R install.package() bug

R install.package() bug

[Stephen P Carrier]

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I would like to report an issue with install.packages() experienced today
using the current R package.

I installed R 4.3.0 on system:

# uname -rs
CYGWIN_NT-10.0-20348 3.4.9-1.x86_64

I tried to install the DBI package, DBI_1.1.3.tar.gz, downloaded from a
mirror.

I used

install.packages("/path/to/DBI_1.1.13.tar.gz", repos = NULL);

What happens is:

-----
Installing package into ‘/usr/lib/R/site-library’
(as ‘lib’ is unspecified)
During startup - Warning message:
package ‘stats’ in options("defaultPackages") was not found
* installing *source* package ‘DBI’ ...
** package ‘DBI’ successfully unpacked and MD5 sums checked
** using staged installation
Error : Invalid DESCRIPTION file

Malformed maintainer field.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ERROR: installing package DESCRIPTION failed for package ‘DBI’
-----

I looked in the manual to see what DESCRIPTION files should look like.  The
encoding is specified as UTF-8 in the file so the umlauts sprinkled
throughout should be fine.  The 'Maintainer:' line contains an umlaut, I
removed it, after which the package installed without error.  Umlauts
elsewhere in the DESCRIPTION file are not a problem.

Seems like a bug.  I don't have R 4.3.0 installed on a Linux system to test
if the bug is upstream from Cygwin, and my immediate problem is solved with
a simple workaround.

Thanks to all for maintaining this fine product (Cygwin kernel and all the
packages).

--Stephen Carrier

Re: R install.package() bug

[Markus Hönicka]

> Stephen P Carrier via Cygwin <cygwin@cygwin.com> hat am 2023-11-28 06:01 CET geschrieben:
> 
>  
> I would like to report an issue with install.packages() experienced today
> using the current R package.
> 
> I installed R 4.3.0 on system:
> 
> # uname -rs
> CYGWIN_NT-10.0-20348 3.4.9-1.x86_64
> 
> I tried to install the DBI package, DBI_1.1.3.tar.gz, downloaded from a
> mirror.
> 
> I used
> 
> install.packages("/path/to/DBI_1.1.13.tar.gz", repos = NULL);
> 
> What happens is:
> 
> -----
> Installing package into ‘/usr/lib/R/site-library’
> (as ‘lib’ is unspecified)
> During startup - Warning message:
> package ‘stats’ in options("defaultPackages") was not found
> * installing *source* package ‘DBI’ ...
> ** package ‘DBI’ successfully unpacked and MD5 sums checked
> ** using staged installation
> Error : Invalid DESCRIPTION file
> 
> Malformed maintainer field.
> 
> See section 'The DESCRIPTION file' in the 'Writing R Extensions'
> manual.
> ERROR: installing package DESCRIPTION failed for package ‘DBI’
> -----
> 
> I looked in the manual to see what DESCRIPTION files should look like.  The
> encoding is specified as UTF-8 in the file so the umlauts sprinkled
> throughout should be fine.  The 'Maintainer:' line contains an umlaut, I
> removed it, after which the package installed without error.  Umlauts
> elsewhere in the DESCRIPTION file are not a problem.
> 
> Seems like a bug.  I don't have R 4.3.0 installed on a Linux system to test
> if the bug is upstream from Cygwin, and my immediate problem is solved with
> a simple workaround.
> 
> Thanks to all for maintaining this fine product (Cygwin kernel and all the
> packages).
> 
> --Stephen Carrier
> 

Hi Stephen,
I came across this type of error with R on Cygwin, but not on FreeBSD or Linux. I'm still running R version 3.6.3 on Cygwin (I don't have root permissions on this box, so I'm forced to upgrade very infrequently) and I have positively seen this error when I set up my current installation. I use the same R packages on my Unix boxes at home and have never seen such an error. I don't think this is an upstream error. Unfortunately this is above my head to debug.
regards,
Markus

Re: R install.package() bug

[Marco Atzeri]

On 28/11/2023 06:01, Stephen P Carrier via Cygwin wrote:
> I would like to report an issue with install.packages() experienced today
> using the current R package.
> 
> I installed R 4.3.0 on system:
> 
> # uname -rs
> CYGWIN_NT-10.0-20348 3.4.9-1.x86_64
> 
> I tried to install the DBI package, DBI_1.1.3.tar.gz, downloaded from a
> mirror.
> 
> I used
> 
> install.packages("/path/to/DBI_1.1.13.tar.gz", repos = NULL);
> 
> What happens is:
> 
> -----
> Installing package into ‘/usr/lib/R/site-library’
> (as ‘lib’ is unspecified)
> During startup - Warning message:
> package ‘stats’ in options("defaultPackages") was not found
> * installing *source* package ‘DBI’ ...
> ** package ‘DBI’ successfully unpacked and MD5 sums checked
> ** using staged installation
> Error : Invalid DESCRIPTION file
> 
> Malformed maintainer field.
> 
> See section 'The DESCRIPTION file' in the 'Writing R Extensions'
> manual.
> ERROR: installing package DESCRIPTION failed for package ‘DBI’
> -----
> 
> I looked in the manual to see what DESCRIPTION files should look like.  The
> encoding is specified as UTF-8 in the file so the umlauts sprinkled
> throughout should be fine.  The 'Maintainer:' line contains an umlaut, I
> removed it, after which the package installed without error.  Umlauts
> elsewhere in the DESCRIPTION file are not a problem.
> 
> Seems like a bug.  I don't have R 4.3.0 installed on a Linux system to test
> if the bug is upstream from Cygwin, and my immediate problem is solved with
> a simple workaround.
> 
> Thanks to all for maintaining this fine product (Cygwin kernel and all the
> packages).
> 
> --Stephen Carrier

It is an UTF8 issue, it will need some time to understand why
the code page interpretation is wrong for R and it is not using UTF8

As work around:

$ tar -xf DBI-1.1.3.tar.gz

$ cd DBI-1.1.3

$ grep Mü DESCRIPTION
     person("Kirill", "Müller", , "krlmlr+r@mailbox.org", role = 
c("aut", "cre"),

$ sed -e "s/Müller/Mueller/" -i DESCRIPTION

$ grep ller DESCRIPTION
     person("Kirill", "Mueller", , "krlmlr+r@mailbox.org", role = 
c("aut", "cre"),

$ cd ..

$ tar -xzf DBI-1.1.3.tar.gz DBI-1.1.3

and then in R:

 > install.packages("/tmp/DBI-1.1.3.tar.gz", repos = NULL);
Installing package into ‘/usr/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘DBI’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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
* DONE (DBI)


Regards Marco

PS: I see only 1.1.3 on https://github.com/r-dbi/DBI/releases

Re: R install.package() bug

[Henry S. Thompson]

Marco Atzeri via Cygwin writes:

> As work around:
>
> $ tar -xf DBI-1.1.3.tar.gz
>
> ...
>
> $ tar -xzf DBI-1.1.3.tar.gz DBI-1.1.3

Argh     ^
I'm pretty sure that will just undo the fix!
Cut-and-paste error?

I think what's wanted is

$ tar -czf DBI-1.1.3.tar.gz DBI-1.1.3

ht
-- 
       Henry S. Thompson, School of Informatics, University of Edinburgh
      10 Crichton Street, Edinburgh EH8 9AB, SCOTLAND -- (44) 131 650-4440
                Fax: (44) 131 650-4587, e-mail: ht@inf.ed.ac.uk
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