R devel - May 2007 - (PR#9691) 'Bug'#424696: R CMD INSTALL -l <path> does not

I looked for evidence that this is supposed to happen, as it was news to 
me that it did on some versions of R.  Possible sources of documentation 
seem to be

R CMD INSTALL --help
?INSTALL
R-intro.texi, R-exts.texi, R-admin.texi

none of which mention this AFAICS, and all seem to be written assuming an 
existing library tree.

DId you find something to suggest otherwise?  Clearly no alpha/beta 
tester expected this to work.

I am not at all sure this would be desirable.  It seems that specifying a 
non-existent library tree would most likely be a typing error, and 
silently creating it would lead to some puzzling errors.  (In fact, I now 
suspect that this has happened to me in the past.)

I've added some much more specific error messages.


On Wed, 16 May 2007, edd at debian.org wrote:
>
> Soeren,
>
> On 16 May 2007 at 23:00, Soeren Sonnenburg wrote:
> | Package: r-base-core
> | Version: 2.5.1~20070513-1    [ aka R-patched as of 20070513 ]
> | Severity: important
> |
> | R CMD INSTALL -l /path/to/lib
> |
> | no longer creates /path/to/lib but assumes it does already exist. This
> | is a change in behaviour as it has worked with R 2.4.X
Yes, but changes in undocumented behaviour are allowed, especially if no 
one knows about them.
> Let me pass that on to R Bugs then as it is in no way related to any Debian
> changes.
>
> Thanks, Dirk
>
>
> | looking at /usr/lib/R/bin/INSTALL, the problem seems to be in the block
starting at line 298:
> |
> |
> |
> | lib=`tilde_expand "${lib}"`
> | if test -z "${lib}"; then
> |   lib=`echo "cat('\n~~~', .libPaths()[1], '\n', sep
= '')" | \
> |     R_DEFAULT_PACKAGES=NULL "${R_EXE}" --no-save --slave | \
> |     grep '^~~~' | sed 's/.*~~~//'`
> |   message "Installing to library '$lib'"
> | else
> |   lib0=${lib}
> |   cd ${lib}        <-------------- PROBLEM directory must not exist
(call MKDIR_P before ?)
> |   lib=`${GETWD}`
> |   cd ${startdir}
> | fi
> |
> |
> | -- System Information:
> | Debian Release: lenny/sid
> |   APT prefers stable
> |   APT policy: (700, 'stable'), (650, 'testing'), (600,
'unstable'), (1, 'experimental')
> | Architecture: i386 (i686)
> |
> | Kernel: Linux 2.6.21.1-sonne (SMP w/2 CPU cores; PREEMPT)
> | Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
> | Shell: /bin/sh linked to /bin/dash
> |
> | Versions of packages r-base-core depends on:
> | ii  atlas3-base [libblas.so.3 3.6.0-20.6     Automatically Tuned Linear
Algebra
> | ii  atlas3-sse2 [libblas.so.3 3.6.0-20.6     Automatically Tuned Linear
Algebra
> | ii  libbz2-1.0                1.0.3-6        high-quality block-sorting
file co
> | ii  libc6                     2.5-7          GNU C Library: Shared
libraries
> | ii  libgfortran1              4.1.2-7        Runtime library for GNU
Fortran ap
> | ii  libice6                   1:1.0.3-2      X11 Inter-Client Exchange
library
> | ii  libjpeg62                 6b-13          The Independent JPEG
Group's JPEG
> | ii  libpaper-utils            1.1.21         Library for handling paper
charact
> | ii  libpcre3                  6.7-1          Perl 5 Compatible Regular
Expressi
> | ii  libpng12-0                1.2.15~beta5-1 PNG library - runtime
> | ii  libreadline5              5.2-2          GNU readline and history
libraries
> | ii  libsm6                    2:1.0.3-1      X11 Session Management
library
> | ii  libx11-6                  2:1.0.3-7      X11 client-side library
> | ii  libxt6                    1:1.0.5-2      X11 toolkit intrinsics
library
> | ii  perl                      5.8.8-7        Larry Wall's Practical
Extraction
> | ii  refblas3 [libblas.so.3]   1.2-8          Basic Linear Algebra
Subroutines 3
> | ii  tcl8.4                    8.4.12-1.1     Tcl (the Tool Command
Language) v8
> | ii  tk8.4                     8.4.12-1       Tk toolkit for Tcl and X11,
v8.4 -
> | ii  unzip                     5.52-9         De-archiver for .zip files
> | ii  zip                       2.32-1         Archiver for .zip files
> | ii  zlib1g                    1:1.2.3-14     compression library -
runtime
> |
> | Versions of packages r-base-core recommends:
> | ii  r-base-dev              2.5.1~20070513-1 GNU R installation of
auxiliary GN
> | ii  r-recommended           2.5.1~20070513-1 GNU R collection of
recommended pa
> |
> | -- no debconf information
> |
>
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

(Added Debian BTS address for this bug report back on CCs  --edd)

Brian,

Thanks for not letting this fall off the wagon.

On 23 May 2007 at 21:08, ripley at stats.ox.ac.uk wrote:
| I looked for evidence that this is supposed to happen, as it was news to 
| me that it did on some versions of R.  Possible sources of documentation 
| seem to be
| 
| R CMD INSTALL --help
| ?INSTALL
| R-intro.texi, R-exts.texi, R-admin.texi
| 
| none of which mention this AFAICS, and all seem to be written assuming an 
| existing library tree.
| 
| DId you find something to suggest otherwise?  Clearly no alpha/beta 
| tester expected this to work.

It was news to me too.  Personally, in the (common) code used for building
all r-cran-* packages, I do create directories explicitly ... simply because
I have to do that for all other Debian packages too. We even have
dh_installdirs for that...

Maybe GNU install is different, I do not know.

| I am not at all sure this would be desirable.  It seems that specifying a 
| non-existent library tree would most likely be a typing error, and 
| silently creating it would lead to some puzzling errors.  (In fact, I now 
| suspect that this has happened to me in the past.)
| 
| I've added some much more specific error messages.

Ok. For Debian, I will close this now as you demonstrated (and Thanks! for
that) that it is/was not documented behaviour.  So I see no bug either.
 
| On Wed, 16 May 2007, edd at debian.org wrote:
| 
| >
| > Soeren,
| >
| > On 16 May 2007 at 23:00, Soeren Sonnenburg wrote:
| > | Package: r-base-core
| > | Version: 2.5.1~20070513-1    [ aka R-patched as of 20070513 ]
| > | Severity: important
| > |
| > | R CMD INSTALL -l /path/to/lib
| > |
| > | no longer creates /path/to/lib but assumes it does already exist. This
| > | is a change in behaviour as it has worked with R 2.4.X
| 
| Yes, but changes in undocumented behaviour are allowed, especially if no 
| one knows about them.

I agree with this.

Best, Dirk


| 
| > Let me pass that on to R Bugs then as it is in no way related to any
Debian
| > changes.
| >
| > Thanks, Dirk
| >
| >
| > | looking at /usr/lib/R/bin/INSTALL, the problem seems to be in the block
starting at line 298:
| > |
| > |
| > |
| > | lib=`tilde_expand "${lib}"`
| > | if test -z "${lib}"; then
| > |   lib=`echo "cat('\n~~~', .libPaths()[1], '\n',
sep = '')" | \
| > |     R_DEFAULT_PACKAGES=NULL "${R_EXE}" --no-save --slave | \
| > |     grep '^~~~' | sed 's/.*~~~//'`
| > |   message "Installing to library '$lib'"
| > | else
| > |   lib0=${lib}
| > |   cd ${lib}        <-------------- PROBLEM directory must not exist
(call MKDIR_P before ?)
| > |   lib=`${GETWD}`
| > |   cd ${startdir}
| > | fi
| > |
| > |
| > | -- System Information:
| > | Debian Release: lenny/sid
| > |   APT prefers stable
| > |   APT policy: (700, 'stable'), (650, 'testing'), (600,
'unstable'), (1, 'experimental')
| > | Architecture: i386 (i686)
| > |
| > | Kernel: Linux 2.6.21.1-sonne (SMP w/2 CPU cores; PREEMPT)
| > | Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
| > | Shell: /bin/sh linked to /bin/dash
| > |
| > | Versions of packages r-base-core depends on:
| > | ii  atlas3-base [libblas.so.3 3.6.0-20.6     Automatically Tuned Linear
Algebra
| > | ii  atlas3-sse2 [libblas.so.3 3.6.0-20.6     Automatically Tuned Linear
Algebra
| > | ii  libbz2-1.0                1.0.3-6        high-quality block-sorting
file co
| > | ii  libc6                     2.5-7          GNU C Library: Shared
libraries
| > | ii  libgfortran1              4.1.2-7        Runtime library for GNU
Fortran ap
| > | ii  libice6                   1:1.0.3-2      X11 Inter-Client Exchange
library
| > | ii  libjpeg62                 6b-13          The Independent JPEG
Group's JPEG
| > | ii  libpaper-utils            1.1.21         Library for handling paper
charact
| > | ii  libpcre3                  6.7-1          Perl 5 Compatible Regular
Expressi
| > | ii  libpng12-0                1.2.15~beta5-1 PNG library - runtime
| > | ii  libreadline5              5.2-2          GNU readline and history
libraries
| > | ii  libsm6                    2:1.0.3-1      X11 Session Management
library
| > | ii  libx11-6                  2:1.0.3-7      X11 client-side library
| > | ii  libxt6                    1:1.0.5-2      X11 toolkit intrinsics
library
| > | ii  perl                      5.8.8-7        Larry Wall's Practical
Extraction
| > | ii  refblas3 [libblas.so.3]   1.2-8          Basic Linear Algebra
Subroutines 3
| > | ii  tcl8.4                    8.4.12-1.1     Tcl (the Tool Command
Language) v8
| > | ii  tk8.4                     8.4.12-1       Tk toolkit for Tcl and
X11, v8.4 -
| > | ii  unzip                     5.52-9         De-archiver for .zip files
| > | ii  zip                       2.32-1         Archiver for .zip files
| > | ii  zlib1g                    1:1.2.3-14     compression library -
runtime
| > |
| > | Versions of packages r-base-core recommends:
| > | ii  r-base-dev              2.5.1~20070513-1 GNU R installation of
auxiliary GN
| > | ii  r-recommended           2.5.1~20070513-1 GNU R collection of
recommended pa
| > |
| > | -- no debconf information
| > |
| >
| >
| 
| -- 
| Brian D. Ripley,                  ripley at stats.ox.ac.uk
| Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
| University of Oxford,             Tel:  +44 1865 272861 (self)
| 1 South Parks Road,                     +44 1865 272866 (PA)
| Oxford OX1 3TG, UK                Fax:  +44 1865 272595
| 
| ______________________________________________
| R-devel at r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel

-- 
Hell, there are no rules here - we're trying to accomplish something. 
                                                  -- Thomas A. Edison