R Development Page
pcalg log file (check_x86_64_linux)
Tue Feb 6 15:47:03 2024: Checking package pcalg (SVN revision 537) ...
* using log directory ‘/srv/rf/building/build_2024-02-06-15-44/RF_PKG_CHECK/PKGS/pcalg.Rcheck’
* using R version 4.3.2 Patched (2024-02-04 r85859)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Debian 12.2.0-14) 12.2.0
GNU Fortran (Debian 12.2.0-14) 12.2.0
* running under: Debian GNU/Linux 12 (bookworm)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘pcalg/DESCRIPTION’ ... OK
* this is package ‘pcalg’ version ‘2.7-10’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/8s] Note_to_CRAN_maintainers
Maintainer: ‘Markus Kalisch ’
* 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 ... [66s/66s] OK
* used C compiler: ‘gcc (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++ (Debian 12.2.0-14) 12.2.0’
* checking installed package size ... NOTE
installed size is 13.7Mb
sub-directories of 1Mb or more:
data 2.1Mb
libs 8.6Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... WARNING
A complete check needs the 'checkbashisms' script.
See section ‘Configure and cleanup’ in the ‘Writing R Extensions’
manual.
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [25s/25s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘unifDAG’
* 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 ... [1s/1s] 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’ ... WARNING
‘gs+qpdf’ made some significant size reductions:
compacted ‘vignette2018.pdf’ from 610Kb to 256Kb
consider running tools::compactPDF(gs_quality = "ebook") on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [26s/26s] OK
* checking examples with --run-donttest ... [51s/51s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test_LINGAM.R’ [2s/2s]
Running ‘test_addBgKnowledge.R’ [2s/2s]
Running ‘test_adjustment.R’ [3s/3s]
Running ‘test_ages.R’ [2s/2s]
Running ‘test_amat2dag.R’ [1s/1s]
Running ‘test_arges.R’ [1s/1s]
Running ‘test_backdoor.R’ [5s/5s]
Comparing ‘test_backdoor.Rout’ to ‘test_backdoor.Rout.save’ ... OK
Running ‘test_bicscore.R’ [2s/2s]
Running ‘test_causalEffect.R’ [1s/1s]
Running ‘test_coercion.R’ [2s/1s]
Running ‘test_compareGraphs.R’ [1s/1s]
Running ‘test_dag2cpdag.R’ [2s/1s]
Running ‘test_dag2essgraph.R’ [2s/2s]
Running ‘test_displayAmat.R’ [1s/1s]
Running ‘test_dsep.R’ [2s/2s]
Running ‘test_dsepAM.R’ [1s/1s]
Running ‘test_dsepAMTest.R’ [2s/2s]
Running ‘test_fci.R’ [1s/1s]
Running ‘test_fciPlus.R’ [2s/2s]
Running ‘test_gSquareBin.R’ [1s/1s]
Running ‘test_gSquareDis.R’ [2s/2s]
Running ‘test_gac.R’ [2s/2s]
Running ‘test_getNextSet.R’ [1s/1s]
Running ‘test_gies.R’ [2s/2s]
Running ‘test_ida.R’ [5s/5s]
Running ‘test_idaFast.R’ [3s/3s]
Running ‘test_isValidGraph.R’ [2s/2s]
Running ‘test_jointIda.R’ [2s/2s]
Running ‘test_mat2targets.R’ [2s/2s]
Running ‘test_optAdjSet.R’ [2s/2s]
Running ‘test_opttarget.R’ [1s/1s]
Running ‘test_pag2anc.R’ [1s/1s]
Running ‘test_pag2conf.R’ [1s/1s]
Running ‘test_pag2edge.R’ [1s/1s]
Running ‘test_pc.R’ [2s/2s]
Running ‘test_pcSelect.R’ [3s/3s]
Running ‘test_pcalg2dagitty.R’ [2s/2s]
Running ‘test_pcorOrder.R’ [1s/1s]
Running ‘test_pdag2allDags.R’ [1s/1s]
Running ‘test_pdag2dag.R’ [1s/1s]
Running ‘test_possDeAn.R’ [2s/2s]
Running ‘test_randDAG.R’ [3s/3s]
Comparing ‘test_randDAG.Rout’ to ‘test_randDAG.Rout.save’ ... OK
Running ‘test_randomDAG.R’ [1s/1s]
Running ‘test_rfci.R’ [3s/3s]
Running ‘test_rmvDAG.R’ [1s/1s]
Running ‘test_searchAM.R’ [1s/1s]
Running ‘test_shd.R’ [1s/1s]
Running ‘test_skeleton.R’ [2s/2s]
Running ‘test_udag2pag.R’ [1s/1s]
Running ‘test_udag2pdag.R’ [4s/4s]
Running ‘test_wgtMatrix.R’ [1s/1s]
[97s/96s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [21s/21s] OK
* checking PDF version of manual ... [8s/8s] OK
* checking HTML version of manual ... [1s/0s] NOTE
Skipping checking HTML validation: no command 'tidy' found
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 WARNINGs, 3 NOTEs
See
‘/srv/rf/building/build_2024-02-06-15-44/RF_PKG_CHECK/PKGS/pcalg.Rcheck/00check.log’
for details.
Run time: 339.46 seconds.
