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BioC 3.2: CHECK report for nem on linux1.bioconductor.org

This page was generated on 2015-10-27 17:23:54 -0400 (Tue, 27 Oct 2015).

Package 700/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nem 2.44.0
Holger Froehlich
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/nem
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: nem
Version: 2.44.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings nem_2.44.0.tar.gz
StartedAt: 2015-10-27 06:14:21 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 06:15:16 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 54.2 seconds
RetCode: 0
Status:  OK 
CheckDir: nem.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings nem_2.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/nem.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nem/DESCRIPTION’ ... OK
* this is package ‘nem’ version ‘2.44.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘nem’ can be installed ... [4s/4s] 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
* 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
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’
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’
* 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
File ‘nem/libs/nem.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘MCMC.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘MCMC.o’

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.

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 ... [7s/7s] 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/nem.Rcheck/00check.log’
for details.


nem.Rcheck/00install.out:

* installing *source* package ‘nem’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -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:455:24: 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]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -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;
         ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -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);
                           ^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o nem.so MCMC.o netlearn.o wrapper.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/nem.Rcheck/nem/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (nem)

nem.Rcheck/nem-Ex.timings:

nameusersystemelapsed
BFSlevel0.0000.0000.001
BoutrosRNAi20020.0380.0000.037
Ivanova2006RNAiTimeSeries0.0020.0000.002
NiederbergerMediator20120.0140.0000.014
SCCgraph0.2660.0080.274
SahinRNAi20080.0030.0000.003
enumerate.models0.0020.0000.003
generateNetwork0.2930.0030.304
infer.edge.type0.1950.0030.202
local.model.prior0.0010.0000.000
nem2.4690.0162.499
nem.bootstrap0.0000.0000.001
nem.calcSignificance0.0000.0000.001
nem.consensus0.0000.0000.001
nem.cont.preprocess0.1680.0000.171
nem.discretize0.0430.0000.043
nem.jackknife0.0000.0000.001
nemModelSelection0.4830.0000.486
network.AIC0.1840.0040.188
plotEffects0.2190.0000.223
prior.EgeneAttach.EB0.2660.0010.268
prune.graph0.0710.0080.087
quicknem0.0000.0000.001
selectEGenes0.3130.0040.316
set.default.parameters0.0010.0000.000
sim.intervention0.0830.0000.084
subsets0.0010.0000.000
transitive.closure0.0620.0000.068
transitive.reduction0.0610.0000.067