* using log directory ‘/srv/hornik/tmp/CRAN/compositions.Rcheck’
* using R Under development (unstable) (2024-01-07 r85787)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (3)
    Debian flang-new version 17.0.6 (3)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘compositions/DESCRIPTION’ ... OK
* this is package ‘compositions’ version ‘2.0-7’
* checking CRAN incoming feasibility ... [5s/6s] NOTE
Maintainer: ‘K. Gerald van den Boogaart <support@boogaart.de>’

Found the following (possibly) invalid URLs:
  URL: https://ima.udg.edu/Activitats/CoDaWork03/
    From: man/acomp.Rd
          man/acomparith.Rd
          man/alr.Rd
          man/compositions.Rd
          man/gsigetbalstruct.Rd
          man/gsimerge2signary.Rd
          man/gsivarwithlosts.Rd
          man/ilr.Rd
          man/ilrBase.Rd
          man/pairwisePlot.Rd
          man/plot.Rd
          man/princompacomp.Rd
          man/pwlr.Rd
          man/pwlrPlot.Rd
          man/zeroreplace.Rd
    Status: Error
    Message: server certificate verification failed. CAfile: none CRLfile: none
      	(Status without verification: OK)
  URL: https://ima.udg.edu/Activitats/CoDaWork05/
    From: man/acomp.Rd
          man/acomparith.Rd
          man/balancebase.Rd
          man/codadendrogram.Rd
          man/compositions.Rd
          man/pairwisePlot.Rd
          man/plot.Rd
          man/princompacomp.Rd
          man/pwlrPlot.Rd
          man/rDirichlet.Rd
          man/zeroreplace.Rd
    Status: Error
    Message: server certificate verification failed. CAfile: none CRLfile: none
      	(Status without verification: OK)
  URL: https://ima.udg.edu/Activitats/CoDaWork08/
    From: man/balancebase.Rd
          man/pairwisePlot.Rd
          man/pwlrPlot.Rd
    Status: Error
    Message: server certificate verification failed. CAfile: none CRLfile: none
      	(Status without verification: OK)
* 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 ‘compositions’ can be installed ... [10s/10s] OK
* used C compiler: ‘Debian clang version 17.0.6 (3)’
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking whether startup messages can be suppressed ... [0s/0s] 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 ... [18s/18s] OK
* checking Rd files ... [1s/1s] 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... 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 ... [29s/29s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [10s/10s] OK
  Running ‘AitchisonTest.R’ [0s/0s]
  Running ‘CheckGeometry.R’ [3s/3s]
  Comparing ‘CheckGeometry.Rout’ to ‘CheckGeometry.Rout.save’ ... OK
  Running ‘RobustTest.R’ [0s/0s]
  Comparing ‘RobustTest.Rout’ to ‘RobustTest.Rout.save’ ... OK
  Running ‘TestMissing.R’ [3s/3s]
  Comparing ‘TestMissing.Rout’ to ‘TestMissing.Rout.save’ ...138c138
< [1] 8.412440e+00 4.201802e+00 3.119081e-01 1.761007e-01 4.592042e-16
---
> [1] 8.412440e+00 4.201802e+00 3.119081e-01 1.761007e-01 7.156429e-17
187c187
< [1] 8.412440e+00 4.201802e+00 3.119081e-01 1.761007e-01 4.592042e-16
---
> [1] 8.412440e+00 4.201802e+00 3.119081e-01 1.761007e-01 7.156429e-17
397d396
< There were 40 warnings (use warnings() to see them)
399d397
< There were 40 warnings (use warnings() to see them)
401d398
< There were 40 warnings (use warnings() to see them)
404c401
< There were 50 or more warnings (use warnings() to see the first 50)
---
> There were 22 warnings (use warnings() to see them)
406,426d402
< Warning messages:
< 1: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 4 does not name a graphical parameter
< 2: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 5 does not name a graphical parameter
< 3: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 4 does not name a graphical parameter
< 4: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 5 does not name a graphical parameter
< 5: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 4 does not name a graphical parameter
< 6: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 5 does not name a graphical parameter
< 7: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 4 does not name a graphical parameter
< 8: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 5 does not name a graphical parameter
< 9: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 4 does not name a graphical parameter
< 10: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 5 does not name a graphical parameter
428c404,405
< There were 41 warnings (use warnings() to see them)
---
> Warning message:
> In acomp(x) : Negative values in composition are used as detection limits
430,450d406
< Warning messages:
< 1: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 4 does not name a graphical parameter
< 2: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 5 does not name a graphical parameter
< 3: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 4 does not name a graphical parameter
< 4: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 5 does not name a graphical parameter
< 5: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 4 does not name a graphical parameter
< 6: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 5 does not name a graphical parameter
< 7: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 4 does not name a graphical parameter
< 8: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 5 does not name a graphical parameter
< 9: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 4 does not name a graphical parameter
< 10: In par(xlog = FALSE, ylog = FALSE, xpd = xpd, par(), opar) :
<   argument 5 does not name a graphical parameter
  Running ‘TestSimp.R’ [2s/2s]
  Comparing ‘TestSimp.Rout’ to ‘TestSimp.Rout.save’ ...1918,1920c1918,1920
< Cu  0.107 -0.410 -0.593  0.681       
< Zn  0.192 -0.576 -0.363 -0.673  0.215
< Pb -0.220  0.571 -0.701 -0.257 -0.262
---
> Cu  0.107 -0.410  0.593  0.681       
> Zn  0.192 -0.576  0.363 -0.673  0.215
> Pb -0.220  0.571  0.701 -0.257 -0.262
1922c1922
< Co  0.607  0.415 -0.134         0.657
---
> Co  0.607  0.415  0.134         0.657
  Running ‘acheck.R’ [0s/0s]
  Running ‘geostat.R’ [0s/0s]
  Running ‘missings.R’ [0s/0s]
  Comparing ‘missings.Rout’ to ‘missings.Rout.save’ ... OK
  Running ‘quickcheck.R’ [0s/0s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [4s/4s] OK
* checking PDF version of manual ... [8s/8s] OK
* checking HTML version of manual ... [5s/5s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 NOTE