##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:Vega.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings Vega_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/Vega.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 ‘Vega/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Vega’ 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 ‘Vega’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'Vega' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.11-bioc/meat/Vega.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
plotSegmentation: no visible global function definition for ‘par’
plotSegmentation: no visible global function definition for ‘lines’
vega: no visible global function definition for ‘sd’
vega: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  lines par sd write.table
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
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
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Vega-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotSegmentation
> ### Title: Plot observations and the respective segmentation.
> ### Aliases: plotSegmentation
> 
> ### ** Examples
> 
> 	
> 	# Import the data
> 	data(G519)
> 	
> 	# Compute the segmentation for all chromosomes
> 	seg <- vega(G519, c(1:22, "X", "Y"))
Processing Chromosome 1
Done

Processing Chromosome 2
Done

Processing Chromosome 3
Done

Processing Chromosome 4
Done

Processing Chromosome 5
Done

Processing Chromosome 6
Done

Processing Chromosome 7
Done

Processing Chromosome 8
Done

Processing Chromosome 9
Done

Processing Chromosome 10
Done

Processing Chromosome 11
Done

Processing Chromosome 12
Done

Processing Chromosome 13
Done

Processing Chromosome 14
Done

Processing Chromosome 15
Done

Processing Chromosome 16
Done

Processing Chromosome 17
Done

Processing Chromosome 18
Done

Processing Chromosome 19
Done

Processing Chromosome 20
Done

Processing Chromosome 21
Done

Processing Chromosome 22
Done

Processing Chromosome X
Done

Processing Chromosome Y
Done

> 	
> 	# Plot the results for all chromosomes in terms of mean of LRRs 
> 	plotSegmentation(G519, seg, c(1:22, "X", "Y"), opt=0)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
Vega
 --- call from context --- 
plotSegmentation(G519, seg, c(1:22, "X", "Y"), opt = 0)
 --- call from argument --- 
if (class(data_table) != "matrix") {
    data_table <- t(as.matrix(data_table))
}
 --- R stacktrace ---
where 1: plotSegmentation(G519, seg, c(1:22, "X", "Y"), opt = 0)

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (CNVdata, segmentation, chromosomes, opt = 0) 
{
    num_of_chroms <- length(chromosomes)
    if (num_of_chroms <= 6) {
        rows <- 1
        cols <- num_of_chroms
    }
    else {
        cols <- 6
        tmp1 <- round(num_of_chroms/cols)
        tmp2 <- num_of_chroms/cols
        diff_tmp <- tmp1 - tmp2
        if (diff_tmp == 0) {
            rows <- tmp1
        }
        else {
            rows <- tmp1 + 1
        }
    }
    par(mfrow = c(rows, cols))
    for (i in 1:num_of_chroms) {
        curr_chr <- chromosomes[i]
        data_table <- CNVdata[which(CNVdata[, 1] == curr_chr), 
            ]
        if (class(data_table) != "matrix") {
            data_table <- t(as.matrix(data_table))
        }
        curr_seg <- segmentation[which(segmentation[, 1] == curr_chr), 
            ]
        if (class(curr_seg) != "matrix") {
            curr_seg <- t(as.matrix(curr_seg))
        }
        min_lrr <- min(as.numeric(data_table[, 4])) - 0.5
        max_lrr <- max(as.numeric(data_table[, 4])) + 0.5
        if (opt == 1 && min_lrr > -1.5) {
            min_lrr <- -1.5
        }
        if (opt == 1 && max_lrr < 1.5) {
            max_lrr <- 1.5
        }
        plot(as.numeric(data_table[, 4]), col = "blue", xaxt = "n", 
            xlab = "", ylab = "LRR", main = paste("chromosome", 
                curr_chr), ylim = c(min_lrr, max_lrr))
        chr_size <- sum(as.numeric(curr_seg[, 4]))
        tmp <- 0 * c(1:chr_size)
        curr = 1
        for (i in 1:nrow(curr_seg)) {
            if (opt == 0) {
                label = as.numeric(curr_seg[i, 5])
            }
            if (opt == 1) {
                label = as.numeric(curr_seg[i, 6])
            }
            tmp[curr:(curr + as.numeric(curr_seg[i, 4]))] <- label
            curr = (curr + as.numeric(curr_seg[i, 4]))
        }
        lines(c(1:length(tmp)), tmp, col = "red", lwd = 2)
    }
}
<bytecode: 0x562e832e24f0>
<environment: namespace:Vega>
 --- function search by body ---
Function plotSegmentation in namespace Vega 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/Vega.Rcheck/00check.log’
for details.

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


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘Vega’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c vega.c -o vega.o
vega.c: In function ‘heap_delete’:
vega.c:201:8: warning: variable ‘deleted’ set but not used [-Wunused-but-set-variable]
   node deleted;
        ^~~~~~~
vega.c: In function ‘vega’:
vega.c:355:13: warning: unused variable ‘maxptr’ [-Wunused-variable]
  node max, *maxptr, tmp_node;
             ^~~~~~
vega.c:348:68: warning: unused variable ‘tmp_lambda2’ [-Wunused-variable]
  double lambda, lambda_gradient, stop_lambda_gradient, tmp_lambda, tmp_lambda2;
                                                                    ^~~~~~~~~~~
vega.c:347:6: warning: unused variable ‘index’ [-Wunused-variable]
  int index;
      ^~~~~
vega.c: In function ‘update_priority’:
vega.c:560:64: warning: unused variable ‘next_mean’ [-Wunused-variable]
  double lambda, first_term, second_term, prev_mean, curr_mean, next_mean;
                                                                ^~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o Vega.so vega.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-Vega/00new/Vega/libs
** R
** data
** 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
Warning: Package 'Vega' 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 'Vega' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (Vega)