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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:nem.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings nem_2.62.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/nem.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.62.0’
* 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]
  Warning: Package 'nem' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.11-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 ... 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 is not available
File ‘/home/biocbuild/bbs-3.11-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 ... ERROR
Running examples in ‘nem-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SCCgraph
> ### Title: Combines Strongly Connected Components into single nodes
> ### Aliases: SCCgraph
> ### Keywords: graphs
> 
> ### ** Examples
> 
>    data("BoutrosRNAi2002")
>    D   <- BoutrosRNAiDiscrete[,9:16]
>    res <- nem(D,control=set.default.parameters(unique(colnames(D)), para=c(.13,.05)))
Greedy hillclimber for 4 S-genes (lambda = 0 )...

 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
nem
 --- call from context --- 
transitive.closure(Phinew, mat = TRUE, loops = TRUE)
 --- call from argument --- 
if (!(class(g) %in% c("graphNEL", "matrix"))) stop("Input must be either graphNEL object or adjacency matrix")
 --- R stacktrace ---
where 1: transitive.closure(Phinew, mat = TRUE, loops = TRUE)
where 2: get.insertions(Phi, control$trans.close)
where 3: nem.greedy(D, initial = models[[1]], control, verbose = verbose)
where 4: nem(D, control = set.default.parameters(unique(colnames(D)), 
    para = c(0.13, 0.05)))

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (g, mat = FALSE, loops = TRUE) 
{
    if (!(class(g) %in% c("graphNEL", "matrix"))) 
        stop("Input must be either graphNEL object or adjacency matrix")
    g <- as(g, "matrix")
    n <- ncol(g)
    matExpIterativ <- function(x, pow, y = x, z = x, i = 1) {
        while (i < pow) {
            z <- z %*% x
            y <- y + z
            i <- i + 1
        }
        return(y)
    }
    h <- matExpIterativ(g, n)
    h <- (h > 0) * 1
    dimnames(h) <- dimnames(g)
    if (!loops) 
        diag(h) <- rep(0, n)
    else diag(h) <- rep(1, n)
    if (!mat) 
        h <- as(h, "graphNEL")
    return(h)
}
<bytecode: 0x55607aee6cd0>
<environment: namespace:nem>
 --- function search by body ---
Function transitive.closure in namespace nem has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
* 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 ERROR, 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/nem.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL nem
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘nem’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-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-3.11-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-3.11-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-3.11-bioc/R/lib -L/usr/local/lib -o nem.so MCMC.o netlearn.o wrapper.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-nem/00new/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 from temporary location
Warning: Package 'nem' is deprecated and will be removed from Bioconductor
  version 3.12
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'nem' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (nem)