --merge-multiarch nem_2.47.0.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL nem_2.47.0.zip  && rm nem_2.47.0.tar.gz nem_2.47.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 4188k  100 4188k    0     0  78.4M      0 --:--:-- --:--:-- --:--:-- 85.2M

install for i386

* installing *source* package 'nem' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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/gcc -shared -s -static-libgcc -o nem.dll tmp.def MCMC.o netlearn.o wrapper.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/nem.buildbin-libdir/nem/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'nem.Rnw' using 'latin1' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'nem' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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/gcc -shared -s -static-libgcc -o nem.dll tmp.def MCMC.o netlearn.o wrapper.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/nem.buildbin-libdir/nem/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'nem' as nem_2.47.0.zip
* DONE (nem)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'nem' successfully unpacked and MD5 sums checked