| Back to "Blame Jeroen" build/check report for BioC 3.11 |
This page was generated on 2020-04-15 03:20:15 -0400 (Wed, 15 Apr 2020).
| These builds are using Rtools40 and R-testing by Jeroen Ooms (available at https://cran.r-project.org/bin/windows/testing/rtools40.html) |
| TO THE DEVELOPERS/MAINTAINERS OF THE nem PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 59/89 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
Holger Froehlich
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | ERROR | OK |
| Package: nem |
| Version: 2.61.1 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/nem_2.61.1.tar.gz && rm -rf nem.buildbin-libdir && mkdir nem.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=nem.buildbin-libdir nem_2.61.1.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL nem_2.61.1.zip && rm nem_2.61.1.tar.gz nem_2.61.1.zip |
| StartedAt: 2020-04-14 18:14:24 -0400 (Tue, 14 Apr 2020) |
| EndedAt: 2020-04-14 18:14:58 -0400 (Tue, 14 Apr 2020) |
| EllapsedTime: 33.6 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/nem_2.61.1.tar.gz && rm -rf nem.buildbin-libdir && mkdir nem.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=nem.buildbin-libdir nem_2.61.1.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL nem_2.61.1.zip && rm nem_2.61.1.tar.gz nem_2.61.1.zip
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install for i386
* installing *source* package 'nem' ...
** using staged installation
** libs
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^~~~~~~~~~
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^~~~~~~~~~
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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);
~~~~~~~^~~
/mingw32/bin/gcc -shared -s -static-libgcc -o nem.dll tmp.def MCMC.o netlearn.o wrapper.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCTE~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/nem.buildbin-libdir/00LOCK-nem/00new/nem/libs/i386
** R
** data
** inst
** byte-compile and prepare 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 from temporary location
Warning: Package 'nem' is deprecated and will be removed from Bioconductor
version 3.12
** 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
install for x64
* installing *source* package 'nem' ...
** libs
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:455:12: warning: 'logPrior_cur' may be used uninitialized in this function [-Wmaybe-uninitialized]
MCMC.c:455:12: warning: 'likelihood' may be used uninitialized in this function [-Wmaybe-uninitialized]
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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;
^~~~~~~~~~
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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);
~~~~~~~^~~
/mingw64/bin/gcc -shared -s -static-libgcc -o nem.dll tmp.def MCMC.o netlearn.o wrapper.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCTE~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/nem.buildbin-libdir/nem/libs/x64
** testing if installed package can be loaded
Warning: Package 'nem' is deprecated and will be removed from Bioconductor
version 3.12
* MD5 sums
packaged installation of 'nem' as nem_2.61.1.zip
* DONE (nem)
* installing to library 'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library'
package 'nem' successfully unpacked and MD5 sums checked