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CHECK report for nem on malbec2

This page was generated on 2018-10-17 08:21:51 -0400 (Wed, 17 Oct 2018).

Package 984/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nem 2.54.0
Holger Froehlich
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/nem
Branch: RELEASE_3_7
Last Commit: 47e6a75
Last Changed Date: 2018-04-30 10:35:05 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: nem
Version: 2.54.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:nem.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings nem_2.54.0.tar.gz
StartedAt: 2018-10-16 02:20:32 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 02:21:23 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 50.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: nem.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:nem.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings nem_2.54.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/nem.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘2.54.0’
* 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 ... 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 ‘/home/biocbuild/bbs-3.7-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
* 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 is not available
File ‘/home/biocbuild/bbs-3.7-bioc/R/library/nem/libs/nem.so’:
  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 ... 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/nem.Rcheck/00check.log’
for details.



Installation output

nem.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL nem
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘nem’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-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:455:12: 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]
gcc -I"/home/biocbuild/bbs-3.7-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 -I"/home/biocbuild/bbs-3.7-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 -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o nem.so MCMC.o netlearn.o wrapper.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/nem/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘nem.Rnw’ using ‘latin1’ 
** testing if installed package can be loaded
* DONE (nem)

Tests output


Example timings

nem.Rcheck/nem-Ex.timings

nameusersystemelapsed
BFSlevel000
BoutrosRNAi20020.0320.0040.038
Ivanova2006RNAiTimeSeries0.0000.0000.001
NiederbergerMediator20120.0120.0000.011
SCCgraph0.3160.0040.322
SahinRNAi20080.0040.0000.003
enumerate.models0.0040.0000.002
generateNetwork0.2040.0080.224
infer.edge.type0.1440.0040.149
local.model.prior0.0000.0000.001
nem1.8040.0121.832
nem.bootstrap0.0000.0000.001
nem.calcSignificance0.0000.0000.001
nem.consensus000
nem.cont.preprocess0.2240.0000.229
nem.discretize0.0440.0000.040
nem.jackknife0.0000.0000.001
nemModelSelection0.4240.0040.431
network.AIC0.1840.0000.186
plotEffects0.1880.0040.198
prior.EgeneAttach.EB0.2080.0000.214
prune.graph0.0840.0000.098
quicknem0.0000.0000.001
selectEGenes0.2680.0040.271
set.default.parameters0.0040.0000.001
sim.intervention0.1480.0000.149
subsets0.0000.0000.001
transitive.closure0.1200.0040.130
transitive.reduction0.1160.0000.124