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 | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf nem.buildbin-libdir nem.Rcheck && mkdir nem.buildbin-libdir nem.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=nem.buildbin-libdir nem_2.47.0.tar.gz >nem.Rcheck\00install.out 2>&1 && cp nem.Rcheck\00install.out nem-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=nem.buildbin-libdir --install="check:nem-install.out" --force-multiarch --no-vignettes --timings nem_2.47.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/nem.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'nem/DESCRIPTION' ... OK
* this is package 'nem' version '2.47.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'nem' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bum.mle: no visible global function definition for 'optim'
bum.negLogLik: no visible global function definition for 'dexp'
nem.bootstrap: no visible global function definition for 'makeCluster'
nem.calcSignificance: no visible global function definition for
'registerDoMC'
nem.calcSignificance: no visible global function definition for
'%dopar%'
nem.calcSignificance: no visible global function definition for
'foreach'
nem.featureselection: no visible global function definition for
'registerDoMC'
nem.featureselection: no visible global function definition for
'%dopar%'
nem.featureselection: no visible global function definition for
'foreach'
nem.featureselection: no visible binding for global variable 'd'
nemModelSelection: no visible global function definition for
'registerDoMC'
nemModelSelection: no visible global function definition for '%dopar%'
nemModelSelection: no visible global function definition for 'foreach'
nemModelSelection: no visible binding for global variable 'lam'
nemModelSelection: no visible binding for global variable 'r'
quicknem: no visible global function definition for 'exprs'
quicknem: no visible global function definition for 'file_test'
score.aux: no visible global function definition for 'registerDoMC'
score.aux: no visible global function definition for '%dopar%'
score.aux: no visible global function definition for 'foreach'
score.aux: no visible binding for global variable 'm'
Undefined global functions or variables:
%dopar% d dexp exprs file_test foreach lam m makeCluster optim r
registerDoMC
Consider adding
importFrom("stats", "dexp", "optim")
importFrom("utils", "file_test")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.4-bioc/meat/nem.buildbin-libdir/nem/libs/i386/nem.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'rand', possibly from 'rand' (C)
Found 'srand', possibly from 'srand' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
'ModuleNetworks1.png'
Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
'D:/biocbld/bbs-3.4-bioc/meat/nem.Rcheck/00check.log'
for details.
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
** 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)