>>>>> Dirk Eddelbuettel <e...@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.
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@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@max:~$
>
> --
> Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com
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