[Rd] R CMD INSTALL warning for S4 replacement functions on R 4.1.0-alpha
Martin Maechler
m@ech|er @end|ng |rom @t@t@m@th@ethz@ch
Sat Apr 24 15:44:56 CEST 2021
>>>>> Felix Ernst
>>>>> on Fri, 23 Apr 2021 17:01:05 +0000 writes:
> Hi all,
> Since R 4.1, R CMD INSTALL throws warning during building the man pages, when installing from source.
> We noticed this first on Windows for man pages involving S4 replacement function:
> * http://bioconductor.org/checkResults/devel/bioc-LATEST/Modstrings/riesling1-checksrc.html
> * http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicAlignments/riesling1-checksrc.html
> However, it's also showing up on linux with a slight twist (file not found instead of invalid argument) for other functions:
> * https://cran.r-project.org/web/checks/check_results_Matrix.html (right at the end)
>> From the messages and the involved offending filenames, we hypothesize that this is triggered by invalid filenames specific to the OS.
> Please note, that the warning is not issued during R CMD CHECK for a given package.
> Can anyone comment on this? Is more information needed? If it is a bug, I am happy to post on the bug tracker.
> Thanks for any advice.
> Best regards,
> Felix
Thanks a lot, Felix, for the heads up -- and for using the
pre-release versions of R ---- you should be role model to the
many readers of 'R-devel' and other R developers -- even doing
it for a living and who are *still* not help the R project by
the relatively simple act of starting to work with
'R x.y.0 alpha'
To the topic, yes, I think there's something we (the R core
team) has not considered when implementing some of the changes
in static help page creation.
This will now get technical .... but that should always be ok /
even desirable for the R-devel list :
The CRAN check on Matrix (with R 4.1.0 alpha, called "R-patched") you mention,
here more directly
https://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/Matrix-00check.html
has the relevant lines
---------------------------------------------------------------------------------------
checking whether package ‘Matrix’ can be installed ... WARNING
Found the following significant warnings:
Rd warning: Previous alias or file overwritten by alias: chol,dsCMatrix-method
Rd warning: Previous alias or file overwritten by alias: chol,lsCMatrix-method
Rd warning: Previous alias or file overwritten by alias: chol,nsCMatrix-method
Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ddiMatrix,ddenseMatrix-method.html’: No such file or directory
Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ddiMatrix,ldenseMatrix-method.html’: No such file or directory
Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ddiMatrix,ndenseMatrix-method.html’: No such file or directory
Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ldiMatrix,ddenseMatrix-method.html’: No such file or directory
Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ldiMatrix,ldenseMatrix-method.html’: No such file or directory
Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ldiMatrix,ndenseMatrix-method.html’: No such file or directory
Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ddiMatrix,Matrix-method.html’: No such file or directory
Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ldiMatrix,Matrix-method.html’: No such file or directory
Rd warning: Previous alias or file overwritten by alias: expand
Rd warning: Previous alias or file overwritten by alias: crossprod-methods
Rd warning: Previous alias or file overwritten by alias: tcrossprod-methods
See https://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/Matrix-00install.html for details.
---------------------------------------------------------------------------------------
and the (quite large, from many C compilation warnings (from
SuiteSparse, not Matrix directly))
00install.html then gives the details:
*** installing help indices
converting help for package ‘Matrix’
finding HTML links ... done
BunchKaufman-methods html
CAex html
[...............]
bandSparse html
bdiag html
boolean-matprod html
REDIRECT:file boolean-matprod.html -> boolean-matprod.html [ SUCCESS ]
cBind html
chol html
Rd warning: Previous alias or file overwritten by alias: chol,dsCMatrix-method
Rd warning: Previous alias or file overwritten by alias: chol,lsCMatrix-method
Rd warning: Previous alias or file overwritten by alias: chol,nsCMatrix-method
chol2inv-methods html
colSums html
compMatrix-class html
condest html
dMatrix-class html
ddenseMatrix-class html
ddiMatrix-class html
denseMatrix-class html
dgCMatrix-class html
dgRMatrix-class html
dgTMatrix-class html
dgeMatrix-class html
diagU2N html
diagonalMatrix-class html
REDIRECT:topic %/%,ddiMatrix,ddenseMatrix-method -> diagonalMatrix-class.html [ FAIL ]
REDIRECT:topic %/%,ddiMatrix,ldenseMatrix-method -> diagonalMatrix-class.html [ FAIL ]
REDIRECT:topic %/%,ddiMatrix,ndenseMatrix-method -> diagonalMatrix-class.html [ FAIL ]
REDIRECT:topic %/%,ldiMatrix,ddenseMatrix-method -> diagonalMatrix-class.html [ FAIL ]
REDIRECT:topic %/%,ldiMatrix,ldenseMatrix-method -> diagonalMatrix-class.html [ FAIL ]
REDIRECT:topic %/%,ldiMatrix,ndenseMatrix-method -> diagonalMatrix-class.html [ FAIL ]
REDIRECT:topic %/%,ddiMatrix,Matrix-method -> diagonalMatrix-class.html [ FAIL ]
REDIRECT:topic %/%,ldiMatrix,Matrix-method -> diagonalMatrix-class.html [ FAIL ]
Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ddiMatrix,ddenseMatrix-method.html’: No such file or directory
Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ddiMatrix,ldenseMatrix-method.html’: No such file or directory
Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ddiMatrix,ndenseMatrix-method.html’: No such file or directory
Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ldiMatrix,ddenseMatrix-method.html’: No such file or directory
Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ldiMatrix,ldenseMatrix-method.html’: No such file or directory
Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ldiMatrix,ndenseMatrix-method.html’: No such file or directory
Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ddiMatrix,Matrix-method.html’: No such file or directory
Rd warning: cannot open file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Matrix/00new/Matrix/help/%/%,ldiMatrix,Matrix-method.html’: No such file or directory
dpoMatrix-class html
drop0 html
dsCMatrix-class html
dsRMatrix-class html
dsparseMatrix-class html
dsyMatrix-class html
dtCMatrix-class html
dtRMatrix-class-def html
REDIRECT:file dtRMatrix-class-def.html -> dtRMatrix-class-def.html [ SUCCESS ]
dtpMatrix-class html
dtrMatrix-class html
[...................]
------------------------------------------------------------------------
What I am really puzzled about is why this only shows for
R 4.1.0 alpha -- which was split off R-devel only Tuesday (Apr
20) .... and we had never seen this issue on R-devel, where
indeed we did change help page HTML link creations on purpose
but really many months ago, starting around here (which has been
a big improvement liked by many who had wished for it!):
---------------------------------------------------------------------------
r79075 | deepayan | 2020-08-25 08:32:39 +0200 (Tue, 25 Aug 2020) | 1 line
Changed paths:
M doc/NEWS.Rd
M doc/manual/R-exts.texi
M src/library/tools/R/Rd2HTML.R
M src/library/tools/R/dynamicHelp.R
help system now prefers topic over filename in external package help links
----------------------------------------------------------------------------
and there quite a few tweaks and improvements to
src/library/tools/R/Rd2HTML.R
after that ... but none happened the last couple of weeks, so
R 4.1.0 and R-devel should be identical here.... but the CRAN
checks using R-devel don't seem to show anything.
...
... hence my deep puzzlement.
Thank you once more for the report,
Martin
--
Martin Maechler
ETH Zurich and R Core team
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