Holger Froehlich
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/nem |
| Branch: RELEASE_3_10 |
| Last Commit: ded87f8 |
| Last Changed Date: 2019-10-29 13:07:44 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:17:48 -0400 (Wed, 15 Apr 2020).
| Package 1141/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| nem 2.60.0 Holger Froehlich
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: nem |
| Version: 2.60.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nem.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings nem_2.60.0.tar.gz |
| StartedAt: 2020-04-15 05:05:45 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:07:11 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 85.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: nem.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nem.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings nem_2.60.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/nem.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '2.60.0'
* 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 ... WARNING
Found the following significant warnings:
MCMC.c:116:62: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
MCMC.c:125:27: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
wrapper.c:107:27: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/nem.Rcheck/00install.out' for details.
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
plot.ModuleNetwork plot.dynoNEM plot.mc.eminem plot.nem plot.nem.BN
plot.nem.bootstrap plot.nem.consensus plot.nem.greedy
plot.nem.greedyMAP plot.nem.jackknife plot.pairwise plot.score
plot.triples print.ModuleNetwork print.dynoNEM print.mc.eminem
print.nem print.nem.BN print.nem.bootstrap print.nem.consensus
print.nem.greedy print.nem.greedyMAP print.nem.jackknife
print.pairwise print.score print.triples
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* 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 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/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)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/nem/libs/x64/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 use Fortran I/O
nor system RNGs. 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: 1 WARNING, 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/nem.Rcheck/00check.log'
for details.
nem.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/nem_2.60.0.tar.gz && rm -rf nem.buildbin-libdir && mkdir nem.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=nem.buildbin-libdir nem_2.60.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL nem_2.60.0.zip && rm nem_2.60.0.tar.gz nem_2.60.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
2 4182k 2 112k 0 0 358k 0 0:00:11 --:--:-- 0:00:11 362k
100 4182k 100 4182k 0 0 6226k 0 --:--:-- --:--:-- --:--:-- 6252k
install for i386
* installing *source* package 'nem' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/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"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/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"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'nem' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/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"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/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"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/nem.buildbin-libdir/nem/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'nem' as nem_2.60.0.zip
* DONE (nem)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'nem' successfully unpacked and MD5 sums checked
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nem.Rcheck/examples_i386/nem-Ex.timings
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nem.Rcheck/examples_x64/nem-Ex.timings
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