Last updated on 2026-07-23 08:49:46 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.7-12 | 86.52 | 352.43 | 438.95 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 2.7-12 | 63.56 | 249.07 | 312.63 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.7-12 | 124.00 | 528.40 | 652.40 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2.7-12 | 70.00 | 234.20 | 304.20 | NOTE | |
| r-devel-windows-x86_64 | 2.7-12 | 108.00 | 385.00 | 493.00 | NOTE | |
| r-patched-linux-x86_64 | 2.7-12 | 90.91 | 337.61 | 428.52 | OK | |
| r-release-linux-x86_64 | 2.7-12 | 87.37 | 337.10 | 424.47 | OK | |
| r-release-macos-arm64 | 2.7-12 | 20.00 | 75.00 | 95.00 | OK | |
| r-release-macos-x86_64 | 2.7-12 | 56.00 | 441.00 | 497.00 | OK | |
| r-release-windows-x86_64 | 2.7-12 | 107.00 | 394.00 | 501.00 | OK | |
| r-oldrel-macos-arm64 | 2.7-12 | OK | ||||
| r-oldrel-macos-x86_64 | 2.7-12 | 51.00 | 312.00 | 363.00 | OK | |
| r-oldrel-windows-x86_64 | 2.7-12 | 125.00 | 526.00 | 651.00 | OK |
Version: 2.7-12
Check: R code for possible problems
Result: NOTE
Found calls to structure() using deprecated special names:
pcalg/tests/test_pcSelect.R (.Dim: 4, .Dimnames: 4)
'.Dim' should be changed to 'dim'.
'.Dimnames' should be changed to 'dimnames'.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64
Version: 2.7-12
Check: Rd contents
Result: NOTE
Rd files without \usage:
‘amatType.Rd’
\arguments should not be documented without \usage.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 2.7-12
Check: tests
Result: ERROR
Running ‘test_LINGAM.R’ [1s/2s]
Running ‘test_addBgKnowledge.R’ [2s/3s]
Running ‘test_adjustment.R’ [3s/4s]
Running ‘test_ages.R’ [2s/2s]
Running ‘test_amat2dag.R’ [1s/2s]
Running ‘test_arges.R’ [1s/2s]
Running ‘test_backdoor.R’ [6s/7s]
Comparing ‘test_backdoor.Rout’ to ‘test_backdoor.Rout.save’ ... OK
Running ‘test_bicscore.R’ [2s/2s]
Running ‘test_causalEffect.R’ [1s/2s]
Running ‘test_coercion.R’ [2s/2s]
Running ‘test_compareGraphs.R’ [1s/2s]
Running ‘test_dag2cpdag.R’ [2s/2s]
Running ‘test_dag2essgraph.R’ [2s/2s]
Running ‘test_displayAmat.R’ [2s/2s]
Running ‘test_dsep.R’ [2s/2s]
Running ‘test_dsepAM.R’ [2s/2s]
Running ‘test_dsepAMTest.R’ [2s/3s]
Running ‘test_fci.R’ [2s/2s]
Running ‘test_fciPlus.R’ [2s/3s]
Running ‘test_gSquareBin.R’ [1s/2s]
Running ‘test_gSquareDis.R’ [2s/3s]
Running ‘test_gac.R’ [3s/5s]
Running ‘test_getNextSet.R’ [1s/1s]
Running ‘test_gies.R’ [3s/4s]
Running ‘test_ida.R’ [7s/9s]
Running ‘test_idaFast.R’ [5s/6s]
Running ‘test_isValidGraph.R’ [3s/3s]
Running ‘test_jointIda.R’ [2s/4s]
Running ‘test_mat2targets.R’ [2s/2s]
Running ‘test_optAdjSet.R’ [2s/3s]
Running ‘test_opttarget.R’ [1s/1s]
Running ‘test_pag2anc.R’ [1s/2s]
Running ‘test_pag2conf.R’ [1s/1s]
Running ‘test_pag2edge.R’ [1s/1s]
Running ‘test_pc.R’ [2s/2s]
Running ‘test_pcSelect.R’ [3s/4s]
Running ‘test_pcalg2dagitty.R’ [2s/3s]
Running ‘test_pcorOrder.R’ [1s/2s]
Running ‘test_pdag2allDags.R’ [1s/2s]
Running ‘test_pdag2dag.R’ [2s/2s]
Running ‘test_possDeAn.R’ [1s/1s]
Running ‘test_randDAG.R’ [3s/3s]
Running ‘test_randomDAG.R’ [2s/2s]
Running ‘test_rfci.R’ [3s/5s]
Running ‘test_rmvDAG.R’ [1s/2s]
Running ‘test_searchAM.R’ [1s/1s]
Running ‘test_shd.R’ [1s/1s]
Running ‘test_skeleton.R’ [3s/3s]
Running ‘test_udag2pag.R’ [1s/1s]
Running ‘test_udag2pdag.R’ [5s/6s]
Running ‘test_wgtMatrix.R’ [1s/2s]
Running the tests in ‘tests/test_LINGAM.R’ failed.
Complete output:
> library(pcalg)
> ## source("/u/kalischm/research/packages/LINGAM/R/lingamFuns.R")
>
> ##--> showProc.time(), assertError(), relErrV(), ...
> R.home(); sessionInfo() # helping package maintainers to debug ...
[1] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build"
R Under development (unstable) (2026-07-21 r90286)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux forky/sid
Matrix products: default
BLAS: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libRblas.so
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.1; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Vienna
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] pcalg_2.7-12
loaded via a namespace (and not attached):
[1] graph_1.90.0 igraph_2.3.3 DEoptimR_1.2-0
[4] clue_0.3-68 magrittr_2.0.5 fastICA_1.2-7
[7] abind_1.4-8 BiocGenerics_0.58.1 pkgconfig_2.0.3
[10] generics_0.1.4 stats4_4.7.0 lifecycle_1.0.5
[13] cli_3.6.6 sfsmisc_1.1-24 ggm_2.5.2
[16] corpcor_1.6.10 robustbase_0.99-7 compiler_4.7.0
[19] RBGL_1.88.0 tools_4.7.0 cluster_2.1.8.2
[22] bdsmatrix_1.3-7 Rcpp_1.1.2 BiocManager_1.30.27
[25] rlang_1.3.0
> .libPaths()
[1] "/home/hornik/tmp/scratch/RtmpXBoM8F/RLIBS_3223746dcca6ea"
[2] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/library"
> packageDescription("pcalg")
Package: pcalg
Version: 2.7-12
Date: 2024-09-12
Title: Methods for Graphical Models and Causal Inference
Description: Functions for causal structure learning and causal
inference using graphical models. The main algorithms for
causal structure learning are PC (for observational data
without hidden variables), FCI and RFCI (for observational data
with hidden variables), and GIES (for a mix of data from
observational studies (i.e. observational data) and data from
experiments involving interventions (i.e. interventional data)
without hidden variables). For causal inference the IDA
algorithm, the Generalized Backdoor Criterion (GBC), the
Generalized Adjustment Criterion (GAC) and some related
functions are implemented. Functions for incorporating
background knowledge are provided.
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>
Authors@R: c(person("Markus","Kalisch",
email="kalisch@stat.math.ethz.ch", role=c("aut","cre")),
person("Alain", "Hauser", role="aut"),
person("Martin","Maechler", role="aut"), person("Diego",
"Colombo", role="ctb"), person("Doris", "Entner", role="ctb"),
person("Patrik", "Hoyer", role="ctb"), person("Antti",
"Hyttinen", role="ctb"), person("Jonas", "Peters", role="ctb"),
person("Nicoletta", "Andri", role="ctb"), person("Emilija",
"Perkovic", role="ctb"), person("Preetam", "Nandy",
role="ctb"), person("Philipp", "Ruetimann",
role="ctb"),person("Daniel", "Stekhoven", role="ctb"),
person("Manuel", "Schuerch", role="ctb"), person("Marco",
"Eigenmann", role="ctb"), person("Leonard", "Henckel", role =
"ctb"),person("Joris", "Mooij", role = "ctb"))
Depends: R (>= 3.5.0)
LinkingTo: Rcpp (>= 0.11.0), RcppArmadillo, BH
Imports: stats, graphics, utils, methods, abind, graph, RBGL, igraph,
ggm, corpcor, robustbase, vcd, Rcpp, bdsmatrix, sfsmisc (>=
1.0-26), fastICA, clue
Suggests: MASS, Matrix, Rgraphviz, mvtnorm, huge, ggplot2, dagitty
NeedsCompilation: yes
Encoding: UTF-8
License: GPL (>= 2)
URL: https://pcalg.r-forge.r-project.org/
Packaged: 2024-09-12 08:25:27 UTC; kalischm
Author: Markus Kalisch [aut, cre], Alain Hauser [aut], Martin Maechler
[aut], Diego Colombo [ctb], Doris Entner [ctb], Patrik Hoyer
[ctb], Antti Hyttinen [ctb], Jonas Peters [ctb], Nicoletta
Andri [ctb], Emilija Perkovic [ctb], Preetam Nandy [ctb],
Philipp Ruetimann [ctb], Daniel Stekhoven [ctb], Manuel
Schuerch [ctb], Marco Eigenmann [ctb], Leonard Henckel [ctb],
Joris Mooij [ctb]
Repository: CRAN
Date/Publication: 2024-09-12 17:40:27 UTC
Built: R 4.7.0; x86_64-pc-linux-gnu; 2026-07-22 09:44:39 UTC; unix
-- File: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/pcalg/Meta/package.rds
> packageDescription("Matrix")
Package: Matrix
Version: 1.7-5
VersionNote: do also bump src/version.h, inst/include/Matrix/version.h
Date: 2026-03-20
Priority: recommended
Title: Sparse and Dense Matrix Classes and Methods
Description: A rich hierarchy of sparse and dense matrix classes,
including general, symmetric, triangular, and diagonal matrices
with numeric, logical, or pattern entries. Efficient methods
for operating on such matrices, often wrapping the 'BLAS',
'LAPACK', and 'SuiteSparse' libraries.
License: GPL (>= 2) | file LICENCE
URL: https://Matrix.R-forge.R-project.org
BugReports: https://R-forge.R-project.org/tracker/?atid=294&group_id=61
Contact: Matrix-authors@R-project.org
Authors@R: c(person("Douglas", "Bates", role = "aut", comment = c(ORCID
= "0000-0001-8316-9503")), person("Martin", "Maechler", role =
c("aut", "cre"), email = "mmaechler+Matrix@gmail.com", comment
= c(ORCID = "0000-0002-8685-9910")), person("Mikael", "Jagan",
role = "aut", comment = c(ORCID = "0000-0002-3542-2938")),
person("Timothy A.", "Davis", role = "ctb", comment = c(ORCID =
"0000-0001-7614-6899", "SuiteSparse libraries", "collaborators
listed in dir(system.file(\"doc\", \"SuiteSparse\",
package=\"Matrix\"), pattern=\"License\", full.names=TRUE,
recursive=TRUE)")), person("George", "Karypis", role = "ctb",
comment = c(ORCID = "0000-0003-2753-1437", "METIS library",
"Copyright: Regents of the University of Minnesota")),
person("Jason", "Riedy", role = "ctb", comment = c(ORCID =
"0000-0002-4345-4200", "GNU Octave's condest() and
onenormest()", "Copyright: Regents of the University of
California")), person("Jens", "Oehlschlägel", role = "ctb",
comment = "initial nearPD()"), person("R Core Team", role =
"ctb", comment = c(ROR = "02zz1nj61", "base R's matrix
implementation")))
Depends: R (>= 4.4), methods
Imports: grDevices, graphics, grid, lattice, stats, utils
Suggests: MASS, datasets, sfsmisc, tools
Enhances: SparseM, graph
LazyData: no
LazyDataNote: not possible, since we use data/*.R and our S4 classes
BuildResaveData: no
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2026-03-20 19:40:14 UTC; maechler
Author: Douglas Bates [aut] (ORCID:
<https://orcid.org/0000-0001-8316-9503>), Martin Maechler [aut,
cre] (ORCID: <https://orcid.org/0000-0002-8685-9910>), Mikael
Jagan [aut] (ORCID: <https://orcid.org/0000-0002-3542-2938>),
Timothy A. Davis [ctb] (ORCID:
<https://orcid.org/0000-0001-7614-6899>, SuiteSparse libraries,
collaborators listed in dir(system.file("doc", "SuiteSparse",
package="Matrix"), pattern="License", full.names=TRUE,
recursive=TRUE)), George Karypis [ctb] (ORCID:
<https://orcid.org/0000-0003-2753-1437>, METIS library,
Copyright: Regents of the University of Minnesota), Jason Riedy
[ctb] (ORCID: <https://orcid.org/0000-0002-4345-4200>, GNU
Octave's condest() and onenormest(), Copyright: Regents of the
University of California), Jens Oehlschlägel [ctb] (initial
nearPD()), R Core Team [ctb] (ROR: <https://ror.org/02zz1nj61>,
base R's matrix implementation)
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Repository: CRAN
Date/Publication: 2026-03-21 14:40:03 UTC
Built: R 4.7.0; x86_64-pc-linux-gnu; 2026-07-22 08:56:15 UTC; unix
-- File: /home/hornik/tmp/scratch/RtmpXBoM8F/RLIBS_3223746dcca6ea/Matrix/Meta/package.rds
> cat("doExtras:", (doExtras <- pcalg:::doExtras()), "\n")
doExtras: FALSE
>
>
> ##################################################
> ## Exp 1
> ##################################################
> set.seed(123)
> n <- 500
> eps1 <- sign(rnorm(n)) * sqrt(abs(rnorm(n)))
> eps2 <- runif(n) - 0.5 # ~ U[-1/2, 1/2]
>
> X <- cbind(A = eps1 + 0.9*eps2,
+ B = eps2)
>
> ## x1 <- x2
> ## adjacency matrix:
> ## 0 0
> ## 1 0
> (trueDAG <- rbind(c(0,0),
+ c(1,0)))
[,1] [,2]
[1,] 0 0
[2,] 1 0
>
> estDAG <- LINGAM(X, verbose = TRUE)
Performing row permutation, nzdiag*() ...
(Small dimensionality, using brute-force method.): Done!
Performing permutation for causal order...
(Small dimensionality, using brute-force method.): Done!
[,1] [,2]
[1,] 0.0000000 0.001722255
[2,] 0.8506492 0.000000000
Causal B nicely triangular. No problems to report here.
Pruning the network connections...
Done!
Warning message:
In LINGAM(X, verbose = TRUE) :*** buffer overflow detected ***: terminated
Aborted
Running the tests in ‘tests/test_udag2pdag.R’ failed.
Complete output:
> library(pcalg)
> suppressWarnings(RNGversion("3.5.0"))
> .libPaths()
[1] "/home/hornik/tmp/scratch/RtmpXBoM8F/RLIBS_3223746dcca6ea"
[2] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/library"
> ## acyclic graphs
>
> nreps <- 30
> p <- 8
> n <- 1000
>
> for(u2pd in c("rand", "retry", "relaxed")) {
+ cat("\n u2pd =", u2pd, "\n ------------\n")
+ cyc.res <- logical(nreps)
+ for (i in 1:nreps) {
+ set.seed(i)
+ myDAG <- randomDAG(p, prob = 0.2)
+ d.mat <- rmvDAG(n, myDAG, errDist = "normal")
+ res <- suppressWarnings(pcAlgo(d.mat, alpha = 0.05, directed=TRUE, u2pd = u2pd))
+ ## ------ directed; u2pd = "rand" --> udag2pdag()
+ res.A <- wgtMatrix(res@graph)
+ res.A[res.A!=0] <- 1
+ undir.A <- res.A + t(res.A)
+ undir.A[undir.A==1] <- 0
+ undir.A[undir.A==2] <- 1
+ res.dir <- res.A - undir.A
+ cyc.res[i] <- ggm::isAcyclic(res.dir)
+ }
+ if (!all(cyc.res)) stop("Test of pcAlgo(*, directed): Cyclic part in PDAG!")
+ } ## for(u2pd ...)
u2pd = rand
------------
u2pd = retry
------------
u2pd = relaxed
------------
> cat('Time elapsed: ', (.pt <- proc.time()),"\n")
Time elapsed: 3.572 0.264 4.828 0.007 0.006
>
> ## find collider correctly
> set.seed(123)
> myDAG <- randomDAG(3, prob = 0.5)
> library(Matrix)
> as(myDAG,"sparseMatrix")
3 x 3 sparse Matrix of class "dgCMatrix"
1 2 3
1 . . 0.4680792
2 . . 0.9464206
3 . . .
> d.mat <- rmvDAG(n, myDAG, errDist = "normal")
> res <- pcAlgo(d.mat, alpha = 0.05, corMethod = "standard",directed=TRUE)
Warning message:
In pcAlgo(d.mat, alpha = 0.05, corMethod = "standard", directed = TRUE) :*** buffer overflow detected ***: terminated
Aborted
Flavor: r-devel-linux-x86_64-debian-gcc