Re: [R-pkg-devel] FW: [CRAN-pretest-archived] CRAN submission RIBMDB 1.0.0

[Binit Kumar]

Hi Ivan,
Thanks for the response. Appreciate.
But,

  1.  Windows: As I can see in the logs of the machine:

platform =  windows , arch =  x64 , R_Version =  R Under development (unstable) 
(2021-02-16 r80015)



So that means the architecture on CRAN machine is 64 bit and not 32 bit.

This is extracted by my code using:

platform = .Platform$OS.type

arch = .Platform$r_arch



The dll is selected based on the architecture, it is not hardcoded.

Please let me know if my understanding is wrong.

2)  Linux: I have already used "configure" and that copies the requisite 
file using "CLIDriver_installer.R" but problem is that R does everything in tmp 
file and then copy to the library folder of R. As you mentioned, "This still may
be insufficient as you might have to instruct the dynamic linker to look
for libdb2.so in the same directory when the package shared object is
loaded by R; on some compilers this may be done by passing the
-rpath='$ORIGIN' argument to the linker, but this is very
platform-dependent (no idea whether it's going to work on Solaris, for
example)."  So the part that is failing is loading. I want to exclude test 
loading using "-c -no-test-load". I tested in my local system and it works fine.

Can you suggest how to move ahead?



Also the CRAN upload has a limitation of 100MB. I have some executables for 
multiple platforms and they together constitute more than 100MB. How to resolve 
this? Can you please help?




Thanks & Regards,
Binit Kumar
From: Ivan Krylov 
Sent: 18 February 2021 01:53
To: Binit Kumar 
Cc: r-package-devel@r-project.org
Subject: Re: [R-pkg-devel] FW: [CRAN-pretest-archived] CRAN submission RIBMDB 
1.0.0

EXTERNAL EMAIL



Hello Binit Kumar,

On Wed, 17 Feb 2021 15:12:53 +
Binit Kumar mailto:bku...@rocketsoftware.com>> wrote:

> Error: Ld:/Compiler/gcc-4.9.3/local330/lib
> -LD:/RCompile/recent/R/bin/i386 -lR clidriver/bin/db2app64.dll: file
> not recognized: file format not recognized
>
> Why is db2app64.dll a non recognized file?

The package is being built for i386 (32-bit) subarchitecture, but the
64-bit dll is being linked to it. I think that the correct way to
identify the target sub-architecture is to inspect the R_ARCH
environment variable from configure.win (in R code, use getenv()).

This is described in WRE 1.2:
>.

> Error: ** testing if installed package can be loaded from temporary
> location
>
> Error: package or namespace load failed for 'RIBMDB' in
> dyn.load(file, DLLpath = DLLpath, ...):
>
> unable to load shared object
> '/srv/hornik/tmp/CRAN/RIBMDB.Rcheck/00LOCK-RIBMDB/00new/RIBMDB/libs/RIBMDB.so':
>
> libdb2.so.1: cannot open shared object file: No such file or
> directory

The bigger problem is trying to manually write under R.home() during
installation. This is not allowed by the CRAN policy and may lead to
problems. (Imagine what would happen if two different packages tried to
write to file.path(R.home(), 'clidriver') and for some reason succeeded
despite it's usually not writable for the end-user on Unix-alikes...)

Instead, you could try to (1) use ./configure to extract the
library to src/ and link to it from there and (2) provide a
src/install.libs.R file to copy libdb2.so from src/ to the same
directory where the package shared object is installed. This still may
be insufficient as you might have to instruct the dynamic linker to look
for libdb2.so in the same directory when the package shared object is
loaded by R; on some compilers this may be done by passing the
-rpath='$ORIGIN' argument to the linker, but this is very
platform-dependent (no idea whether it's going to work on Solaris, for
example).

See WRE 1.1.5 for more info on install.libs.R:
https://cran.r-project.org/doc/manuals/R-exts.html#Package-subdirectories

In short, linking an R package to a binary dependency not provided by a
system package is painful, but not explicitly prohibited by CRAN policy
("Source packages may not contain any form of binary executable code",
and yours downloads binaries when it's built, but doesn't contain any;
"Downloads of additional software <...> as part of package installation
<...> should only use secure download mechanisms", which yours does).

--
Best regards,
Ivan


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[R-pkg-devel] Cannot reproduce CRAN error (Solaris i386)

[Daeyoung Lim]

Hello,

I have a package on CRAN called 'metapack' and received a message from
Professor Ripley that the error must be resolved for the package to be
safely retained in CRAN. I've encountered this error on R-CMD-check on
GitHub but cannot replicate it on any of my local machines to save my life.
The reproducible code snippet is as follows (I use Rcpp/RcppArmadillo):

library(metapack)
data("cholesterol")
Outcome <- model.matrix(~ pldlc + phdlc + ptg, data = cholesterol)
SD <- model.matrix(~ sdldl + sdhdl + sdtg, data = cholesterol)
Trial <- cholesterol$Trial
Treat <- cholesterol$trt
Npt <- cholesterol$Npt
XCovariate <- model.matrix(~ 0 + bldlc + bhdlc + btg + age + durat +
white + male + dm, data = cholesterol)
WCovariate <- model.matrix(~ trt, data = cholesterol)

fmodel <- 1
set.seed(2797542)
fit <- bayes.parobs(Outcome, SD, XCovariate, WCovariate, Treat, Trial,
  Npt, fmodel, mcmc = list(ndiscard = 1, nskip = 1, nkeep = 1),
  scale_x = TRUE, group = cholesterol$onstat, verbose = FALSE)

which gives me the following error:

warning: chol(): given matrix is not symmetric  error: chol():
decomposition failed

This can't be true because (1) it runs without problem on other machines,
(2) every matrix that is Cholesky-decomposed is ensured to be symmetric
through Sig = 0.5 * (Sig + Sig.t());. Even with Sig = arma::symmatu(Sig)
doesn't seem to guarantee symmetry.

Has anyone encountered something similar to this?
Thank you for your time.

*Daeyoung Lim, MS*

Ph.D. Student

Department of Statistics

University of Connecticut

Philip E. Austin, 215 Glenbrook Road


Storrs Mansfield, CT 06269-4120 

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Re: [Bioc-devel] How to change the name of a package on Bioconductor

[Yu Huihui]

Thank you, Martin,


I have renamed 'vasp' to "VaSP" in release and devel branches. I will wait for 
the build result. If it success, I will keep the name "VaSP" and just maintain 
"VaSP".


Huihui






--Original--
From:   
 "Martin Morgan"

https://bioconductor.org/packages/VaSP will point to the new landing page. 
The user will install it with `BiocManager::install("VaSP")`. The user will use 
the package with `library("VaSP")`.

The old version of your package, with the original name, will remain available 
at https://bioconductor.org/packages/3.11/vasp.

Note that your users who have already installed your package may experience 
problems, e.g., on some operating systems that respect differences in directory 
case, library(vasp) and library(VaSP) will return different versions of the 
package. On operating systems with file systems that do not differentiate 
between case their previous installation of vasp will be replaced by VaSP, and 
library(vasp) will no longer work. This problem will only persist for existing 
users of Bioconductor version 3.12.

Issues like this make renaming packages very tedious. A more formal approach 
would have deprecated 'vasp' over two release cycles (introduce deprecation in 
devel, wait for next release, remove from devel, leading to final removal two 
releases from now) and at the same time introduce a new package into devel. But 
the new package could not have been named 'VaSP', for the file naming reasons 
mentioned. So you would have had to rename your package something else, 
SuperVaSP, but then you would not have addressed your concern, that you had 
published your package under the name VaSP rather than vasp.

I chose to simply replace 'vasp' with 'VaSP', in both the release and devel 
branches, rather than force you though these hoops.

We will not create and maintain a special redirect for your package.

Martin


From: Yu Huihui http://bioconductor.org/packages/vasp and 
http://bioconductor.org/packages/VaSP can jump to 
http://bioconductor.org/packages/release/bioc/html/vasp.html. Is that possible? 
Currently the link http://bioconductor.org/packages/VaSP will jump to 
http://bioconductor.org/about/removed-packages/.; Please give me your 
suggestions.

Thanks,
Huihui


-- Original --
From: "Yu Huihui" http://bioconductor.org/packages/vasp). Recently I had a manuscript about this 
package publishednbsp;on New Physiologist 
(https://nph.onlinelibrary.wiley.com/doi/10./nph.17189). However, on the 
manuscript, the link to the package is http://bioconductor.org/packages/VaSP. I 
want to change the name of the package to VaSP from vasp.nbsp; I changed 
the package name and updated it innbsp;git.bioconductor.org, but the build 
failed and it said "ERRORnbsp; (Bad DESCRIPTION file)".nbsp;


Can I change the name of a package existing on Bioconductor? How can I do that?


Thanks,
Huihui
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Re: [Rd] issue with print()ing multibyte characters on R 4.0.4

[Hiroaki Yutani]

I filed an issue for this on R's Bugzilla as well, in case this makes
it easier to track (This is my first time to submit a bug report,
please excuse me if I'm failing to follow the appropriate steps to do
this).

https://bugs.r-project.org/bugzilla/show_bug.cgi?id=18059

2021年2月17日(水) 22:47 Hiroaki Yutani :
>
> Thanks for confirming and investigating.
>
> > but it was no one reported in the run up to 4.0.4.
>
> Yes, it was unfortunate that no one had reported it to the right place
> before the release...
>
> 2021年2月17日(水) 19:20 Prof Brian Ripley :
>
> >
> > On 17/02/2021 04:58, Hiroaki Yutani wrote:
> > > Hi all,
> > >
> > > I saw several people on Japanese locale claim that, on R 4.0.4,
> > > print() doesn't display
> > > Japanese characters correctly. This seems to happen only on Windows
> > > and on macOS (I
> > > usually use Linux and I don't see this problem).
> > >
> > > For example, in the result below, "鬼" and "外" are displayed in
> > > "\u" format. What's
> > > curious here is that "は" is displayed as it is, by the way.
> > >
> > >> "鬼は外"
> > > [1] "\u9b3cは\u5916"
> > >
> > > But, if I use such functions as message() or cat(), the string is
> > > displayed as it is.
> > >
> > >> message("鬼は外")
> > > 鬼は外
> >
> > that does not escape non-printable characters, so as expected.
> > >
> > > Considering the fact that it seems only Windows and macOS are
> > > affected, I suspect this
> > > is somehow related to this change described in the release note,
> > > (though I have no idea
> > > what change this is):
> > >
> > >  The internal table for iswprint (used on Windows, macOS and AIX) has 
> > > been
> > >  updated to include many recent Unicode characters.
> > >  (https://cran.r-project.org/doc/manuals/r-release/NEWS.html)
> > >
> > > Before I'm going to file this issue on Bugzilla, I'd like to confirm
> > > if this is not the intended
> > > change, and, if this is actually intended, I want to discuss how to
> > > improve this behaviour.
> >
> > I am sorry: this was not intended but it was no one reported in the run
> > up to 4.0.4.  It seems to be working in R-devel so I suggest you check
> > that or go back to 4.0.3.
> >
> > It looks like a line in the iswprint table got deleted in the merge from
> > R-devel.  I will try to set up some automated checks to see if I can
> > find any other problems, but that will take a few days.
> >
> > --
> > Brian D. Ripley,  rip...@stats.ox.ac.uk
> > Emeritus Professor of Applied Statistics, University of Oxford

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Re: [Bioc-devel] How to change the name of a package on Bioconductor

[Martin Morgan]

Your package will build under the new name. When it builds successfully, the 
url https://bioconductor.org/packages/VaSP will point to the new landing page. 
The user will install it with `BiocManager::install("VaSP")`. The user will use 
the package with `library("VaSP")`.

The old version of your package, with the original name, will remain available 
at https://bioconductor.org/packages/3.11/vasp.

Note that your users who have already installed your package may experience 
problems, e.g., on some operating systems that respect differences in directory 
case, library(vasp) and library(VaSP) will return different versions of the 
package. On operating systems with file systems that do not differentiate 
between case their previous installation of vasp will be replaced by VaSP, and 
library(vasp) will no longer work. This problem will only persist for existing 
users of Bioconductor version 3.12.

Issues like this make renaming packages very tedious. A more formal approach 
would have deprecated 'vasp' over two release cycles (introduce deprecation in 
devel, wait for next release, remove from devel, leading to final removal two 
releases from now) and at the same time introduce a new package into devel. But 
the new package could not have been named 'VaSP', for the file naming reasons 
mentioned. So you would have had to rename your package something else, 
SuperVaSP, but then you would not have addressed your concern, that you had 
published your package under the name VaSP rather than vasp.

I chose to simply replace 'vasp' with 'VaSP', in both the release and devel 
branches, rather than force you though these hoops.

We will not create and maintain a special redirect for your package.

Martin


From: Yu Huihui 
Date: Wednesday, February 17, 2021 at 4:59 PM
To: "mtmorgan.bioc" , "nturaga.bioc" 

Cc: bioc-devel 
Subject: Re:[Bioc-devel] How to change the name of a package on Bioconductor

Hello,

I am just following my last email. I find it is a bad way to change package 
name. An alternative way is to let the link jump to the package webpage, that 
is both http://bioconductor.org/packages/vasp and 
http://bioconductor.org/packages/VaSP can jump to 
http://bioconductor.org/packages/release/bioc/html/vasp.html. Is that possible? 
Currently the link http://bioconductor.org/packages/VaSP will jump to 
http://bioconductor.org/about/removed-packages/.  Please give me your 
suggestions.

Thanks,
Huihui


-- Original --
From: "Yu Huihui" ;
Date: Wed, Feb 17, 2021 11:55 AM
To: "mtmorgan.bioc";
Cc: "bioc-devel";
Subject: [Bioc-devel] How to change the name of a package on Bioconductor

Hello,

I have released a package vasp toBioconductor 
(http://bioconductor.org/packages/vasp). Recently I had a manuscript about this 
package publishedon New Physiologist 
(https://nph.onlinelibrary.wiley.com/doi/10./nph.17189). However, on the 
manuscript, the link to the package is http://bioconductor.org/packages/VaSP. I 
want to change the name of the package to VaSP from vasp. I changed the 
package name and updated it ingit.bioconductor.org, but the build failed 
and it said "ERROR (Bad DESCRIPTION file)".


Can I change the name of a package existing on Bioconductor? How can I do that?


Thanks,
Huihui
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Re: [Bioc-devel] How to change the name of a package on Bioconductor

[Yu Huihui]

Hello,


I am just following my last email. I find it is a bad way to change package 
name. An alternative way is to let the link jump to the package webpage, that 
is both http://bioconductor.org/packages/vasp and 
http://bioconductor.org/packages/VaSP can jump to 
http://bioconductor.org/packages/release/bioc/html/vasp.html. Is that possible? 
Currently the link http://bioconductor.org/packages/VaSP will jump to 
http://bioconductor.org/about/removed-packages/. Please give me your 
suggestions.


Thanks,
Huihui




-- Original --
From:   
 "Yu Huihui"

http://bioconductor.org/packages/vasp). Recently I had a manuscript about this 
package publishednbsp;on New Physiologist 
(https://nph.onlinelibrary.wiley.com/doi/10./nph.17189). However, on the 
manuscript, the link to the package is http://bioconductor.org/packages/VaSP. I 
want to change the name of the package to VaSP from vasp.nbsp; I changed 
the package name and updated it innbsp;git.bioconductor.org, but the build 
failed and it said "ERRORnbsp; (Bad DESCRIPTION file)".nbsp;


Can I change the name of a package existing on Bioconductor? How can I do that?


Thanks,
Huihui
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Re: [R-pkg-devel] How to R CMD build / check using LTO

[Bill Dunlap]

I suspect your problem is that, at least with the recent gnu
compilers, the Fortran 'c_logical' maps to the C _Bool, not the C int.

-Bill

On Wed, Feb 17, 2021 at 11:38 AM Paul Schmidt-Walter
 wrote:
>
> Dear Team,
>
> My package 'LWFBrook90R' (https://github.com/pschmidtwalter/LWFBrook90R)
> was recently released on CRAN, but there are additional LTO Issues
> (https://www.stats.ox.ac.uk/pub/bdr/LTO/LWFBrook90R.out) with the
> compiled code, that need to be fixed soon.
>
> I would like to reproduce the LTO warnings locally to see if possible
> solutions fix them, but dont know how to build and check with LTO. I am
> a newbie on Ubuntu 18.04 and hope to get help in this case.
>
> There is information provided on how to configure R to reproduce the
> test (https://www.stats.ox.ac.uk/pub/bdr/LTO/README.txt), but I simply
> don't know how to "build with configure --enable-lto" and I also can't
> find the "config.site" file on my system to enable the respective
> compiler flags (see below).
>
> Any help is appreciated!
>
> Paul
>
> ---
>
> LTO-Readme.txt:
>
> Compilation logs for CRAN packages using x86_64 Fedora 32 Linux
> (currently using GCC 10.1)built with configure --enable-lto and
> config.site:
>
> CFLAGS="-g -O2 -Wall -pedantic -mtune=native"
> FFLAGS="-g -O2 -mtune=native -Wall -pedantic"
> CXXFLAGS="-g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes
> -Wno-deprecated-declarations -Wno-parentheses"
> AR=gcc-ar
> RANLIB=gcc-ranlib
>
> Look for [-Wlto-type-mismatch] warnings.  In some cases these involve
> Fortran CHARACTER arguments where the length is passed as a 'hidden'
> argument at the end, giving mismatches such as
>
> sblas.f:3951:14: note: type ‘long int’ should match type ‘void’
>
> To work around these, define USE_FC_LEN_T and include Rconfig.h
> (perhaps via R.h) before including BLAS.h or Lapack.h or your own
> C proptypes for Fortran functions.  Then amend the actual calls to include
> character length arguments: see the example of
> src/library/stats/src/rWishart.c
>
> in the R sources.
>
> ---
>
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Re: [Bioc-devel] R-CMD-check fails on ubuntu-20.04 (release)

[Catherine Ross]

Hi Robert, Martin,

Thank you both for your responses!

I wasn’t able to recreate the issue on the Ubuntu docker image (only when you 
try to fail do you not fail… ), but adding the line `sudo apt-get install -y 
libglpk-dev` to my Github Action workflow did the trick.

Catherine

On Feb 16, 2021, at 7:39 PM, Martin Morgan 
mailto:mtmorgan.b...@gmail.com>> wrote:

EXTERNAL EMAIL:

The key is that libglpk.so.40 cannot be loaded.

I'm guessing that igraph was installed from the RStudio package manager as a 
'binary'. The RSPM had a libglpk installed when the igraph binary was built, so 
the binary package expects this library to be available. It was not on the 
image where the installation failed.

The solution is to arrange for libglpk to be installed on whatever image you 
are using  for your CI, maybe sudo apt-get install -y libglpk-dev.

Several interesting points.

Binary packages are installed, but unlike source packages R does not try to 
load them after they are installed, somehow assuming that the installation was 
correct. So the igraph failure is not apparent until later.

igraph's dependency on libglpk is optional, so if you'd installed it from 
source rather than from RSPM this would not have been an issue.

This issue came up immediately before the Bioc2020 annual conference, where the 
bioconductor/bioconductor_docker:devel image did not have libglpk because the 
rocker base image did not use RSPM at the time the Bioconductor docker file was 
created; it was introduced as an upstream change that was picked up when 
bioconductor/bioconductor_docker:devel image was rebuilt from source.

Martin Morgan

On 2/16/21, 7:01 PM, "Bioc-devel on behalf of Robert M. Flight" 
mailto:bioc-devel-boun...@r-project.org> on 
behalf of rfligh...@gmail.com> wrote:

   Hi Catherine,

   It looks like igraph is not installed, which RCy3 depends on. This seems
   odd, because my own package categoryCompare depends on RCy3 and igraph, and
   it is building fine in the Bioconductor release and dev.

   I would see if you can recreate this issue locally on the Ubuntu docker
   image, or even use another github repo that just tries to install igraph or
   RCy3 on Ubuntu-release. igraph is still on CRAN, so it should be able to
   install.

   Regards,

   -Robert

   On Tue, Feb 16, 2021 at 6:10 PM Catherine Ross <
   catherinem.r...@mail.utoronto.ca> 
wrote:

Hello,

I’m running the following Github R-CMD-check workflow file on my package
repository.
https://github.com/r-lib/actions/tree/master/examples#standard-ci-workflow

It passes on 3/4 operating systems — windows-latest (release),
macOS-latest (release), ubuntu-20.04 (devel) — but fails on ubuntu-20.04
(release).
I get the following error at the ‘Install dependencies’ section:

* installing *source* package ‘RCy3’ ... ** using staged installation ** R
** inst ** byte-compile and prepare package for lazy loading Error in
dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object
'/home/runner/work/_temp/Library/igraph/libs/igraph.so': libglpk.so.40:
cannot open shared object file: No such file or directory Calls:
 ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted ERROR: lazy loading failed for package ‘RCy3’ * removing
‘/home/runner/work/_temp/Library/RCy3’

Then this error during ‘Check’:

Run options(crayon.enabled = TRUE) ── R CMD build
─ *
checking for file ‘/home/runner/work/FEDUP/FEDUP/DESCRIPTION’ ... OK *
preparing ‘FEDUP’: * checking DESCRIPTION meta-information ... OK *
installing the package to build vignettes
--- ERROR: dependency ‘RCy3’ is not
available for package ‘FEDUP’ * removing
‘/tmp/RtmpQdTGMd/Rinst3f8b26ef4bf5/FEDUP’
--- ERROR: package installation failed
Error: Error in proc$get_built_file() : Build process failed Calls:
 ... build_package -> with_envvar -> force -> 
Execution halted Error: Process completed with exit code 1.

I run into no issues when running devtools::check() locally on my system
(macOS Big Sur 11.2).

Any ideas on how to fix this issue?

Thanks,
Catherine

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Re: [R-pkg-devel] How to R CMD build / check using LTO

[Gábor Csárdi]

You can use this Docker container:
https://hub.docker.com/repository/docker/rhub/debian-gcc-devel-lto

It is somewhat old, but chances are that it will reproduce the LTO
issues. I'll update it in a minute, anyway.

Gabor

On Wed, Feb 17, 2021 at 9:33 PM Ivan Krylov  wrote:
>
> On Wed, 17 Feb 2021 20:04:34 +0100
> Paul Schmidt-Walter  wrote:
>
> > I simply don't know how to "build with configure --enable-lto"
>
> "R Installation and Administration"
> 
> contains a detailed set of instructions on how to compile R, including
> section 2.7.4 about the use of LTO. Start with Appendix A, which lists
> the packages you would need to install on your Ubuntu (basically,
> build-essential, gfortran and the libraries mentioned there). Good luck!
>
> --
> Best regards,
> Ivan
>
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Re: [R-pkg-devel] How to R CMD build / check using LTO

[Ivan Krylov]

On Wed, 17 Feb 2021 20:04:34 +0100
Paul Schmidt-Walter  wrote:

> I simply don't know how to "build with configure --enable-lto"

"R Installation and Administration"

contains a detailed set of instructions on how to compile R, including
section 2.7.4 about the use of LTO. Start with Appendix A, which lists
the packages you would need to install on your Ubuntu (basically,
build-essential, gfortran and the libraries mentioned there). Good luck!

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] FW: [CRAN-pretest-archived] CRAN submission RIBMDB 1.0.0

[Ivan Krylov]

Hello Binit Kumar,

On Wed, 17 Feb 2021 15:12:53 +
Binit Kumar  wrote:

> Error: Ld:/Compiler/gcc-4.9.3/local330/lib
> -LD:/RCompile/recent/R/bin/i386 -lR clidriver/bin/db2app64.dll: file
> not recognized: file format not recognized
> 
> Why is db2app64.dll a non recognized file?

The package is being built for i386 (32-bit) subarchitecture, but the
64-bit dll is being linked to it. I think that the correct way to
identify the target sub-architecture is to inspect the R_ARCH
environment variable from configure.win (in R code, use getenv()).

This is described in WRE 1.2:
.

> Error: ** testing if installed package can be loaded from temporary
> location
> 
> Error: package or namespace load failed for 'RIBMDB' in
> dyn.load(file, DLLpath = DLLpath, ...):
> 
>  unable to load shared object
> '/srv/hornik/tmp/CRAN/RIBMDB.Rcheck/00LOCK-RIBMDB/00new/RIBMDB/libs/RIBMDB.so':
> 
>   libdb2.so.1: cannot open shared object file: No such file or
> directory

The bigger problem is trying to manually write under R.home() during
installation. This is not allowed by the CRAN policy and may lead to
problems. (Imagine what would happen if two different packages tried to
write to file.path(R.home(), 'clidriver') and for some reason succeeded
despite it's usually not writable for the end-user on Unix-alikes...)

Instead, you could try to (1) use ./configure to extract the
library to src/ and link to it from there and (2) provide a
src/install.libs.R file to copy libdb2.so from src/ to the same
directory where the package shared object is installed. This still may
be insufficient as you might have to instruct the dynamic linker to look
for libdb2.so in the same directory when the package shared object is
loaded by R; on some compilers this may be done by passing the
-rpath='$ORIGIN' argument to the linker, but this is very
platform-dependent (no idea whether it's going to work on Solaris, for
example).

See WRE 1.1.5 for more info on install.libs.R:
https://cran.r-project.org/doc/manuals/R-exts.html#Package-subdirectories

In short, linking an R package to a binary dependency not provided by a
system package is painful, but not explicitly prohibited by CRAN policy
("Source packages may not contain any form of binary executable code",
and yours downloads binaries when it's built, but doesn't contain any;
"Downloads of additional software <...> as part of package installation
<...> should only use secure download mechanisms", which yours does).

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] Unicode errors when building a package

[Ibon Tamayo]

Thanks Max and Fernando,

The Max's solution was the one worked for me.
Thanks,
All the best,
Ibon

El mié, 17 feb 2021 a las 20:14, Max Turgeon ()
escribió:

> Hi Ibon,
>
> It looks like you have a couple non-ASCII characters in your documentation
> files. You can find which ones by running the command showNonASCIIfile in
> the tools package.
>
> To address these warnings, you have two options:
>
>1. Replace these non-ASCII characters with similar/equivalent ASCII
>ones.
>2. Specify the encoding for the doc files; see this section of WRE:
>https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Encoding
>
> Best,
>
> Max Turgeon
> --
> *From:* R-package-devel  on behalf
> of Ibon Tamayo 
> *Sent:* Wednesday, February 17, 2021 11:13 AM
> *To:* r-package-devel@r-project.org 
> *Subject:* [R-pkg-devel] Unicode errors when building a package
>
> 
> Caution: This message was sent from outside the University of Manitoba.
> 
>
> Dear all,
>
> I am trying to fix all the error of my package. Most of them I know how to
> solve them. But there are some errors related with unicode that I don't
> know how to fix.
>
> Flavor: r-devel-windows-ix86+x86_64
> Check: PDF version of manual, Result: WARNING
>   LaTeX errors when creating PDF version.
>   This typically indicates Rd problems.
>   LaTeX errors found:
>   ! Package inputenc Error: Unicode char Ì‚ (U+302)
>   (inputenc)not set up for use with LaTeX.
>
>   See the inputenc package documentation for explanation.
>   Type  H   for immediate help.
>   ! Package inputenc Error: Unicode char Ï„ (U+3C4)
>   (inputenc)not set up for use with LaTeX.
>
>   See the inputenc package documentation for explanation.
>   Type  H   for immediate help.
>   ! Package inputenc Error: Unicode char Ï„ (U+3C4)
>   (inputenc)not set up for use with LaTeX.
>
>
> Any help will be appreciated,
> All the best,
> Ibon
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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[Bioc-devel] CRAN checks failed by downloading ‘reactome.db’ package (WARNING Ubuntu, OK for Windows)

[JEANNERET Florian]

Hello all !

I need some help to "build my package" using reactome.db for reactomePA 
functions.

In fact, builds and remote downloads have failed for Ubuntu but not for Windows 
10 at reactome.db downloading.
The same appears when I try to download reactome.db alone.

Archive downloading [url][1] works manually from Bioconductor page.

With this command:

BiocManager::install("reactome.db")

I get these messages:

Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'reactome.db'
essai de l'URL 
'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/reactome.db_1.70.0.tar.gz'
Content type 'application/x-gzip' length 454979427 bytes (433.9 MB)

downloaded 348.9 MB

Error in download.file(url, destfile, method, mode = "wb", ...) :
  download from 
'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/reactome.db_1.70.0.tar.gz'
 failed
De plus : Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 365895769 != reported length 454979427
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 
'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/reactome.db_1.70.0.tar.gz':
 Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package �reactome.db� failed
Installation path not writeable, unable to update packages: littler, boot, 
class, cluster,
  codetools, foreign, KernSmooth, MASS, Matrix, mgcv, nlme, nnet, spatial


__

In case of personal use, I can change the timeout option:

options(timeout = 300)  # five minutes



But in case of package building, this warning is an issue, so how should we 
manage it ?

For CRAN checks for instance on Ubuntu,
I get in logs:

...
trying URL 
'https://bioconductor.org/packages/3.13/data/annotation/src/contrib/reactome.db_1.74.0.tar.gz'
Content type 'application/x-gzip' length 430092992 bytes (410.2 MB)
==
downloaded 410.2 MB
...

Then:

* installing *source* package �reactome.db� ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation 
path
* creating tarball
Build timed out (after 20 minutes). Marking the build as failed.
Build was aborted

Again a question of time, so my question is, how to manage this ? Or this 
package could be a part of  Bioconductor despite this warning ?

Complete logs are here : 
https://builder.r-hub.io/status/original/MOANI_0.99.0.tar.gz-20213007616144e596072fe64e5e7127

Any ideas ?
Thanks !


  [1]: 
https://bioconductor.org/packages/3.12/data/annotation/src/contrib/reactome.db_1.74.0.tar.gz

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[R-pkg-devel] How to R CMD build / check using LTO

[Paul Schmidt-Walter]

Dear Team,

My package 'LWFBrook90R' (https://github.com/pschmidtwalter/LWFBrook90R) 
was recently released on CRAN, but there are additional LTO Issues 
(https://www.stats.ox.ac.uk/pub/bdr/LTO/LWFBrook90R.out) with the 
compiled code, that need to be fixed soon.


I would like to reproduce the LTO warnings locally to see if possible 
solutions fix them, but dont know how to build and check with LTO. I am 
a newbie on Ubuntu 18.04 and hope to get help in this case.


There is information provided on how to configure R to reproduce the 
test (https://www.stats.ox.ac.uk/pub/bdr/LTO/README.txt), but I simply 
don't know how to "build with configure --enable-lto" and I also can't 
find the "config.site" file on my system to enable the respective 
compiler flags (see below).


Any help is appreciated!

Paul

---

LTO-Readme.txt:

Compilation logs for CRAN packages using x86_64 Fedora 32 Linux
(currently using GCC 10.1)built with configure --enable-lto and 
config.site:


CFLAGS="-g -O2 -Wall -pedantic -mtune=native"
FFLAGS="-g -O2 -mtune=native -Wall -pedantic"
CXXFLAGS="-g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes 
-Wno-deprecated-declarations -Wno-parentheses"

AR=gcc-ar
RANLIB=gcc-ranlib

Look for [-Wlto-type-mismatch] warnings.  In some cases these involve
Fortran CHARACTER arguments where the length is passed as a 'hidden'
argument at the end, giving mismatches such as

sblas.f:3951:14: note: type ‘long int’ should match type ‘void’

To work around these, define USE_FC_LEN_T and include Rconfig.h
(perhaps via R.h) before including BLAS.h or Lapack.h or your own
C proptypes for Fortran functions.  Then amend the actual calls to include
character length arguments: see the example of 
src/library/stats/src/rWishart.c


in the R sources.

---

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Re: [R-pkg-devel] Unicode errors when building a package

[Max Turgeon]

Hi Ibon,

It looks like you have a couple non-ASCII characters in your documentation 
files. You can find which ones by running the command showNonASCIIfile in the 
tools package.

To address these warnings, you have two options:

  1.  Replace these non-ASCII characters with similar/equivalent ASCII ones.
  2.  Specify the encoding for the doc files; see this section of WRE: 
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Encoding

Best,

Max Turgeon

From: R-package-devel  on behalf of Ibon 
Tamayo 
Sent: Wednesday, February 17, 2021 11:13 AM
To: r-package-devel@r-project.org 
Subject: [R-pkg-devel] Unicode errors when building a package


Caution: This message was sent from outside the University of Manitoba.


Dear all,

I am trying to fix all the error of my package. Most of them I know how to
solve them. But there are some errors related with unicode that I don't
know how to fix.

Flavor: r-devel-windows-ix86+x86_64
Check: PDF version of manual, Result: WARNING
  LaTeX errors when creating PDF version.
  This typically indicates Rd problems.
  LaTeX errors found:
  ! Package inputenc Error: Unicode char ̂ (U+302)
  (inputenc)not set up for use with LaTeX.

  See the inputenc package documentation for explanation.
  Type  H   for immediate help.
  ! Package inputenc Error: Unicode char τ (U+3C4)
  (inputenc)not set up for use with LaTeX.

  See the inputenc package documentation for explanation.
  Type  H   for immediate help.
  ! Package inputenc Error: Unicode char τ (U+3C4)
  (inputenc)not set up for use with LaTeX.


Any help will be appreciated,
All the best,
Ibon

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Re: [R-pkg-devel] URL in RMarkdown file (libcurl error code 35)

[Vincent van Hees]

Sorry, you can ignore my question:
Uwe Liges clarified to me that the other error in my CRAN submission check
is definitely a problem I need to address.
And from this post by Hadley on Twitter I conclude that the URL warning can
be ignored: https://twitter.com/hadleywickham/status/1358170607314235392
Best,
Vincent




On Wed, 17 Feb 2021 at 16:32, Vincent van Hees 
wrote:

> Hello,
> My R package submission got rejected today because of the URL libcurl
> error code 35 issue below (see heading Attempt 1). It seems I have a
> subscription to these errors, because I have been getting them a lot
> through the years. Next, I edited the URL and submitted the package to
> R-devel on win-builder.r-project.org, but there it got flagged again. I
> am struggling to resolve this. Please find below an overview of all my
> attempts so far..
> Could anyone tell me what I am doing wrong?
> Thanks, Vincent
>
> Attempt 1: Warning after CRAN submission
>
> Flavor: r-devel-windows-ix86+x86_64 Check: CRAN incoming feasibility,
> Result: NOTE Maintainer: 'Vincent T van Hees '
> Found the following (possibly) invalid URLs: URL:
> https://journals.humankinetics.com/view/journals/jmpb/2/3/article-p188.xml
> From: inst/doc/GGIR.html Status: Error Message: libcurl error code 35:
> schannel: next InitializeSecurityContext failed: SEC_E_ILLEGAL_MESSAGE
> (0x80090326) - This error usually occurs when a fatal SSL/TLS alert is
> received (e.g. handshake failed).
>
> Attemp 2: This is what I submitted to win-builder R-devel. In comparison
> to the CRAN submission this has the doi URL instead of the full journal
> URL.:
>
> Found the following (possibly) invalid URLs: URL:
> https://doi.org/10.1123/jmpb.2018-0063 From: inst/doc/GGIR.html Status:
> Error Message: libcurl error code 35: schannel: next
> InitializeSecurityContext failed: SEC_E_ILLEGAL_MESSAGE (0x80090326) - This
> error usually occurs when a fatal SSL/TLS alert is received (e.g. handshake
> failed).
>
> Attempt 3:
> Putting a URLencode() statement around the URL was suggested somewhere,
> e.g.
> [link](URLencode("https://doi.org/10.1123/jmpb.2018-0063;)),  but this
> breaks the URL on my local machine.
>
> Attempt 4: Curl test (in Ubuntu with curl version 7.68) for the journal
> url to see whether this provides any insight:
>
> vincent@vincent:~$ curl -Is
> https://journals.humankinetics.com/view/journals/jmpb/2/3/article-p188.xml
> HTTP/1.1 200 OK
> server: Apache-Coyote/1.1
> set-cookie: JSESSIONID=AF4859DD2D01CF4E1C16EE530712A13F; Path=/; Secure;
> HttpOnly
> content-type: text/html;charset=UTF-8
> transfer-encoding: chunked
> date: Wed, 17 Feb 2021 15:14:04 GMT
> content-security-policy: frame-ancestors 'self'
> set-cookie: ServerID=hk-web-live-bot24; path=/
>

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Re: [Bioc-devel] Change of package mantainer

[Nitesh Turaga]

Hi,

You have to change the name on the DESCRIPTION file. Everything else is taken 
care of.

Best,

Nitesh

From: Luo Weijun 
Date: Wednesday, February 17, 2021 at 11:53 AM
To: Nitesh Turaga 
Subject: Re: Change of package mantainer

Great, thank you Nitesh. We will work on it.
Note that I has been a co-maintainer, Xiaoxi Dong was the maintainer. Can you 
replace him with me as the maintainer as he is not part of the team anymore? We 
will update the package correspondingly and push some major updates soon. 
thanks.
Weijun Luo


On Tuesday, February 16, 2021, 02:48:37 PM EST, Nitesh Turaga 
 wrote:


Hi,

Thanks for the update.

You will have to do a few things yourself in this process once I gave access to 
the new maintainers.

You will first have to change the maintainer field in your package's 
description file; then, the new maintainer will have to subscribe to the 
bioc-devel mailing list.

Please note every package can only have one maintainer, and it seems like 
Weijin Luo is already listed as a maintainer on the package. Kovidh has a new 
BiocCredentials account that has to be activated at 
https://git.bioconductor.org/BiocCredentials/account_activation. Once that is 
done and SSH keys are added to the account, Kovidh will get access.

Best,

Nitesh


On Mon, Feb 15, 2021 at 3:48 PM Luo Weijun 
mailto:luo_wei...@yahoo.com>> wrote:
Dear Nitesh and Bioc team,
We need to change the maintainer for SBGNview and SBGNview.data packages. 
Xiaoxi Dong has left our team.
Please make Weijun Luo (luo_wei...@yahoo.com) and 
Kovidh Vegesna (kvege...@uncc.edu) the maintainers. 
Thank you!
Weijun Luo

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Re: [R-pkg-devel] URL in RMarkdown file (libcurl error code 35)

[Gábor Csárdi]

I suspect that this is an issue with the CRAN Windows machine, not
with your package.

If you want to work around it in the incoming checks, you can remove
the URL. Maybe it is enough to remove the `https://` from the
beginning, but I am not sure.

Gabor

On Wed, Feb 17, 2021 at 4:33 PM Vincent van Hees
 wrote:
>
> Hello,
> My R package submission got rejected today because of the URL libcurl error
> code 35 issue below (see heading Attempt 1). It seems I have a subscription
> to these errors, because I have been getting them a lot through the years.
> Next, I edited the URL and submitted the package to R-devel on
> win-builder.r-project.org, but there it got flagged again. I am struggling
> to resolve this. Please find below an overview of all my attempts so far..
> Could anyone tell me what I am doing wrong?
> Thanks, Vincent
>
> Attempt 1: Warning after CRAN submission
>
> Flavor: r-devel-windows-ix86+x86_64 Check: CRAN incoming feasibility,
> Result: NOTE Maintainer: 'Vincent T van Hees '
> Found the following (possibly) invalid URLs: URL:
> https://journals.humankinetics.com/view/journals/jmpb/2/3/article-p188.xml
> From: inst/doc/GGIR.html Status: Error Message: libcurl error code 35:
> schannel: next InitializeSecurityContext failed: SEC_E_ILLEGAL_MESSAGE
> (0x80090326) - This error usually occurs when a fatal SSL/TLS alert is
> received (e.g. handshake failed).
>
> Attemp 2: This is what I submitted to win-builder R-devel. In comparison to
> the CRAN submission this has the doi URL instead of the full journal URL.:
>
> Found the following (possibly) invalid URLs: URL:
> https://doi.org/10.1123/jmpb.2018-0063 From: inst/doc/GGIR.html Status:
> Error Message: libcurl error code 35: schannel: next
> InitializeSecurityContext failed: SEC_E_ILLEGAL_MESSAGE (0x80090326) - This
> error usually occurs when a fatal SSL/TLS alert is received (e.g. handshake
> failed).
>
> Attempt 3:
> Putting a URLencode() statement around the URL was suggested somewhere, e.g.
> [link](URLencode("https://doi.org/10.1123/jmpb.2018-0063;)),  but this
> breaks the URL on my local machine.
>
> Attempt 4: Curl test (in Ubuntu with curl version 7.68) for the journal url
> to see whether this provides any insight:
>
> vincent@vincent:~$ curl -Is
> https://journals.humankinetics.com/view/journals/jmpb/2/3/article-p188.xml
> HTTP/1.1 200 OK
> server: Apache-Coyote/1.1
> set-cookie: JSESSIONID=AF4859DD2D01CF4E1C16EE530712A13F; Path=/; Secure;
> HttpOnly
> content-type: text/html;charset=UTF-8
> transfer-encoding: chunked
> date: Wed, 17 Feb 2021 15:14:04 GMT
> content-security-policy: frame-ancestors 'self'
> set-cookie: ServerID=hk-web-live-bot24; path=/
>
> [[alternative HTML version deleted]]
>
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[R-pkg-devel] URL in RMarkdown file (libcurl error code 35)

[Vincent van Hees]

Hello,
My R package submission got rejected today because of the URL libcurl error
code 35 issue below (see heading Attempt 1). It seems I have a subscription
to these errors, because I have been getting them a lot through the years.
Next, I edited the URL and submitted the package to R-devel on
win-builder.r-project.org, but there it got flagged again. I am struggling
to resolve this. Please find below an overview of all my attempts so far..
Could anyone tell me what I am doing wrong?
Thanks, Vincent

Attempt 1: Warning after CRAN submission

Flavor: r-devel-windows-ix86+x86_64 Check: CRAN incoming feasibility,
Result: NOTE Maintainer: 'Vincent T van Hees '
Found the following (possibly) invalid URLs: URL:
https://journals.humankinetics.com/view/journals/jmpb/2/3/article-p188.xml
From: inst/doc/GGIR.html Status: Error Message: libcurl error code 35:
schannel: next InitializeSecurityContext failed: SEC_E_ILLEGAL_MESSAGE
(0x80090326) - This error usually occurs when a fatal SSL/TLS alert is
received (e.g. handshake failed).

Attemp 2: This is what I submitted to win-builder R-devel. In comparison to
the CRAN submission this has the doi URL instead of the full journal URL.:

Found the following (possibly) invalid URLs: URL:
https://doi.org/10.1123/jmpb.2018-0063 From: inst/doc/GGIR.html Status:
Error Message: libcurl error code 35: schannel: next
InitializeSecurityContext failed: SEC_E_ILLEGAL_MESSAGE (0x80090326) - This
error usually occurs when a fatal SSL/TLS alert is received (e.g. handshake
failed).

Attempt 3:
Putting a URLencode() statement around the URL was suggested somewhere, e.g.
[link](URLencode("https://doi.org/10.1123/jmpb.2018-0063;)),  but this
breaks the URL on my local machine.

Attempt 4: Curl test (in Ubuntu with curl version 7.68) for the journal url
to see whether this provides any insight:

vincent@vincent:~$ curl -Is
https://journals.humankinetics.com/view/journals/jmpb/2/3/article-p188.xml
HTTP/1.1 200 OK
server: Apache-Coyote/1.1
set-cookie: JSESSIONID=AF4859DD2D01CF4E1C16EE530712A13F; Path=/; Secure;
HttpOnly
content-type: text/html;charset=UTF-8
transfer-encoding: chunked
date: Wed, 17 Feb 2021 15:14:04 GMT
content-security-policy: frame-ancestors 'self'
set-cookie: ServerID=hk-web-live-bot24; path=/

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[R-pkg-devel] FW: [CRAN-pretest-archived] CRAN submission RIBMDB 1.0.0

[Binit Kumar]

Hi Team,
I uploaded a package in CRAN and it failed with the attached error.
My question:

  1.  Windows:

Error: Ld:/Compiler/gcc-4.9.3/local330/lib -LD:/RCompile/recent/R/bin/i386 -lR
clidriver/bin/db2app64.dll: file not recognized: file format not recognized

Why is db2app64.dll a non recognized file? What is the problem exactly if  
someone can explain please.



  1.  Debian:

Error: ** testing if installed package can be loaded from temporary location

Error: package or namespace load failed for 'RIBMDB' in dyn.load(file, DLLpath 
= DLLpath, ...):

 unable to load shared object 
'/srv/hornik/tmp/CRAN/RIBMDB.Rcheck/00LOCK-RIBMDB/00new/RIBMDB/libs/RIBMDB.so':

  libdb2.so.1: cannot open shared object file: No such file or directory

Error: loading failed

Execution halted

ERROR: loading failed



Not sure why this error comes even though the file libdb2.so.1 is present in 
"clidriver" folder. Can someone please let me know how to fix this?


Thanks & Regards,
Binit Kumar
From: lig...@statistik.tu-dortmund.de 
Sent: 17 February 2021 20:29
To: Binit Kumar 
Cc: cran-submissi...@r-project.org
Subject: [CRAN-pretest-archived] CRAN submission RIBMDB 1.0.0

EXTERNAL EMAIL



Dear maintainer,

package RIBMDB_1.0.0.tar.gz does not pass the incoming checks automatically, 
please see the following pre-tests:
Windows: 
>
Status: 1 ERROR, 1 NOTE
Debian: 
>
Status: 1 ERROR, 1 NOTE



Please fix all problems and resubmit a fixed version via the webform.
If you are not sure how to fix the problems shown, please ask for help on the 
R-package-devel mailing list:
>
If you are fairly certain the rejection is a false positive, please reply-all 
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Flavor: r-devel-windows-ix86+x86_64
Check: CRAN incoming feasibility, Result: NOTE
  Maintainer: 'ROCKET SOFTWARE '
  
  New submission
  
  Possibly mis-spelled words in DESCRIPTION:
ODBC (8:17)
  
  Found the following (possibly) invalid URLs:
URL: http://msdn.microsoft.com/en-us/library/ms711683(VS.85).aspx
  From: man/sqlColumns.Rd
  Status: 403
  Message: Forbidden
URL: http://msdn.microsoft.com/en-us/library/ms714602(VS.85).aspx
  From: man/sqlColumns.Rd
  Status: 403
  Message: Forbidden
URL: http://msdn.microsoft.com/en-us/library/ms714632(VS.85).aspx
  From: man/sqlTypeInfo.Rd
  Status: 403
  Message: Forbidden
URL: https://cran.r-project.org/web/packages/RODBCDBI/index.html
  From: README.md
  Status: 200
  Message: OK
  CRAN URL not in canonical form
URL: 
https://github.com/ibmdb/RIBMDB/blob/master/contributing/CONTRIBUTING.md
  From: README.md
  Status: 404
  Message: Not Found
The canonical URL of the CRAN page for a package is 
  https://CRAN.R-project.org/package=pkgname
  
  The Date field is over a month old.
  
  Size of tarball: 51165800 bytes

Flavor: r-devel-windows-ix86+x86_64
Check: whether package can be installed, Result: ERROR
  Installation failed.
  See 'd:/RCompile/CRANincoming/R-devel/RIBMDB.Rcheck/00install.out' for 
details.

Flavor: r-devel-linux-x86_64-debian-gcc
Check: CRAN incoming feasibility, Result: NOTE
  Maintainer: 'ROCKET SOFTWARE '
  
  New submission
  
  Possibly mis-spelled words in DESCRIPTION:
ODBC (8:17)
  
  Found the following (possibly) invalid URLs:
URL: 

Re: [Rd] issue with print()ing multibyte characters on R 4.0.4

[Hiroaki Yutani]

Thanks for confirming and investigating.

> but it was no one reported in the run up to 4.0.4.

Yes, it was unfortunate that no one had reported it to the right place
before the release...

2021年2月17日(水) 19:20 Prof Brian Ripley :

>
> On 17/02/2021 04:58, Hiroaki Yutani wrote:
> > Hi all,
> >
> > I saw several people on Japanese locale claim that, on R 4.0.4,
> > print() doesn't display
> > Japanese characters correctly. This seems to happen only on Windows
> > and on macOS (I
> > usually use Linux and I don't see this problem).
> >
> > For example, in the result below, "鬼" and "外" are displayed in
> > "\u" format. What's
> > curious here is that "は" is displayed as it is, by the way.
> >
> >> "鬼は外"
> > [1] "\u9b3cは\u5916"
> >
> > But, if I use such functions as message() or cat(), the string is
> > displayed as it is.
> >
> >> message("鬼は外")
> > 鬼は外
>
> that does not escape non-printable characters, so as expected.
> >
> > Considering the fact that it seems only Windows and macOS are
> > affected, I suspect this
> > is somehow related to this change described in the release note,
> > (though I have no idea
> > what change this is):
> >
> >  The internal table for iswprint (used on Windows, macOS and AIX) has 
> > been
> >  updated to include many recent Unicode characters.
> >  (https://cran.r-project.org/doc/manuals/r-release/NEWS.html)
> >
> > Before I'm going to file this issue on Bugzilla, I'd like to confirm
> > if this is not the intended
> > change, and, if this is actually intended, I want to discuss how to
> > improve this behaviour.
>
> I am sorry: this was not intended but it was no one reported in the run
> up to 4.0.4.  It seems to be working in R-devel so I suggest you check
> that or go back to 4.0.3.
>
> It looks like a line in the iswprint table got deleted in the merge from
> R-devel.  I will try to set up some automated checks to see if I can
> find any other problems, but that will take a few days.
>
> --
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford

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Re: [Rd] issue with print()ing multibyte characters on R 4.0.4

[Prof Brian Ripley]

On 17/02/2021 04:58, Hiroaki Yutani wrote:

Hi all,

I saw several people on Japanese locale claim that, on R 4.0.4,
print() doesn't display
Japanese characters correctly. This seems to happen only on Windows
and on macOS (I
usually use Linux and I don't see this problem).

For example, in the result below, "鬼" and "外" are displayed in
"\u" format. What's
curious here is that "は" is displayed as it is, by the way.


"鬼は外"

[1] "\u9b3cは\u5916"

But, if I use such functions as message() or cat(), the string is
displayed as it is.


message("鬼は外")

鬼は外


that does not escape non-printable characters, so as expected.


Considering the fact that it seems only Windows and macOS are
affected, I suspect this
is somehow related to this change described in the release note,
(though I have no idea
what change this is):

 The internal table for iswprint (used on Windows, macOS and AIX) has been
 updated to include many recent Unicode characters.
 (https://cran.r-project.org/doc/manuals/r-release/NEWS.html)

Before I'm going to file this issue on Bugzilla, I'd like to confirm
if this is not the intended
change, and, if this is actually intended, I want to discuss how to
improve this behaviour.


I am sorry: this was not intended but it was no one reported in the run 
up to 4.0.4.  It seems to be working in R-devel so I suggest you check 
that or go back to 4.0.3.


It looks like a line in the iswprint table got deleted in the merge from 
R-devel.  I will try to set up some automated checks to see if I can 
find any other problems, but that will take a few days.


--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

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Re: [Rd] issue with print()ing multibyte characters on R 4.0.4

[Tomas Kalibera]

Thanks for the report, I can reproduce this on Windows, we'll investigate.

Best
Tomas

On 2/17/21 5:58 AM, Hiroaki Yutani wrote:

Hi all,

I saw several people on Japanese locale claim that, on R 4.0.4,
print() doesn't display
Japanese characters correctly. This seems to happen only on Windows
and on macOS (I
usually use Linux and I don't see this problem).

For example, in the result below, "鬼" and "外" are displayed in
"\u" format. What's
curious here is that "は" is displayed as it is, by the way.


"鬼は外"

[1] "\u9b3cは\u5916"

But, if I use such functions as message() or cat(), the string is
displayed as it is.


message("鬼は外")

鬼は外

Considering the fact that it seems only Windows and macOS are
affected, I suspect this
is somehow related to this change described in the release note,
(though I have no idea
what change this is):

 The internal table for iswprint (used on Windows, macOS and AIX) has been
 updated to include many recent Unicode characters.
 (https://cran.r-project.org/doc/manuals/r-release/NEWS.html)

Before I'm going to file this issue on Bugzilla, I'd like to confirm
if this is not the intended
change, and, if this is actually intended, I want to discuss how to
improve this behaviour.

Best,
Hiroaki Yutani

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Re: [Rd] issue with data()

[David Scott]

I would recommend option 2. I have done that when changes to xtable broke some 
packages. xtable has a number of dependencies but not on the scale of survival. 
Just 4 packages out of 868 seems minimal to me.

David Scott

On 17/02/2021 3:39 am, Therneau, Terry M., Ph.D. via R-devel wrote:
I am testing out the next release of survival, which involves running R CMD 
check on 868
CRAN packages that import, depend or suggest it.

The survival package has a lot of data sets, most of which are non-trivial real 
examples
(something I'm proud of).  To save space I've bundled many of them, .e.g., 
data/cancer.rda
has 19 different dataframes.

This caused failures in 4 packages, each because they have a line such as 
"data(lung)"  or
data(breast, package= "survival"); and the data() command looks for a file name.

This is a question about which option is considered the best (perhaps more of a 
poll),
between two choices

1. unbundle them again  (it does save 1/3 of the space, and I do get complaints 
from R CMD
build about size)
2. send notes to the 4 maintainers.  The help files for the data sets have the 
usage
documented as  "lung" or "breast", and not data(lung), so I am technically 
legal to claim
they have a mistake.

A third option to make the data sets a separate package is not on the table.  I 
use them
heavily in my help files and test suite, and since survival is a recommended 
package I
can't add library(x) statements for  !(x %in% recommended).   I am guessing 
that this
would also break many dependent packages.

Terry T.

--
Terry M Therneau, PhD
Department of Health Science Research
Mayo Clinic
thern...@mayo.edu

"TERR-ree THUR-noh"


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--
_
David Scott
Department of Statistics
The University of Auckland, PB 92019
Auckland 1142,NEW ZEALAND
Email:d.sc...@auckland.ac.nz

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