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CHECK report for nem on tokay1

This page was generated on 2019-04-13 11:20:03 -0400 (Sat, 13 Apr 2019).

Package 1045/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nem 2.56.0
Holger Froehlich
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/nem
Branch: RELEASE_3_8
Last Commit: d6f277a
Last Changed Date: 2018-10-30 11:41:43 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: nem
Version: 2.56.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nem.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings nem_2.56.0.tar.gz
StartedAt: 2019-04-13 04:08:17 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:10:29 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 132.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: nem.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nem.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings nem_2.56.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/nem.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '2.56.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-3.8-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 ... 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 'C:/Users/biocbuild/bbs-3.8-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)

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, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/nem.Rcheck/00check.log'
for details.



Installation output

nem.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/nem_2.56.0.tar.gz && rm -rf nem.buildbin-libdir && mkdir nem.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=nem.buildbin-libdir nem_2.56.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL nem_2.56.0.zip && rm nem_2.56.0.tar.gz nem_2.56.0.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
100 4182k  100 4182k    0     0  24.2M      0 --:--:-- --:--:-- --:--:-- 24.7M

install for i386

* installing *source* package 'nem' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/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/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˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/nem.buildbin-libdir/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
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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/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˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/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/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˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/nem.buildbin-libdir/nem/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'nem' as nem_2.56.0.zip
* DONE (nem)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'nem' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

nem.Rcheck/examples_i386/nem-Ex.timings

nameusersystemelapsed
BFSlevel000
BoutrosRNAi20020.070.000.06
Ivanova2006RNAiTimeSeries000
NiederbergerMediator20120.030.000.03
SCCgraph0.390.020.41
SahinRNAi2008000
enumerate.models000
generateNetwork0.160.010.17
infer.edge.type0.140.020.15
local.model.prior000
nem1.290.001.32
nem.bootstrap000
nem.calcSignificance000
nem.consensus000
nem.cont.preprocess0.110.010.12
nem.discretize0.030.020.05
nem.jackknife000
nemModelSelection0.240.020.25
network.AIC0.120.000.12
plotEffects0.160.000.16
prior.EgeneAttach.EB0.220.030.25
prune.graph0.080.000.08
quicknem000
selectEGenes0.220.000.22
set.default.parameters000
sim.intervention0.090.000.09
subsets000
transitive.closure0.080.000.08
transitive.reduction0.060.000.06

nem.Rcheck/examples_x64/nem-Ex.timings

nameusersystemelapsed
BFSlevel000
BoutrosRNAi20020.040.000.03
Ivanova2006RNAiTimeSeries000
NiederbergerMediator20120.020.000.02
SCCgraph0.360.000.36
SahinRNAi2008000
enumerate.models000
generateNetwork0.180.020.22
infer.edge.type0.140.010.15
local.model.prior000
nem1.540.041.57
nem.bootstrap000
nem.calcSignificance000
nem.consensus000
nem.cont.preprocess0.140.000.14
nem.discretize0.030.000.03
nem.jackknife000
nemModelSelection0.270.000.27
network.AIC0.120.000.12
plotEffects0.160.010.18
prior.EgeneAttach.EB0.370.020.39
prune.graph0.140.000.14
quicknem000
selectEGenes0.360.000.36
set.default.parameters000
sim.intervention0.140.010.16
subsets000
transitive.closure0.100.020.11
transitive.reduction0.120.000.12