On Jun 15, 2013, at 2:42 PM, Martin Maechler wrote: >>>>>> 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. >
I fully agree. Also thanks for summarizing the discussion earlier today - it was dead on. 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@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 > > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
