* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/pcalg.Rcheck’
* using R Under development (unstable) (2024-05-01 r86507)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 18.1.4
    flang-new version 18.1.4
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘pcalg/DESCRIPTION’ ... OK
* this is package ‘pcalg’ version ‘2.7-11’
* 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 whether package ‘pcalg’ can be installed ... [3m/13m] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/pcalg-00install.html' for details.
* used C compiler: ‘clang version 18.1.4’
* used C++ compiler: ‘clang version 18.1.4’
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [3s/10s] 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 loading without being on the library search path ... [3s/10s] 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 ... [81s/268s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Undeclared packages ‘combinat’, ‘unifDAG’ in Rd xrefs
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [50s/197s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [4m/18m] OK
  Running ‘test_LINGAM.R’ [6s/28s]
  Running ‘test_addBgKnowledge.R’ [4s/18s]
  Running ‘test_adjustment.R’ [8s/30s]
  Running ‘test_ages.R’ [4s/17s]
  Running ‘test_amat2dag.R’ [3s/13s]
  Running ‘test_arges.R’ [3s/13s]
  Running ‘test_backdoor.R’ [15s/60s]
  Comparing ‘test_backdoor.Rout’ to ‘test_backdoor.Rout.save’ ... OK
  Running ‘test_bicscore.R’ [4s/19s]
  Running ‘test_causalEffect.R’ [3s/11s]
  Running ‘test_coercion.R’ [4s/15s]
  Running ‘test_compareGraphs.R’ [3s/13s]
  Running ‘test_dag2cpdag.R’ [4s/16s]
  Running ‘test_dag2essgraph.R’ [4s/18s]
  Running ‘test_displayAmat.R’ [4s/15s]
  Running ‘test_dsep.R’ [4s/15s]
  Running ‘test_dsepAM.R’ [3s/14s]
  Running ‘test_dsepAMTest.R’ [4s/16s]
  Running ‘test_fci.R’ [3s/14s]
  Running ‘test_fciPlus.R’ [4s/16s]
  Running ‘test_gSquareBin.R’ [3s/14s]
  Running ‘test_gSquareDis.R’ [6s/25s]
  Running ‘test_gac.R’ [7s/29s]
  Running ‘test_getNextSet.R’ [3s/12s]
  Running ‘test_gies.R’ [7s/27s]
  Running ‘test_ida.R’ [17s/71s]
  Running ‘test_idaFast.R’ [10s/41s]
  Running ‘test_isValidGraph.R’ [7s/31s]
  Running ‘test_jointIda.R’ [4s/18s]
  Running ‘test_mat2targets.R’ [4s/18s]
  Running ‘test_optAdjSet.R’ [4s/19s]
  Running ‘test_opttarget.R’ [3s/13s]
  Running ‘test_pag2anc.R’ [3s/13s]
  Running ‘test_pag2conf.R’ [3s/13s]
  Running ‘test_pag2edge.R’ [3s/12s]
  Running ‘test_pc.R’ [5s/23s]
  Running ‘test_pcSelect.R’ [6s/27s]
  Running ‘test_pcalg2dagitty.R’ [5s/19s]
  Running ‘test_pcorOrder.R’ [3s/13s]
  Running ‘test_pdag2allDags.R’ [3s/13s]
  Running ‘test_pdag2dag.R’ [3s/15s]
  Running ‘test_possDeAn.R’ [4s/18s]
  Running ‘test_randDAG.R’ [8s/34s]
  Comparing ‘test_randDAG.Rout’ to ‘test_randDAG.Rout.save’ ...1a2,16
> R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
> Copyright (C) 2023 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
> 
> R ist freie Software und kommt OHNE JEGLICHE GARANTIE.
> Sie sind eingeladen, es unter bestimmten Bedingungen weiter zu verbreiten.
> Tippen Sie 'license()' or 'licence()' für Details dazu.
> 
> R ist ein Gemeinschaftsprojekt mit vielen Beitragenden.
> Tippen Sie 'contributors()' für mehr Information und 'citation()',
> um zu erfahren, wie R oder R packages in Publikationen zitiert werden können.
> 
> Tippen Sie 'demo()' für einige Demos, 'help()' für on-line Hilfe, oder
> 'help.start()' für eine HTML Browserschnittstelle zur Hilfe.
> Tippen Sie 'q()', um R zu verlassen.
56c71
< Number of Edges = 21 
---
> Number of Edges = 0 
61c76
< Number of Edges = 13 
---
> Number of Edges = 12 
66c81
< Number of Edges = 16 
---
> Number of Edges = 13 
71c86
< Number of Edges = 19 
---
> Number of Edges = 16 
90,93c105,108
<  $ barabasi : chr "4"
<  $ geometric: chr [1:3] "3" "4" "7"
<  $ power    : chr [1:4] "2" "7" "8" "9"
<  $ interEr  : chr [1:2] "3" "7"
---
>  $ barabasi : chr [1:10] "1" "2" "3" "4" ...
>  $ geometric: chr [1:3] "2" "6" "10"
>  $ power    : chr [1:4] "2" "4" "5" "10"
>  $ interEr  : chr [1:2] "5" "6"
108,111c123,126
<  $ barabasi : chr [1:3] "1" "6" "7"
<  $ geometric: chr [1:3] "5" "6" "9"
<  $ power    : chr [1:3] "4" "5" "10"
<  $ interEr  : chr [1:2] "2" "4"
---
>  $ barabasi : chr [1:10] "1" "2" "3" "4" ...
>  $ geometric: chr [1:4] "1" "3" "5" "10"
>  $ power    : chr [1:4] "1" "6" "7" "8"
>  $ interEr  : chr [1:3] "1" "3" "8"
145c160
< Number of Edges = 13 
---
> Number of Edges = 0 
150c165
< Number of Edges = 6 
---
> Number of Edges = 12 
155c170
< Number of Edges = 11 
---
> Number of Edges = 13 
160c175
< Number of Edges = 10 
---
> Number of Edges = 11 
174a190
> Lade nötiges Paket: Matrix
240,242c256,258
< 1  . . . . | . . . | .
< 2  . . . | | . . | | .
< 3  . | . | . . . | | .
---
> 1  . . . . . . . . . .
> 2  . . . . . . . . . .
> 3  . . . . . . . . . .
244,249c260,265
< 5  . . . . . . . | . .
< 6  . | | . | . . . . |
< 7  . | . | . . . . . .
< 8  . . . | . . . . . .
< 9  . . . | . . . . . .
< 10 . . | . | . . . . .
---
> 5  . . . . . . . . . .
> 6  . . . . . . . . . .
> 7  . . . . . . . . . .
> 8  . . . . . . . . . .
> 9  . . . . . . . . . .
> 10 . . . . . . . . . .
255,264c271,280
< 1  . . | . . . . . . .
< 2  . . . . . . | . . .
< 3  . . . . . . . . . .
< 4  . . . . . . . . . .
< 5  . | . . . . | . . |
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---
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> 2  . . . . . . . . . .
> 3  . | . | . . . . . .
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> 10 . . . . . . . . . .
270c286
< 1  . . . . . . | . . .
---
> 1  . . | . | . . . | .
272,279c288,295
< 3  | | . . . . | | | .
< 4  | . | . . | | . . .
< 5  . . | . . . . . . .
< 6  . . . . . . | . . .
< 7  . . . . . . . . . .
< 8  . . . . . . . . . .
< 9  . . . . . . . . . .
< 10 | . | . . . | . | .
---
> 3  . . . | . . . . . .
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> 7  . . . | . . . . | |
> 8  . . . | . . . . | .
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> 10 . . . . . . . . . .
285,294c301,310
< 1  . . . . . . . . . |
< 2  | . | . . . . . | |
< 3  . . . . . . . . . .
< 4  . . . . | | | | . .
< 5  . . . . . . | . . .
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< 8  | . . . | . . . . .
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---
> 1  . . . . | . . . . |
> 2  . . . . . | . . | .
> 3  . | . . . | | . | .
> 4  . . . . | . . . . .
> 5  . . . . . . . . . .
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369,372c385,388
< 1  . . . . . | . . . . . .
< 2  | . . . . . . . . . | .
< 3  | . . . . . . . . . . |
< 4  | . . . . . . . . . . .
---
> 1  . . . . . . . . . . . .
> 2  . . . . . . . . . . . .
> 3  . . . . . . . . . . . .
> 4  . . . . . . . . . . . .
375,379c391,395
< 7  | . . . . . . . . . . .
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386,387c402,403
< 1  . . . . . . . . | . . .
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> 2  . . . . . . . . . . . .
389c405
< 4  . . . . . . . . . | . .
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391c407
< 6  . . . . . . . . . . . |
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> 6  . | . . . . . | . | . .
393,394c409,410
< 8  . . . . . . . . . . . .
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> 9  . . | | . . . . . . . .
396,397c412,413
< 11 . . | . . . . . . . . .
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> 11 . . . . . . . . . . . .
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403,407c419,423
< 1  . . . . . | | . . . . |
< 2  . . . . . . | . . . . .
< 3  | . . . . . . . . . . .
< 4  . . . . . . | . . . . .
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---
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> 2  . . . . . . . . . . . .
> 3  . . . . . . . . . . . .
> 4  . . . . . . . . . . . .
> 5  . . . . . . . . . . . .
410,414c426,430
< 8  . . . . . . | . | . . .
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< 10 . . . . . . | . . . . .
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---
> 8  | | . | | . . . . . . |
> 9  . . | . . . . . . . . .
> 10 . | . . . . . | . . . .
> 11 . . . . . . . . | . . .
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420,422c436,438
< 1  . . . . . . . . . . . .
< 2  . . . . | . . . . . . .
< 3  . . . . . . | . . . | .
---
> 1  . . . . . . . . . . . |
> 2  | . . . . . . | . . . .
> 3  . . . . . . . . . . . |
425,431c441,447
< 6  . . . . . . . . . . . .
< 7  . . . . | . . . . . . .
< 8  . . . . . . . . . . . .
< 9  | . . . . . . . . . . .
< 10 . . . . . . | | . . . .
< 11 . . . . | . . . . . . .
< 12 | . . . . | . . . . . .
---
> 6  | . . . . . . . . . . |
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> 9  . . . | | . . . . . . .
> 10 | . . . . . . . . . . .
> 11 . . . . . . . . . . . .
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523,525c539,541
< 1  . . . . | . . . | .
< 2  . . . | | . . | | .
< 3  . | . | . . . | | .
---
> 1  . . . . . . . . . .
> 2  . . . . . . . . . .
> 3  . . . . . . . . . .
527,532c543,548
< 5  . . . . . . . | . .
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< 7  . | . | . . . . . .
< 8  . . . | . . . . . .
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< 10 . . | . | . . . . .
---
> 5  . . . . . . . . . .
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538,547c554,563
< 1  . . | . . . . . . .
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553c569
< 1  . . . . . . | . . .
---
> 1  . . | . | . . . | .
555,562c571,578
< 3  | | . . . . | | | .
< 4  | . | . . | | . . .
< 5  . . | . . . . . . .
< 6  . . . . . . | . . .
< 7  . . . . . . . . . .
< 8  . . . . . . . . . .
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< 10 | . | . . . | . | .
---
> 3  . . . | . . . . . .
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> 8  . . . | . . . . | .
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568,577c584,593
< 1  . . . . . . . . . |
< 2  | . | . . . . . | |
< 3  . . . . . . . . . .
< 4  . . . . | | | | . .
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652,655c668,671
< 1  . . . . . | . . . . . .
< 2  | . . . . . . . . . | .
< 3  | . . . . . . . . . . |
< 4  | . . . . . . . . . . .
---
> 1  . . . . . . . . . . . .
> 2  . . . . . . . . . . . .
> 3  . . . . . . . . . . . .
> 4  . . . . . . . . . . . .
658,662c674,678
< 7  | . . . . . . . . . . .
< 8  | . . . . . . . . . . .
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669,670c685,686
< 1  . . . . . . . . | . . .
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---
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> 2  . . . . . . . . . . . .
672c688
< 4  . . . . . . . . . | . .
---
> 4  . . | . . . . . . | . .
674c690
< 6  . . . . . . . . . . . |
---
> 6  . | . . . . . | . | . .
676,677c692,693
< 8  . . . . . . . . . . . .
< 9  . . . . . . . . . . . .
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> 8  . | . . | . . . . | . .
> 9  . . | | . . . . . . . .
679,680c695,696
< 11 . . | . . . . . . . . .
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> 11 . . . . . . . . . . . .
> 12 . . | . . . . . | . . .
686,690c702,706
< 1  . . . . . | | . . . . |
< 2  . . . . . . | . . . . .
< 3  | . . . . . . . . . . .
< 4  . . . . . . | . . . . .
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> 1  . . . . . . . . . . . .
> 2  . . . . . . . . . . . .
> 3  . . . . . . . . . . . .
> 4  . . . . . . . . . . . .
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693,697c709,713
< 8  . . . . . . | . | . . .
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703,705c719,721
< 1  . . . . . . . . . . . .
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> 2  | . . . . . . | . . . .
> 3  . . . . . . . . . . . |
708,714c724,730
< 6  . . . . . . . . . . . .
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  Running ‘test_randomDAG.R’ [4s/16s]
  Running ‘test_rfci.R’ [6s/27s]
  Running ‘test_rmvDAG.R’ [3s/14s]
  Running ‘test_searchAM.R’ [3s/13s]
  Running ‘test_shd.R’ [3s/14s]
  Running ‘test_skeleton.R’ [7s/27s]
  Running ‘test_udag2pag.R’ [3s/11s]
  Running ‘test_udag2pdag.R’ [11s/46s]
  Running ‘test_wgtMatrix.R’ [4s/15s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [47s/178s] OK
* checking PDF version of manual ... [21s/82s] OK
* checking HTML version of manual ... [14s/53s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 NOTEs