- using R version 4.4.2 (2024-10-31)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-14 (Debian 14.2.0-6) 14.2.0
GNU Fortran (Debian 14.2.0-6) 14.2.0
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘netdiffuseR/DESCRIPTION’ ... OK
- this is package ‘netdiffuseR’ version ‘1.22.6’
- package encoding: UTF-8
- 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 executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking serialization versions ... OK
- checking whether package ‘netdiffuseR’ can be installed ... OK
See the install log for details.
- used C++ compiler: ‘g++-14 (Debian 14.2.0-6) 14.2.0’
- checking package directory ... OK
- checking for future file timestamps ... 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 code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [3s/4s] OK
- checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
- checking whether the package can be unloaded cleanly ... [2s/3s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
- checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
- checking loading without being on the library search path ... [3s/3s] OK
- checking whether startup messages can be suppressed ... [3s/3s] OK
- checking use of S3 registration ... 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 ... [32s/43s] OK
- checking Rd files ... [2s/2s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... 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 ... [2s/3s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in shell scripts ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [14s/16s] ERROR
Running examples in ‘netdiffuseR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: exposure
> ### Title: Ego exposure
> ### Aliases: exposure
> ### Keywords: univar
>
> ### ** Examples
>
> # Calculating lagged exposure -----------------------------------------------
>
> set.seed(8)
> graph <- rdiffnet(20, 4)
Warning in (function (graph, p, algorithm = "endpoints", both.ends = FALSE, :
The option -copy.first- is set to TRUE. In this case, the first graph will be treated as a baseline, and thus, networks after T=1 will be replaced with T-1.
>
> expo0 <- exposure(graph)
> expo1 <- exposure(graph, lags = 1)
>
> # These should be equivalent
> stopifnot(all(expo0[, -4] == expo1[, -1])) # No stop!
>
>
> # Calculating the exposure based on Structural Equivalence ------------------
> set.seed(113132)
> graph <- rdiffnet(100, 4)
Warning in (function (graph, p, algorithm = "endpoints", both.ends = FALSE, :
The option -copy.first- is set to TRUE. In this case, the first graph will be treated as a baseline, and thus, networks after T=1 will be replaced with T-1.
>
> SE <- lapply(struct_equiv(graph), "[[", "SE")
> SE <- lapply(SE, function(x) {
+ x <- 1/x
+ x[!is.finite(x)] <- 0
+ x
+ })
>
>
> # These three lines are equivalent to:
> expo_se2 <- exposure(graph, alt.graph="se", valued=TRUE)
> # Notice that we are setting valued=TRUE, but this is not necesary since when
> # alt.graph = "se" the function checks this to be setted equal to TRUE
>
> # Weighted Exposure using degree --------------------------------------------
> eDE <- exposure(graph, attrs=dgr(graph))
>
> # Which is equivalent to
> graph[["deg"]] <- dgr(graph)
> eDE2 <- exposure(graph, attrs="deg")
>
> # Comparing using incoming edges -------------------------------------------
> eIN <- exposure(graph, outgoing=FALSE)
>
> # Structral equivalence for different communities ---------------------------
> data(medInnovationsDiffNet)
>
> # Only using 4 time slides, this is for convenience
> medInnovationsDiffNet <- medInnovationsDiffNet[, , 1:4]
>
> # METHOD 1: Using the c.diffnet method:
>
> # Creating subsets by city
> cities <- unique(medInnovationsDiffNet[["city"]])
>
> diffnet <- medInnovationsDiffNet[medInnovationsDiffNet[["city"]] == cities[1]]
> diffnet[["expo_se"]] <- exposure(diffnet, alt.graph="se", valued=TRUE)
*** caught segfault ***
address (nil), cause 'unknown'
Traceback:
1: .nextMethod(.Object = .Object, ... = ...)
2: callNextMethod()
3: initialize(value, ...)
4: initialize(value, ...)
5: new("dgTMatrix", Dim = d, Dimnames = dn, i = i, j = j, x = x)
6: newTMat(i = c(ij1[, 1], ij2[, 1]), j = c(ij1[, 2], ij2[, 2]), x = if (Generic == "+") c(e1@x, e2@x) else c(e1@x, -e2@x))
7: .M2C(newTMat(i = c(ij1[, 1], ij2[, 1]), j = c(ij1[, 2], ij2[, 2]), x = if (Generic == "+") c(e1@x, e2@x) else c(e1@x, -e2@x)))
8: .Arith.Csparse(e1, e2, .Generic, class. = "dgCMatrix")
9: d[, ids[, 1]] - d[, ids[, 2]]
10: d[, ids[, 1]] - d[, ids[, 2]]
11: euclidean_distance(gdist)
12: struct_equiv_new(geod, v)
13: struct_equiv.dgCMatrix(methods::as(graph[[i]], "dgCMatrix"), v, inf.replace, groupvar, ...)
14: struct_equiv.list(graph, v, inf.replace, groupvar, ...)
15: struct_equiv(graph, groupvar = groupvar, ...)
16: lapply(struct_equiv(graph, groupvar = groupvar, ...), "[[", "SE")
17: exposure(diffnet, alt.graph = "se", valued = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [71s/90s] OK
Running ‘testthat.R’ [70s/89s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [123s/131s] OK
- checking PDF version of manual ... [11s/16s] OK
- checking HTML version of manual ... [8s/12s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR