severity 913982 wishlist
thanks
Hi Pavel,
Thanks for taking the time to write this up.
On 18 November 2018 at 11:15, Pavel N. Krivitsky wrote:
| Package: r-base-core
| Version: 3.5.1-1+b2
| Severity: important
|
| Dear Maintainer,
|
| # To reproduce:
|
| Attempt to execute on the command line,
|
| $ Rscript -e 'message("OK")'
|
| or
|
| $ R -e 'message("OK")'
|
| # Expected result:
|
| R starts, prints "OK", and then exits.
|
| # Actual result:
|
| /usr/lib/R/bin/R: line 193: /usr/bin/sed: No such file or directory
| ERROR: option '-e' requires a non-empty argument
|
| or
|
| /usr/bin/R: line 193: /usr/bin/sed: No such file or directory
| ERROR: option '-e' requires a non-empty argument
|
| respectively.
Not here (using the r-base Docker container I maintain which uses Debian
testing)
root@03c3abf866d1:/# COLUMNS=100 dpkg -l | grep r-base-core
ii r-base-core 3.5.1-1 amd64 GNU R core of statistical
computation and g
root@03c3abf866d1:/#
root@03c3abf866d1:/# Rscript -e 'message("OK")'
OK
root@03c3abf866d1:/#
And once I update in the same container:
root@03c3abf866d1:/# dpkg -l | grep r-base-core
ii r-base-core 3.5.1-1+b2 amd64 GNU R
core of statistical computation and graphics system
root@03c3abf866d1:/# Rscript -e 'message("OK")'
OK
root@03c3abf866d1:/# R -q -e 'message("OK")'
> message("OK")
OK
>
>
root@03c3abf866d1:/#
So I cannot reproduce this. Which is why I lowered the severity above and
would suggest closing this.
| # Other notes:
|
| The severity is bordering on "grave", but, since it technically does not break
| *all* usage (including just starting R without arguments), I am flagging it as
| "important".
|
| The problem appears to be on line 122 of /usr/lib/R/bin/R and /usr/bin/R,
where
| between r-base-core 3.5.1-1+b1 and 3.5.1-1+b2,
|
| SED=/bin/sed
I just checked and this is where it started from in configure.ac -- see eg
https://salsa.debian.org/edd/r-base/blob/master/configure.ac#L582 -- where we
have
## we would like a POSIX sed, and need one on Solaris
AC_PATH_PROGS(SED, sed, /bin/sed, [/usr/xpg4/bin:$PATH])
| changed to
|
| SED=/usr/bin/sed
root@03c3abf866d1:/# grep sed /usr/bin/R
--encoding=ENC Specify encoding to be used for stdin
## some systems have a more portable sed, e.g. /usr/xpg4/bin/sed on Solaris,
## so make sure that is used.
SED=/usr/bin/sed
root@03c3abf866d1:/# which sed
/usr/bin/sed
root@03c3abf866d1:/#
But all fine here. Something does not make sense here.
The package I shipped it correct. The package I am currently testing is correct.
| whereas Debian puts the executable in question in /bin/sed . I've grepped
| through the R-related files for "/usr/bin/sed", and these might be affected:
|
| /usr/lib/R/bin/R
| /usr/lib/R/bin/libtool
| /usr/lib/R/etc/Renviron.orig
| /usr/lib/R/etc/Renviron.ucf
| /usr/bin/R
R is pretty well organized that way -- configure will govern the R script and
that will flow from /usr/bin/R.
Again, I see no bug.
Dirk
|
| -- System Information:
| Debian Release: buster/sid
| APT prefers testing
| APT policy: (990, 'testing'), (500, 'stable-updates'), (500, 'unstable'),
(500, 'stable'), (500, 'oldstable'), (1, 'experimental')
| Architecture: amd64 (x86_64)
|
| Kernel: Linux 4.18.0-2-amd64 (SMP w/8 CPU cores)
| Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8),
LANGUAGE=en_AU.UTF-8 (charmap=UTF-8)
| Shell: /bin/sh linked to /bin/dash
| Init: systemd (via /run/systemd/system)
| LSM: AppArmor: enabled
|
| Versions of packages r-base-core depends on:
| ii ca-certificates 20170717
| ii libblas3 [libblas.so.3] 3.8.0-1+b1
| ii libbz2-1.0 1.0.6-9
| ii libc6 2.27-8
| ii libcairo2 1.16.0-1
| ii libcurl4 7.61.0-1
| ii libgfortran5 8.2.0-9
| ii libglib2.0-0 2.58.1-2
| ii libgomp1 8.2.0-9
| ii libice6 2:1.0.9-2
| ii libicu63 63.1-4
| ii libjpeg62-turbo 1:1.5.2-2+b1
| ii liblapack3 [liblapack.so.3] 3.8.0-1+b1
| ii liblzma5 5.2.2-1.3
| ii libpango-1.0-0 1.42.4-3
| ii libpangocairo-1.0-0 1.42.4-3
| ii libpaper-utils 1.1.24+nmu5
| ii libpcre3 2:8.39-11
| ii libpng16-16 1.6.34-2
| ii libquadmath0 8.2.0-9
| ii libreadline7 7.0-5
| ii libsm6 2:1.2.2-1+b3
| ii libtcl8.6 8.6.8+dfsg-4
| ii libtiff5 4.0.9+git181026-1
| ii libtk8.6 8.6.8-4
| ii libx11-6 2:1.6.7-1
| ii libxext6 2:1.3.3-1+b2
| ii libxss1 1:1.2.3-1
| ii libxt6 1:1.1.5-1
| ii ucf 3.0038
| ii unzip 6.0-21
| ii xdg-utils 1.1.3-1
| ii zip 3.0-11+b1
| ii zlib1g 1:1.2.11.dfsg-1
|
| Versions of packages r-base-core recommends:
| ii r-base-dev 3.5.1-1
| ii r-doc-html 3.5.1-1
| ii r-recommended 3.5.1-1
|
| Versions of packages r-base-core suggests:
| pn ess <none>
| ii r-base-html 3.5.1-1
| pn r-doc-info | r-doc-pdf <none>
| pn r-mathlib <none>
|
| -- no debconf information
--
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
