come to an understanding of why graphBAM unit tests failed with recent R-devel

[vjcitn]

I blocked one test to get this to pass check in the devel container. Let's see if BBS is happy. If so we can study the problem with the unit test and possibly restore it.

[rcastelo]

Hi, after uncommenting the problematic line, building and installing the package, I cannot reproduce the error when I execute the unit test that triggers the problem line by line:

library(graph)
library(RUnit)

make_smallBAM <- function() {
    from = c("a", "a", "a", "x", "x", "c")
    to   = c("b", "c", "x", "y", "c", "a")
    weight=c(3.4, 2.6, 1.7, 5.3, 1.6, 7.9)
    df <- data.frame(from, to, weight, stringsAsFactors = TRUE)
    g1 <- graphBAM(df, edgemode = "directed")
    g1
}

g1 <- make_smallBAM()
## removing nothing does nothing
c0 <- character(0)
checkEquals(edges(g1), edges(removeEdge(c0, c0, g1)))
[1] TRUE

sessionInfo()
R Under development (unstable) (2024-11-03 r87286)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS:   /projects_fg/soft/R/R-devel/lib/R/lib/libRblas.so 
LAPACK: /projects_fg/soft/R/R-devel/lib/R/lib/libRlapack.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Madrid
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RUnit_0.4.33        graph_1.85.2        BiocGenerics_0.53.6
[4] generics_0.1.3      colorout_1.3-0     

loaded via a namespace (and not attached):
[1] compiler_4.5.0 tools_4.5.0    stats4_4.5.0  

[rcastelo]

Hi again, I have updated my version of R-devel and been able to reproduce the error:

library(graph)
library(RUnit)

make_smallBAM <- function() {
    from = c("a", "a", "a", "x", "x", "c")
    to   = c("b", "c", "x", "y", "c", "a")
    weight=c(3.4, 2.6, 1.7, 5.3, 1.6, 7.9)
    df <- data.frame(from, to, weight, stringsAsFactors = TRUE)
    g1 <- graphBAM(df, edgemode = "directed")
    g1
}

g1 <- make_smallBAM()
## removing nothing does nothing
c0 <- character(0)
checkEquals(edges(g1), edges(removeEdge(c0, c0, g1)))

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: .remEdge(from, to, graph)
 2: removeEdge(c0, c0, g1)
 3: removeEdge(c0, c0, g1)
 4: edges(removeEdge(c0, c0, g1))
 5: mode(current)
 6: attr.all.equal(target, current, ...)
 7: all.equal.list(target, current, tolerance = tolerance, ...)
 8: all.equal(target, current, tolerance = tolerance, ...)
 9: checkEquals(edges(g1), edges(removeEdge(c0, c0, g1)))

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 

Here's the session information loaded separately:

R Under development (unstable) (2025-03-07 r87894)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS:   /projects_fg/soft/R/R-devel/lib/R/lib/libRblas.so 
LAPACK: /projects_fg/soft/R/R-devel/lib/R/lib/libRlapack.so;  LAPACK version 3.12.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Madrid
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RUnit_0.4.33        graph_1.85.2        BiocGenerics_0.53.6
[4] generics_0.1.3      colorout_1.3-0     

loaded via a namespace (and not attached):
[1] compiler_4.5.0 stats4_4.5.0  

[rcastelo]

I've just submitted a PR that in principle solves this problem.