R devel - Jun 2013 - R CMD INSTALL and file permission settings

Summary:   

  The directory /usr/local/lib/R/site-library can be used for site-wide
  multi-user installations of R.  

  This is even the default on Debian and Ubuntu (following a suggestion by
  Kurt and Fritz a decade ago over beers -- what could be better).  However,
  R enforces wrong permissions on directories and files there (removing
  group-write) which effectively defeats this purpose, and breaks multiuser
  installation:  if Tom, Dick and Harry are members of group 'r-users',
each
  one can install in the directory, but neither can _upgrade_ a package
  installed by one of the others.  

  I would like to correct this.


Details:   

  For a while now, R CMD INSTALL dispatches installation work to the R
  function tools:::.install_packages() from the file tools/install.R. The
  function does a lot of hardcoded 'chmod' with constant arguments:

  edd at max:~/svn/r-devel/src/library/tools/R$ grep Sys.chmod install.R 
                  if (!WINDOWS) Sys.chmod(file.path(dest, files),
"755")
                      Sys.chmod(file.path(instdir, f), "644")
                  Sys.chmod(Sys.glob(file.path(instdir, "data",
"*")), "644")
              Sys.chmod(Sys.glob(file.path(instdir, "demo",
"*")), "644")
                      Sys.chmod(Sys.glob(file.path(instdir, "exec",
"*")), "755")
                  Sys.chmod(i2_files[execs], "755")
  edd at max:~/svn/r-devel/src/library/tools/R$ 

  Moreover, it also calls a C function for cleanup cleanup:

  edd at max:~/svn/r-devel/src/library/tools/R$ grep ".Call(dir"
install.R
          .Call(dirchmod, instdir)
                      .Call(dirchmod, ss)
                              .Call(dirchmod, ss)
              ## tree, since the later .Call(dirchmod) call will
  edd at max:~/svn/r-devel/src/library/tools/R$

  which also uses unconditional 644 / 755

      mode_t mask = S_IRUSR | S_IRGRP | S_IROTH | S_IWUSR, /* 0644 */
          dirmask = mask | S_IXUSR | S_IXGRP | S_IXOTH; /* 0755 */


Proposal:

  Add a new option() [with a to-be-determined name] which, if enabled, turns
  on group-write modes for files and directories, ie "664" and
"775".

  One way would be to set two character vars at the beginning of
  _install_packages and to pass a flag to the dirchmod call as so that
  'S_IWGRP' (the 00020 "write by group" permission) can be
set.

  I would be happy to write such a patch (including documentation updates) if
  someone from R Core can signal willigness to look at it.


Thanks,  Dirk

-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com

Hi all,

Dirk Eddelbuettel <edd at debian.org> writes:
> Summary:   
>
>   The directory /usr/local/lib/R/site-library can be used for site-wide
>   multi-user installations of R.  
>
>   This is even the default on Debian and Ubuntu (following a suggestion by
>   Kurt and Fritz a decade ago over beers -- what could be better). 
However,
>   R enforces wrong permissions on directories and files there (removing
>   group-write) which effectively defeats this purpose, and breaks multiuser
>   installation:  if Tom, Dick and Harry are members of group
'r-users', each
>   one can install in the directory, but neither can _upgrade_ a package
>   installed by one of the others.  
>
>   I would like to correct this.
>
This is just a message from a user who would greatly appreciate such a
change.  We have written a script based on inotify to correct that group
writing permissions which we would gladly dismiss again.

Best,
Andreas

>>>>> Dirk Eddelbuettel <edd at debian.org>
>>>>>     on Sat, 8 Jun 2013 11:22:56 -0500 writes:
    > Summary:   

    > The directory /usr/local/lib/R/site-library can be used for site-wide
    > multi-user installations of R.  

    > This is even the default on Debian and Ubuntu (following a suggestion
by
    > Kurt and Fritz a decade ago over beers -- what could be better). 
However,
    > R enforces wrong permissions on directories and files there (removing
    > group-write) which effectively defeats this purpose, and breaks
multiuser
    > installation:  if Tom, Dick and Harry are members of group
'r-users', each
    > one can install in the directory, but neither can _upgrade_ a package
    > installed by one of the others.  

    > I would like to correct this.


    > Details:   

[..........]


    > Proposal:

    > Add a new option() [with a to-be-determined name] which, if enabled,
turns
    > on group-write modes for files and directories, ie "664" and
"775".

[.........]

    > I would be happy to write such a patch (including documentation
updates) if
    > someone from R Core can signal willigness to look at it.

"signal!"
:-)

Regards, 
Martin

On Sat, Jun 15, 2013 at 4:38 PM, Simon Urbanek
<simon.urbanek at r-project.org> wrote:
>
> On Jun 15, 2013, at 2:42 PM, Martin Maechler wrote:
>
>>>>>>> Dirk Eddelbuettel <edd at debian.org>
>>>>>>>    on Sat, 15 Jun 2013 10:45:04 -0500 writes:
>>
>>> On 15 June 2013 at 07:00, Dirk Eddelbuettel wrote:
>>> |
>>> | On 15 June 2013 at 07:47, Simon Urbanek wrote: | |
>>> Because update.packages() doesn't restore the
>>> group-writable bit. Which leads us to my point that this
>>> is not what you really want.
>>> |
>>> | Ooops. I'll take another look.
>>
>>> Done.  "It works."  For fairly generous definitions of
>>> working. I'll detail:
>>
>>> i) My initial patch only used options() to set things.
>>> Martin was not to enthralled with this and guided the
>>> patch towards using --group-writable as an option.
>>
>>> ii) With --group-writable, installation works but updates
>>> fail as noticed by Simon.
>>
>>> iii) If we fall back to using options() [ or an
>>> environment variable ], things works.  A log is below.
>>
>> Hmm, but this only works if everyone who calls  update.packages() also
has
>> this options() setting, no?
>> Why would the update keep the package files group writable otherwise ?
>> If the updater has no group-writable option she can still update
>> the package you installed, but you can no longer, right?
>>
>> I still think the approach to abolish all settings and just
>> trigger group-writable package installation *when* the library
>> directory is group writable is so simple we should adopt it,
>> and can forget all options/ command line arguments / environment
>> variables about this topic.
>>
>
> I fully agree. Also thanks for summarizing the discussion earlier today -
it was dead on.
>
Picking up a somewhat old thread...what is the final status of this?
It doesn't look like an option was added to control the permissions of
installed package files.
It also seems that the --group-writable option to R CMD INSTALL is not
present in R-3.0.1.

So are we back to where we started?

FWIW, I'd prefer a solution that respects the umask and is honored in
install.packages(), update.packages(), etc. In my use case users will
be installing packages most often within R with install.packages() (as
opposed to R CMD INSTALL from the command line), and they will
probably use install.packages() rather than update.packages() even for
packages that are already installed.

I'll probably use the inotify hack suggested earlier in the short term.

Thanks,
Dan


> Thanks,
> Simon
>
>
>
>> Martin
>>
>>> iv) I guess those of you who want the --group-writeable
>>> option need to ensure it also works for update.packages()
>>> as new option?
>>
>>> I am happy with what we have right now as it works in the
>>> context established by my patch.  Martin's addition of
>>> --group-writable is a bit more ambitious and we may need
>>> to enhance update.package(), or tell everybody to also
>>> (??)  use the option() setting, or environment variable.
>>
>>> Two things follow, a quick test script and a log from the
>>> script.
>>
>>> Dirk
>>
>>
>>> Script
>>>
>>> #!/bin/bash
>>>
>>> ## we use digest as an example as it is pretty small
>>> cd ~/svn/digest
>>> ls -l digest_0.6.?.tar.gz
>>>
>>> ## we make two assumptions:
>>> ##
>>> ## a) R-devel (called via a shell script wrapper)
>>> ~/bin/R-devel.sh --version | head -1
>>> ##
>>> ## b) An option has been set
>>> cat /usr/local/lib/R-devel/lib/R/etc/Rprofile.site
>>>
>>> ## now install an older version so that we can upgrade later
>>> ## this is running as 'edd' ie me
>>> ~/bin/R-devel.sh CMD INSTALL digest_0.6.2.tar.gz
>>>
>>> ls -ld /usr/local/lib/R/site-library/digest/
>>> ls -lR /usr/local/lib/R/site-library/digest/
>>>
>>> ## now try the upgrade as another user in the group
>>> sudo su lmp -c '~edd/bin/R-devel.sh -e
"update.packages(repos=\"http://cran.r-project.org\", ask=FALSE,
lib.loc=\"/usr/local/lib/R/site-library\")"'
>>>
>>> ls -ld /usr/local/lib/R/site-library/digest/
>>> ls -lR /usr/local/lib/R/site-library/digest/
>>>
>>>
>>>
>>> Session log
>>>
>>> edd at max:~$ /tmp/testRupgrade.sh
>>> -rw-r--r-- 1 edd edd 53344 Nov 25  2012 digest_0.6.0.tar.gz
>>> -rw-r--r-- 1 edd edd 76839 Jan 21 09:25 digest_0.6.1.tar.gz
>>> -rw-r--r-- 1 edd edd 76771 Jan 25 11:33 digest_0.6.2.tar.gz
>>> -rw-r--r-- 1 edd edd 78002 Feb 16 06:35 digest_0.6.3.tar.gz
>>> R Under development (unstable) (2013-06-14 r62964) --
"Unsuffered Consequences"
>>> options("group.writable.pkgs"=TRUE)
>>> * installing to library ?/usr/local/lib/R/site-library?
>>> * installing *source* package ?digest? ...
>>> ** libs
>>> ccache gcc-4.7 -I/usr/local/lib/R-devel/lib/R/include -DNDEBUG 
-I/usr/local/include    -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99  -c
aes.c -o aes.o
>>> ccache gcc-4.7 -I/usr/local/lib/R-devel/lib/R/include -DNDEBUG 
-I/usr/local/include    -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99  -c
crc32.c -o crc32.o
>>> ccache gcc-4.7 -I/usr/local/lib/R-devel/lib/R/include -DNDEBUG 
-I/usr/local/include    -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99  -c
digest.c -o digest.o
>>> ccache gcc-4.7 -I/usr/local/lib/R-devel/lib/R/include -DNDEBUG 
-I/usr/local/include    -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99  -c
md5.c -o md5.o
>>> ccache gcc-4.7 -I/usr/local/lib/R-devel/lib/R/include -DNDEBUG 
-I/usr/local/include    -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99  -c
raes.c -o raes.o
>>> ccache gcc-4.7 -I/usr/local/lib/R-devel/lib/R/include -DNDEBUG 
-I/usr/local/include    -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99  -c
sha1.c -o sha1.o
>>> ccache gcc-4.7 -I/usr/local/lib/R-devel/lib/R/include -DNDEBUG 
-I/usr/local/include    -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99  -c
sha2.c -o sha2.o
>>> ccache gcc-4.7 -I/usr/local/lib/R-devel/lib/R/include -DNDEBUG 
-I/usr/local/include    -fpic  -O3 -g0 -Wall -pipe -pedantic -std=gnu99  -c
sha256.c -o sha256.o
>>> sha2.c: In function ?SHA256_Final?:
>>> sha2.c:606:3: warning: dereferencing type-punned pointer will break
strict-aliasing rules [-Wstrict-aliasing]
>>> sha2.c: In function ?SHA512_Last?:
>>> sha2.c:923:2: warning: dereferencing type-punned pointer will break
strict-aliasing rules [-Wstrict-aliasing]
>>> sha2.c:924:2: warning: dereferencing type-punned pointer will break
strict-aliasing rules [-Wstrict-aliasing]
>>> ccache gcc-4.7 -shared -L/usr/local/lib -o digest.so aes.o crc32.o
digest.o md5.o raes.o sha1.o sha2.o sha256.o -L/usr/local/lib/R-devel/lib/R/lib
-lR
>>> installing to /usr/local/lib/R/site-library/digest/libs
>>> ** R
>>> ** inst
>>> ** preparing package for lazy loading
>>> ** help
>>> *** installing help indices
>>> ** building package indices
>>> ** testing if installed package can be loaded
>>> * DONE (digest)
>>> drwxrwxr-x 7 edd staff 4096 Jun 15 10:42
/usr/local/lib/R/site-library/digest/
>>> /usr/local/lib/R/site-library/digest/:
>>> total 52
>>> -rw-rw-r-- 1 edd staff  1605 Jun 15 10:42 DESCRIPTION
>>> -rw-rw-r-- 1 edd staff 18092 Jun 15 10:42 GPL-2
>>> drwxrwxr-x 2 edd staff  4096 Jun 15 10:42 help
>>> drwxrwxr-x 2 edd staff  4096 Jun 15 10:42 html
>>> -rw-rw-r-- 1 edd staff   271 Jun 15 10:42 INDEX
>>> drwxrwxr-x 2 edd staff  4096 Jun 15 10:42 libs
>>> drwxrwxr-x 2 edd staff  4096 Jun 15 10:42 Meta
>>> -rw-rw-r-- 1 edd staff   140 Jun 15 10:42 NAMESPACE
>>> drwxrwxr-x 2 edd staff  4096 Jun 15 10:42 R
>>>
>>> /usr/local/lib/R/site-library/digest/help:
>>> total 36
>>> -rw-rw-r-- 1 edd staff    80 Jun 15 10:42 aliases.rds
>>> -rw-rw-r-- 1 edd staff    32 Jun 15 10:42 AnIndex
>>> -rw-rw-r-- 1 edd staff 17857 Jun 15 10:42 digest.rdb
>>> -rw-rw-r-- 1 edd staff   193 Jun 15 10:42 digest.rdx
>>> -rw-rw-r-- 1 edd staff   140 Jun 15 10:42 paths.rds
>>>
>>> /usr/local/lib/R/site-library/digest/html:
>>> total 8
>>> -rw-rw-r-- 1 edd staff 1236 Jun 15 10:42 00Index.html
>>> -rw-rw-r-- 1 edd staff 1179 Jun 15 10:42 R.css
>>>
>>> /usr/local/lib/R/site-library/digest/libs:
>>> total 120
>>> -rwxrwxr-x 1 edd staff 118956 Jun 15 10:42 digest.so
>>>
>>> /usr/local/lib/R/site-library/digest/Meta:
>>> total 20
>>> -rw-rw-r-- 1 edd staff  351 Jun 15 10:42 hsearch.rds
>>> -rw-rw-r-- 1 edd staff  117 Jun 15 10:42 links.rds
>>> -rw-rw-r-- 1 edd staff  224 Jun 15 10:42 nsInfo.rds
>>> -rw-rw-r-- 1 edd staff 1271 Jun 15 10:42 package.rds
>>> -rw-rw-r-- 1 edd staff  331 Jun 15 10:42 Rd.rds
>>>
>>> /usr/local/lib/R/site-library/digest/R:
>>> total 16
>>> -rw-rw-r-- 1 edd staff 1056 Jun 15 10:42 digest
>>> -rw-rw-r-- 1 edd staff 4168 Jun 15 10:42 digest.rdb
>>> -rw-rw-r-- 1 edd staff  388 Jun 15 10:42 digest.rdx
>>>
>>> R Under development (unstable) (2013-06-14 r62964) --
"Unsuffered Consequences"
>>> Copyright (C) 2013 The R Foundation for Statistical Computing
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>> You are welcome to redistribute it under certain conditions.
>>> Type 'license()' or 'licence()' for distribution
details.
>>>
>>>  Natural language support but running in an English locale
>>>
>>> R is a collaborative project with many contributors.
>>> Type 'contributors()' for more information and
>>> 'citation()' on how to cite R or R packages in
publications.
>>>
>>> Type 'demo()' for some demos, 'help()' for on-line
help, or
>>> 'help.start()' for an HTML browser interface to help.
>>> Type 'q()' to quit R.
>>>
>>>> update.packages(repos="http://cran.r-project.org",
ask=FALSE, lib.loc="/usr/local/lib/R/site-library")
>>> trying URL
'http://cran.r-project.org/src/contrib/digest_0.6.3.tar.gz'
>>> Content type 'application/x-gzip' length 80083 bytes (78
Kb)
>>> opened URL
>>> =================================================>>>
downloaded 78 Kb
>>>
>>> * installing *source* package ?digest? ...
>>> ** package ?digest? successfully unpacked and MD5 sums checked
>>> ** libs
>>> ccache gcc -I/usr/local/lib/R-devel/lib/R/include -DNDEBUG 
-I/usr/local/include    -fpic  -ggdb -pipe -std=gnu99 -Wall -pedantic  -c aes.c
-o aes.o
>>> ccache gcc -I/usr/local/lib/R-devel/lib/R/include -DNDEBUG 
-I/usr/local/include    -fpic  -ggdb -pipe -std=gnu99 -Wall -pedantic  -c
crc32.c -o crc32.o
>>> ccache gcc -I/usr/local/lib/R-devel/lib/R/include -DNDEBUG 
-I/usr/local/include    -fpic  -ggdb -pipe -std=gnu99 -Wall -pedantic  -c
digest.c -o digest.o
>>> ccache gcc -I/usr/local/lib/R-devel/lib/R/include -DNDEBUG 
-I/usr/local/include    -fpic  -ggdb -pipe -std=gnu99 -Wall -pedantic  -c md5.c
-o md5.o
>>> ccache gcc -I/usr/local/lib/R-devel/lib/R/include -DNDEBUG 
-I/usr/local/include    -fpic  -ggdb -pipe -std=gnu99 -Wall -pedantic  -c raes.c
-o raes.o
>>> ccache gcc -I/usr/local/lib/R-devel/lib/R/include -DNDEBUG 
-I/usr/local/include    -fpic  -ggdb -pipe -std=gnu99 -Wall -pedantic  -c sha1.c
-o sha1.o
>>> ccache gcc -I/usr/local/lib/R-devel/lib/R/include -DNDEBUG 
-I/usr/local/include    -fpic  -ggdb -pipe -std=gnu99 -Wall -pedantic  -c sha2.c
-o sha2.o
>>> ccache gcc -I/usr/local/lib/R-devel/lib/R/include -DNDEBUG 
-I/usr/local/include    -fpic  -ggdb -pipe -std=gnu99 -Wall -pedantic  -c
sha256.c -o sha256.o
>>> ccache gcc -shared -L/usr/local/lib -o digest.so aes.o crc32.o
digest.o md5.o raes.o sha1.o sha2.o sha256.o -L/usr/local/lib/R-devel/lib/R/lib
-lR
>>> installing to /usr/local/lib/R/site-library/digest/libs
>>> ** R
>>> ** inst
>>> ** preparing package for lazy loading
>>> ** help
>>> *** installing help indices
>>> ** building package indices
>>> ** testing if installed package can be loaded
>>> * DONE (digest)
>>>
>>> The downloaded source packages are in
>>>      ?/tmp/RtmpxJgmSB/downloaded_packages?
>>>>
>>>>
>>> drwxrwxr-x 7 lmp staff 4096 Jun 15 10:42
/usr/local/lib/R/site-library/digest/
>>> /usr/local/lib/R/site-library/digest/:
>>> total 52
>>> -rw-rw-r-- 1 lmp staff  1767 Jun 15 10:42 DESCRIPTION
>>> -rw-rw-r-- 1 lmp staff 18092 Jun 15 10:42 GPL-2
>>> drwxrwxr-x 2 lmp staff  4096 Jun 15 10:42 help
>>> drwxrwxr-x 2 lmp staff  4096 Jun 15 10:42 html
>>> -rw-rw-r-- 1 lmp staff   253 Jun 15 10:42 INDEX
>>> drwxrwxr-x 2 lmp staff  4096 Jun 15 10:42 libs
>>> drwxrwxr-x 2 lmp staff  4096 Jun 15 10:42 Meta
>>> -rw-rw-r-- 1 lmp staff   140 Jun 15 10:42 NAMESPACE
>>> drwxrwxr-x 2 lmp staff  4096 Jun 15 10:42 R
>>>
>>> /usr/local/lib/R/site-library/digest/help:
>>> total 36
>>> -rw-rw-r-- 1 lmp staff    80 Jun 15 10:42 aliases.rds
>>> -rw-rw-r-- 1 lmp staff    32 Jun 15 10:42 AnIndex
>>> -rw-rw-r-- 1 lmp staff 17871 Jun 15 10:42 digest.rdb
>>> -rw-rw-r-- 1 lmp staff   195 Jun 15 10:42 digest.rdx
>>> -rw-rw-r-- 1 lmp staff   140 Jun 15 10:42 paths.rds
>>>
>>> /usr/local/lib/R/site-library/digest/html:
>>> total 8
>>> -rw-rw-r-- 1 lmp staff 1236 Jun 15 10:42 00Index.html
>>> -rw-rw-r-- 1 lmp staff 1179 Jun 15 10:42 R.css
>>>
>>> /usr/local/lib/R/site-library/digest/libs:
>>> total 172
>>> -rwxrwxr-x 1 lmp staff 175154 Jun 15 10:42 digest.so
>>>
>>> /usr/local/lib/R/site-library/digest/Meta:
>>> total 20
>>> -rw-rw-r-- 1 lmp staff  351 Jun 15 10:42 hsearch.rds
>>> -rw-rw-r-- 1 lmp staff  117 Jun 15 10:42 links.rds
>>> -rw-rw-r-- 1 lmp staff  224 Jun 15 10:42 nsInfo.rds
>>> -rw-rw-r-- 1 lmp staff 1325 Jun 15 10:42 package.rds
>>> -rw-rw-r-- 1 lmp staff  331 Jun 15 10:42 Rd.rds
>>>
>>> /usr/local/lib/R/site-library/digest/R:
>>> total 16
>>> -rw-rw-r-- 1 lmp staff 1056 Jun 15 10:42 digest
>>> -rw-rw-r-- 1 lmp staff 4205 Jun 15 10:42 digest.rdb
>>> -rw-rw-r-- 1 lmp staff  385 Jun 15 10:42 digest.rdx
>>> edd at max:~$
>>>
>>> --
>>> Dirk Eddelbuettel | edd at debian.org |
http://dirk.eddelbuettel.com
>>
>>
>
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