##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:joda.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings joda_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/joda.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 ‘joda/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘joda’ version ‘1.36.0’
* 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 ‘joda’ can be installed ... 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 ... NOTE
Packages in Depends field not imported from:
  ‘RBGL’ ‘bgmm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
infer.probabilities: no visible global function definition for ‘par’
infer.probabilities : getProbs: no visible global function definition
  for ‘unsupervised’
infer.probabilities : getProbs: no visible global function definition
  for ‘DEprobs’
infer.probabilities : getProbs: no visible global function definition
  for ‘belief’
infer.probabilities : getProbs: no visible global function definition
  for ‘title’
infer.probabilities : getProbs: no visible global function definition
  for ‘legend’
regulation.scores: no visible global function definition for ‘as’
regulation.scores: no visible global function definition for
  ‘transitive.closure’
Undefined global functions or variables:
  DEprobs as belief legend par title transitive.closure unsupervised
Consider adding
  importFrom("graphics", "legend", "par", "title")
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘joda-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: differential.probs
> ### Title: Calculating probabilities of differential expression in
> ###   perturbation experiments
> ### Aliases: differential.probs
> 
> ### ** Examples
> 
> 	
> data(damage)
> 	
> # Get the probabilities of differential expression
> # for the knockout of p53 in healthy cells
> probs.healthy.p53= differential.probs(data.healthy[,"p53",FALSE],
+ 					beliefs.healthy["p53"], TRUE,TRUE)
joda: Input correctly defined 

Inferring probabilities of differential expression under the knockdown of  p53 ... 
Applying belief-based mixture modeling
The parameters of the model for p53: 
                    differential    unchanged
Mixing proportions:   0.50634787  0.493652126
Means:                0.05503342 -0.072353721
Variances:            0.04807592  0.007986199
> 	
> # Get the probabilities of differential expression
> # for the knockout of Ste12 under pheromone treatment 	
> library(bgmm)
> data(Ste12)
> data=as.matrix(Ste12Data)
> colnames(data)="Ste12"
> beliefs=list(Ste12=Ste12Beliefs)
> diff.p=differential.probs(data,beliefs,TRUE,TRUE)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
joda
 --- call from context --- 
sanity.check.beliefs(data, beliefs)
 --- call from argument --- 
if (!class(data) %in% c("matrix", "data.frame")) stop(paste("\ndifferential.probs Error: data must be a matrix."))
 --- R stacktrace ---
where 1: sanity.check.beliefs(data, beliefs)
where 2: differential.probs(data, beliefs, TRUE, TRUE)

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (data, beliefs) 
{
    if (is.null(beliefs)) 
        beliefs = list()
    if (!class(data) %in% c("matrix", "data.frame")) 
        stop(paste("\ndifferential.probs Error: data must be a matrix."))
    if (!class(beliefs) == "list") 
        stop(paste("\ndifferential.probs Error: beliefs must be a list."))
    regs = colnames(data)
    c1 <- all(names(beliefs) %in% regs)
    if (!c1) 
        stop(paste("\ndifferential.probs Error: beliefs must be a list of  matrices, with names as subset of the data columns (regulators)."))
    ck <- function(kn) {
        k = beliefs[[kn]]
        OK <- TRUE
        if (!is.null(k)) {
            if (!is.matrix(k)) {
                cat(" \n Error:. For a given regulator, the beliefs must be given as a matrix\n")
                return(FALSE)
            }
            gens = rownames(data)
            if (!all(rownames(k) %in% gens)) {
                cat("\n Error: the rownames of the belief matrices must be a subset of the rownames of the data'\n")
                return(FALSE)
            }
            if (!ncol(k) %in% c(2, 3)) {
                cat("\n Error: the belief matrices must have either two or three columns\n")
                return(FALSE)
            }
            OK <- all(k <= 1)
            OK <- all(k >= 0)
            OK <- all(apply(k, 1, sum) == 1)
            if (!OK) 
                cat("\n Error: the belief matrices must have values in (0,1), each row being a distribution over the columns.\n")
        }
        OK
    }
    c2 <- all(sapply(regs, ck))
    if (!(c2)) 
        stop("")
}
<bytecode: 0x556db93355e8>
<environment: namespace:joda>
 --- function search by body ---
Function sanity.check.beliefs in namespace joda 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/joda.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL joda
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘joda’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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
* DONE (joda)