[Distr-commits] r1510 - / pkg

[noreply at r-forge.r-project.org]

Author: ruckdeschel
Date: 2025-05-06 21:14:58 +0200 (Tue, 06 May 2025)
New Revision: 1510

Added:
   20240905WriteUpKHornikS3Methods.txt
   pkg/20250116HintsAsToR-CMD-issue.txt
Log:
yet some remainder writeups

Added: 20240905WriteUpKHornikS3Methods.txt
===================================================================
--- 20240905WriteUpKHornikS3Methods.txt	                        (rev 0)
+++ 20240905WriteUpKHornikS3Methods.txt	2025-05-06 19:14:58 UTC (rev 1510)
@@ -0,0 +1,36 @@
+    ## Check S3 generics and methods consistency.
+
+     ## Unfortunately, what is an S3 method is not clear.
+     ## These days, S3 methods for a generic GEN are found
+     ## A. via GEN.CLS lookup from the callenv to its topenv;
+     ## B. the S3 registry;
+     ## C. GEN.CLS lookup from the parent of the topenv to baseenv,
+     ##    skipping everything on the search path between globalenv and
+     ##    baseenv.
+     ## Thus if "package code" calls GEN, we first look in the package
+     ## namespace itself, then in the registry, and then in the package
+     ## imports and .BaseNamespaceEnv (and globalenv and baseenv again).
+     ##
+     ## Clearly, everything registered via S3method() should be an S3
+     ## method.  Interestingly, we seem to have some registrations for
+     ## non-generics, such as grDevices::axis().  These are "harmless"
+     ## but likely not "as intended", and hence inconsistencies are not
+     ## ignored.
+     ##
+     ## If the package namespace has a function named GEN.CLS, it is used
+     ## as an S3 method for an S3 generic named GEN (and hence "is an S3
+     ## method") only if the package code actually calls GEN (see A
+     ## above).  So one could argue that we should not be looking at all
+     ## GEN.CLS matches with GEN a generic in the package itself, its
+     ## imports or base, but restrict to only the ones where the package
+     ## code calls GEN.  Doable, but not straightforward (calls could be
+     ## PKG::GEN) and possibly quite time consuming.  For generics from
+     ## the package itself or its imports, not restricting should not
+     ## make a difference (why define or import when not calling?), but
+     ## for generics from base it may: hence we filter out the mismatches
+     ## for base GEN not called in the package.
+     ##
+     ## If a package provides an S3 generic GEN, there is no need to
+     ## register GEN.CLS functions for "internal use" (see above).
+     ## However, if GEN is exported then likely all GEN.CLS functions
+     ## should be registered as S3 methods.
\ No newline at end of file

Added: pkg/20250116HintsAsToR-CMD-issue.txt
===================================================================
--- pkg/20250116HintsAsToR-CMD-issue.txt	                        (rev 0)
+++ pkg/20250116HintsAsToR-CMD-issue.txt	2025-05-06 19:14:58 UTC (rev 1510)
@@ -0,0 +1,91 @@
+## -----------------------------------------------------------------
+## UTF-8 encoding issue with R CMD check with install-args="--latex"
+## -----------------------------------------------------------------
+## Peter Ruckdeschel, Oldenburg University
+## -----------------------------------------------------------------
+# peter.ruckdeschel at uol.de, peter.ruckdeschel at web.de
+# 2025-01-16
+## -----------------------------------------------------------------
+
+This reports first insights into the error thrown at
+
+R CMD check --install-args="--latex" <pkg>\_<version>.tar.gz  
+  
+Seen error message:  
+  
+===
+* checking PDF version of manual ... WARNING
+LaTeX errors when creating PDF version.
+This typically indicates Rd problems.
+LaTeX errors found:
+! Undefined control sequence.
+l.37 \inputencoding
+                   {utf8}
+The control sequence at the end of the top line
+of your error message was never \def'ed. If you have
+===
+
+Digging deeper into it, I find that     
+
+    tools:::.Rd2pdf() 
+
+starting in code line 576 of Rd2pdf.R inserts the following line 
+into the TeX file of the manual
+
+    \makeatletter\@ifl at t@r\fmtversion{2018/04/01}{}{\usepackage[utf8]{inputenc}}\makeatother
+
+[and this is the only location in the R code of pkg tools where such a string is written.]
+I.e., in recent TeX-versions the following line is _not_ inserted to the TeX file of the manual
+
+    \usepackage[utf8]{inputenc}
+
+and consequently (as the alternatives to inputenc are not reached either in my case) pdfLaTeX will
+not know command \inputencoding which causes the error described above.
+
+We also note that line 576 is only reached (in if clauses) if logical variable asUTF8 is TRUE.
+However, the code of tools:::.Rd2pdf starting from line 641 in file Rd2pdf.R writes the lines
+
+    \Rdcontents{Contents}
+    \inputencoding{utf8}
+
+into the TeX file of the manual, [and againg, this is the only location in the R code of pkg tools where
+such strings are written.] Of these two lines the latter is only reached if asUTF is FALSE.
+
+So I suppose option --install-args="--latex" somehow interferes with this so that asUTF inbetween
+lines 576 and 641 gets changed, but I have not been able to identify where and how this could
+happen.
+
+=============================================================================
+> sessionInfo()
+R Under development (unstable) (2025-01-10 r87562 ucrt)
+Platform: x86_64-w64-mingw32/x64
+Running under: Windows 11 x64 (build 26100)
+
+Matrix products: default
+  LAPACK version 3.12.0
+
+locale:
+[1] LC_COLLATE=German_Germany.utf8  LC_CTYPE=German_Germany.utf8   
+[3] LC_MONETARY=German_Germany.utf8 LC_NUMERIC=C                   
+[5] LC_TIME=German_Germany.utf8    
+
+time zone: Europe/Berlin
+tzcode source: internal
+
+attached base packages:
+[1] stats     graphics  grDevices utils     datasets  methods   base     
+
+loaded via a namespace (and not attached):
+ [1] utf8_1.2.4       R6_2.5.1         magrittr_2.0.3   gtable_0.3.5    
+ [5] glue_1.7.0       tibble_3.2.1     pkgconfig_2.0.3  lifecycle_1.0.4
+ [9] ggplot2_3.5.1    cli_3.6.3        fansi_1.0.6      scales_1.3.0    
+[13] grid_4.5.0       vctrs_0.6.5      compiler_4.5.0   munsell_0.5.1   
+[17] pillar_1.9.0     colorspace_2.1-1 rlang_1.1.4  
+
+=============================================================================
+As to MikTeX, see:This is pdfTeX, Version 3.141592653-2.6-1.40.26 (MiKTeX 24.4) 
+(preloaded format=pdflatex 2025.1.11)  11 JAN 2025 20:25
+entering extended mode
+ restricted \write18 enabled.
+ %&-line parsing enabled.
+=============================================================================