Re: [R] dev-lang/R-3.1.0: biocLite(vsn) removes all files in /
On 2014-05-18 20:43, peter dalgaard wrote: On 18 May 2014, at 07:38 , Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: Then you had best not do it again if you don't like that result. 1) This is not the right mailing list for issues having to do with bioconductor. Please go to the bioconductor mailing list for that. Hmm, this is one case where I'd really rather not scare people off R-help. Non-BioC users do use BioC packages from time to time and what Juergen did is what the BioConductor web pages tells new users to do (probably minus the as-root bit). A warn-off on R-help seems entirely warranted. Good to see that Martin Morgan is taking the issue very seriously in his post below. As a non-BioC user using BioC packages I've always wondered why the standard R functionality isn't enough. Can someone, please, tell me why 'biocLite()' should be used? I've always succeeded installing BioC packages using the standard R tools (as indicated by Uwe in his reply). Henric Winell 2) Running random scripts straight from the internet as root without reviewing them is exactly the kind of thing any experienced *nix user would never do. That is why user-level accounts have limits on the things they can do. I doubt you are supposed to be running anything with your current directory set to /, ever, especially not logged in as root. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On May 17, 2014 10:16:46 PM PDT, Juergen Rose r...@rz.uni-potsdam.de wrote: I had the following files in /: root@caiman:/root(8)# ll / total 160301 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ -rw-r--r-- 1 root root 38673 May 14 14:22 boot_local-d.log lrwxrwxrwx 1 root root11 Jan 22 2011 data - data_caiman/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ lrwxrwxrwx 1 root root23 Dec 29 13:43 data_impala - /net/impala/data_impala/ lrwxrwxrwx 1 root root21 Jan 27 08:13 data_lynx2 - /net/lynx2/data_lynx2/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ -rw--- 1 root root 15687 Dec 26 13:42 grub.cfg_old lrwxrwxrwx 1 root root11 Jan 23 2011 home - home_caiman/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ lrwxrwxrwx 1 root root23 Dec 29 13:43 home_impala - /net/impala/home_impala/ lrwxrwxrwx 1 root root21 Jan 27 08:13 home_lynx2 - /net/lynx2/home_lynx2/ lrwxrwxrwx 1 root root 5 Mar 30 04:25 lib - lib64/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ -rw-r--r-- 1 root root 1797418 May 14 14:22 login.log drwx-- 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 4 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 270 root root 0 May 14 14:21 proc/ drwx-- 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ -rw-r--r-- 1 root root 162191459 Jan 13 2011 stage3-amd64-20110113.tar.bz2 dr-xr-xr-x 12 root root 0 May 14 14:21 sys/ drwxrwxrwt 16 root root 1648 May 17 17:14 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ Then I did as root: R source(http://bioconductor.org/biocLite.R;) biocLite(vsn) Save workspace image? [y/n/c]: n root@caiman:/root(15)# ll / total 93 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ drwx-- 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 2 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 272 root root 0 May 14 14:21 proc/ drwx-- 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21
Re: [R] dev-lang/R-3.1.0: biocLite(vsn) removes all files in /
On 05/19/2014 01:09 AM, Henric Winell wrote: On 2014-05-18 20:43, peter dalgaard wrote: On 18 May 2014, at 07:38 , Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: Then you had best not do it again if you don't like that result. 1) This is not the right mailing list for issues having to do with bioconductor. Please go to the bioconductor mailing list for that. Hmm, this is one case where I'd really rather not scare people off R-help. Non-BioC users do use BioC packages from time to time and what Juergen did is what the BioConductor web pages tells new users to do (probably minus the as-root bit). A warn-off on R-help seems entirely warranted. Good to see that Martin Morgan is taking the issue very seriously in his post below. As a non-BioC user using BioC packages I've always wondered why the standard R functionality isn't enough. Can someone, please, tell me why 'biocLite()' should be used? I've always succeeded installing BioC packages using the standard R tools (as indicated by Uwe in his reply). Conversely, I've always succeeded in installing CRAN and Bioc packages via source(http://bioconductor.org/biocLite.R;) biocLite(...) and am more-or-less flummoxed by the extra steps I'm asked to perform (to choose and set repositories) when I take that rare foray into install.packages()-land! One point is that http://bioconductor.org actually points to an Amazon CloudFront address, which means that the content comes from a geographically proximate and reliable location (this makes choice of repository mostly irrelevant for normal users, just point to bioconductor.org) Bioconductor has a repository and release schedule that differs from R (Bioconductor has a 'devel' branch to which new packages and updates are introduced, and a stable 'release' branch emitted once every 6 months to which bug fixes but not new features are introduced). A consequences of the mismatch between R and Bioconductor release schedules is that the Bioconductor version identified by Uwe's method is sometimes not the most recent 'release' available. For instance, R 3.1.1 will likely be introduced some months before the next Bioc release. After the Bioc release, 3.1.1 users will be pointed to an out-of-date version of Bioconductor. A consequence of the distinct 'devel' branch is that Uwe's method sometimes points only to the 'release' repository, whereas Bioconductor developers and users wanting leading-edge features wish to access the Bioconductor 'devel' repository. For instance, the next Bioc release will be available for R.3.1.x, so Bioconductor developers and leading-edge users need to be able to install the devel version of Bioconductor packages into the same version (though perhaps different instance or at least library location) of R that currently supports the release version. An indirect consequence of the structured release is that Bioconductor packages generally have more extensive dependencies with one another, both explicitly via the usual package mechanisms and implicitly because the repository, release structure, and Bioconductor community interactions favor re-use of data representations and analysis concepts across packages. There is thus a higher premium on knowing that packages are from the same release, and that all packages are current within the release. These days, the main purpose of source(http://bioconductor.org/biocLite.R;) is to install and attach the 'BiocInstaller' package. In a new installation, the script installs the most recent version of the BiocInstaller package relevant to the version of R in use, regardless of the relative times of R and Bioconductor release cycles. The BiocInstaller package serves as the primary way to identify the version of Bioconductor in use library(BiocInstaller) Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help Since new features are often appealing to users, but at the same time require an updated version of Bioconductor, the source() command evaluated in an out-of-date R will nudge users to upgrade, e.g., in R-2.15.3 source(http://bioconductor.org/biocLite.R;) A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install The biocLite() function is provided by BiocInstaller. This is a wrapper around install.packages, but with the repository chosen according to the version of Bioconductor in use, rather than to the version relevant at the time of the release of R. biocLite also nudges users to remain current within a release, by default checking for out-of-date packages and asking if the user would like to update biocLite() BioC_mirror: http://bioconductor.org Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version 3.1.0. Old packages: 'BBmisc', 'genefilter', 'GenomicAlignments', 'GenomicRanges', 'IRanges', 'MASS', 'reshape2', 'Rgraphviz', 'RJSONIO', 'rtracklayer' Update all/some/none?
Re: [R] dev-lang/R-3.1.0: biocLite(vsn) removes all files in /
As alternative, just use R itself for it: chooseBioCmirror() setRepositories() # select BioC repositories here install.packages(vsn) Which should so the trick without any additional tools not shiped with R directly. Best, Uwe Ligges On 18.05.2014 07:38, Jeff Newmiller wrote: Then you had best not do it again if you don't like that result. 1) This is not the right mailing list for issues having to do with bioconductor. Please go to the bioconductor mailing list for that. 2) Running random scripts straight from the internet as root without reviewing them is exactly the kind of thing any experienced *nix user would never do. That is why user-level accounts have limits on the things they can do. I doubt you are supposed to be running anything with your current directory set to /, ever, especially not logged in as root. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On May 17, 2014 10:16:46 PM PDT, Juergen Rose r...@rz.uni-potsdam.de wrote: I had the following files in /: root@caiman:/root(8)# ll / total 160301 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ -rw-r--r-- 1 root root 38673 May 14 14:22 boot_local-d.log lrwxrwxrwx 1 root root11 Jan 22 2011 data - data_caiman/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ lrwxrwxrwx 1 root root23 Dec 29 13:43 data_impala - /net/impala/data_impala/ lrwxrwxrwx 1 root root21 Jan 27 08:13 data_lynx2 - /net/lynx2/data_lynx2/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ -rw--- 1 root root 15687 Dec 26 13:42 grub.cfg_old lrwxrwxrwx 1 root root11 Jan 23 2011 home - home_caiman/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ lrwxrwxrwx 1 root root23 Dec 29 13:43 home_impala - /net/impala/home_impala/ lrwxrwxrwx 1 root root21 Jan 27 08:13 home_lynx2 - /net/lynx2/home_lynx2/ lrwxrwxrwx 1 root root 5 Mar 30 04:25 lib - lib64/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ -rw-r--r-- 1 root root 1797418 May 14 14:22 login.log drwx-- 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 4 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 270 root root 0 May 14 14:21 proc/ drwx-- 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ -rw-r--r-- 1 root root 162191459 Jan 13 2011 stage3-amd64-20110113.tar.bz2 dr-xr-xr-x 12 root root 0 May 14 14:21 sys/ drwxrwxrwt 16 root root 1648 May 17 17:14 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ Then I did as root: R source(http://bioconductor.org/biocLite.R;) biocLite(vsn) Save workspace image? [y/n/c]: n root@caiman:/root(15)# ll / total 93 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ drwx-- 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 2 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 272 root root 0 May 14 14:21 proc/ drwx-- 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ dr-xr-xr-x 12 root root 0 May 17 17:38 sys/ drwxrwxrwt 19 root root 1752 May 17 18:33 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ I.e., all not directory files in / disappeared. This happens on two systems. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
Re: [R] dev-lang/R-3.1.0: biocLite(vsn) removes all files in /
This would be very bad and certainly unintended if it were the responsibility of biocLite. Can we communicate off-list about this? In particular can you report noquote(readLines(http://bioconductor.org/biocLite.R;)) ? Martin Morgan On 05/17/2014 10:16 PM, Juergen Rose wrote: I had the following files in /: root@caiman:/root(8)# ll / total 160301 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ -rw-r--r-- 1 root root 38673 May 14 14:22 boot_local-d.log lrwxrwxrwx 1 root root11 Jan 22 2011 data - data_caiman/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ lrwxrwxrwx 1 root root23 Dec 29 13:43 data_impala - /net/impala/data_impala/ lrwxrwxrwx 1 root root21 Jan 27 08:13 data_lynx2 - /net/lynx2/data_lynx2/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ -rw--- 1 root root 15687 Dec 26 13:42 grub.cfg_old lrwxrwxrwx 1 root root11 Jan 23 2011 home - home_caiman/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ lrwxrwxrwx 1 root root23 Dec 29 13:43 home_impala - /net/impala/home_impala/ lrwxrwxrwx 1 root root21 Jan 27 08:13 home_lynx2 - /net/lynx2/home_lynx2/ lrwxrwxrwx 1 root root 5 Mar 30 04:25 lib - lib64/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ -rw-r--r-- 1 root root 1797418 May 14 14:22 login.log drwx-- 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 4 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 270 root root 0 May 14 14:21 proc/ drwx-- 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ -rw-r--r-- 1 root root 162191459 Jan 13 2011 stage3-amd64-20110113.tar.bz2 dr-xr-xr-x 12 root root 0 May 14 14:21 sys/ drwxrwxrwt 16 root root 1648 May 17 17:14 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ Then I did as root: R source(http://bioconductor.org/biocLite.R;) biocLite(vsn) Save workspace image? [y/n/c]: n root@caiman:/root(15)# ll / total 93 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ drwx-- 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 2 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 272 root root 0 May 14 14:21 proc/ drwx-- 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ dr-xr-xr-x 12 root root 0 May 17 17:38 sys/ drwxrwxrwt 19 root root 1752 May 17 18:33 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ I.e., all not directory files in / disappeared. This happens on two systems. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] dev-lang/R-3.1.0: biocLite(vsn) removes all files in /
On 18 May 2014, at 07:38 , Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: Then you had best not do it again if you don't like that result. 1) This is not the right mailing list for issues having to do with bioconductor. Please go to the bioconductor mailing list for that. Hmm, this is one case where I'd really rather not scare people off R-help. Non-BioC users do use BioC packages from time to time and what Juergen did is what the BioConductor web pages tells new users to do (probably minus the as-root bit). A warn-off on R-help seems entirely warranted. Good to see that Martin Morgan is taking the issue very seriously in his post below. 2) Running random scripts straight from the internet as root without reviewing them is exactly the kind of thing any experienced *nix user would never do. That is why user-level accounts have limits on the things they can do. I doubt you are supposed to be running anything with your current directory set to /, ever, especially not logged in as root. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On May 17, 2014 10:16:46 PM PDT, Juergen Rose r...@rz.uni-potsdam.de wrote: I had the following files in /: root@caiman:/root(8)# ll / total 160301 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ -rw-r--r-- 1 root root 38673 May 14 14:22 boot_local-d.log lrwxrwxrwx 1 root root11 Jan 22 2011 data - data_caiman/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ lrwxrwxrwx 1 root root23 Dec 29 13:43 data_impala - /net/impala/data_impala/ lrwxrwxrwx 1 root root21 Jan 27 08:13 data_lynx2 - /net/lynx2/data_lynx2/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ -rw--- 1 root root 15687 Dec 26 13:42 grub.cfg_old lrwxrwxrwx 1 root root11 Jan 23 2011 home - home_caiman/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ lrwxrwxrwx 1 root root23 Dec 29 13:43 home_impala - /net/impala/home_impala/ lrwxrwxrwx 1 root root21 Jan 27 08:13 home_lynx2 - /net/lynx2/home_lynx2/ lrwxrwxrwx 1 root root 5 Mar 30 04:25 lib - lib64/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ -rw-r--r-- 1 root root 1797418 May 14 14:22 login.log drwx-- 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 4 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 270 root root 0 May 14 14:21 proc/ drwx-- 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ -rw-r--r-- 1 root root 162191459 Jan 13 2011 stage3-amd64-20110113.tar.bz2 dr-xr-xr-x 12 root root 0 May 14 14:21 sys/ drwxrwxrwt 16 root root 1648 May 17 17:14 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ Then I did as root: R source(http://bioconductor.org/biocLite.R;) biocLite(vsn) Save workspace image? [y/n/c]: n root@caiman:/root(15)# ll / total 93 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ drwx-- 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 2 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 272 root root 0 May 14 14:21 proc/ drwx-- 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ dr-xr-xr-x 12 root root 0 May 17 17:38 sys/ drwxrwxrwt 19 root root 1752 May 17 18:33 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ I.e., all not
Re: [R] dev-lang/R-3.1.0: biocLite(vsn) removes all files in /
On Sun, 18 May 2014 07:16:46 +0200 Juergen Rose r...@rz.uni-potsdam.de wrote: What disappeared are links and three files. The links are recreatable, although they would be better placed in user space rather than under /. Of the three files, the *bz2 appears to be part of a Gentoo release, the second a grub configuration backup - not needed, and the last a log file. While the locaton of these files and links might be an idiosyncrasy of the Linux distribution you are using, most distributions are inherently more careful in configuration. You should get into the habit of creating a user with more limited scope than root and learn to use su and sudo if you need super-user rights. Working from root could seriously imperil your system and your work's integrity. JWDougherty __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] dev-lang/R-3.1.0: biocLite(vsn) removes all files in /
I had the following files in /: root@caiman:/root(8)# ll / total 160301 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ -rw-r--r-- 1 root root 38673 May 14 14:22 boot_local-d.log lrwxrwxrwx 1 root root11 Jan 22 2011 data - data_caiman/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ lrwxrwxrwx 1 root root23 Dec 29 13:43 data_impala - /net/impala/data_impala/ lrwxrwxrwx 1 root root21 Jan 27 08:13 data_lynx2 - /net/lynx2/data_lynx2/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ -rw--- 1 root root 15687 Dec 26 13:42 grub.cfg_old lrwxrwxrwx 1 root root11 Jan 23 2011 home - home_caiman/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ lrwxrwxrwx 1 root root23 Dec 29 13:43 home_impala - /net/impala/home_impala/ lrwxrwxrwx 1 root root21 Jan 27 08:13 home_lynx2 - /net/lynx2/home_lynx2/ lrwxrwxrwx 1 root root 5 Mar 30 04:25 lib - lib64/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ -rw-r--r-- 1 root root 1797418 May 14 14:22 login.log drwx-- 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 4 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 270 root root 0 May 14 14:21 proc/ drwx-- 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ -rw-r--r-- 1 root root 162191459 Jan 13 2011 stage3-amd64-20110113.tar.bz2 dr-xr-xr-x 12 root root 0 May 14 14:21 sys/ drwxrwxrwt 16 root root 1648 May 17 17:14 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ Then I did as root: R source(http://bioconductor.org/biocLite.R;) biocLite(vsn) Save workspace image? [y/n/c]: n root@caiman:/root(15)# ll / total 93 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ drwx-- 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 2 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 272 root root 0 May 14 14:21 proc/ drwx-- 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ dr-xr-xr-x 12 root root 0 May 17 17:38 sys/ drwxrwxrwt 19 root root 1752 May 17 18:33 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ I.e., all not directory files in / disappeared. This happens on two systems. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] dev-lang/R-3.1.0: biocLite(vsn) removes all files in /
Then you had best not do it again if you don't like that result. 1) This is not the right mailing list for issues having to do with bioconductor. Please go to the bioconductor mailing list for that. 2) Running random scripts straight from the internet as root without reviewing them is exactly the kind of thing any experienced *nix user would never do. That is why user-level accounts have limits on the things they can do. I doubt you are supposed to be running anything with your current directory set to /, ever, especially not logged in as root. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On May 17, 2014 10:16:46 PM PDT, Juergen Rose r...@rz.uni-potsdam.de wrote: I had the following files in /: root@caiman:/root(8)# ll / total 160301 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ -rw-r--r-- 1 root root 38673 May 14 14:22 boot_local-d.log lrwxrwxrwx 1 root root11 Jan 22 2011 data - data_caiman/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ lrwxrwxrwx 1 root root23 Dec 29 13:43 data_impala - /net/impala/data_impala/ lrwxrwxrwx 1 root root21 Jan 27 08:13 data_lynx2 - /net/lynx2/data_lynx2/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ -rw--- 1 root root 15687 Dec 26 13:42 grub.cfg_old lrwxrwxrwx 1 root root11 Jan 23 2011 home - home_caiman/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ lrwxrwxrwx 1 root root23 Dec 29 13:43 home_impala - /net/impala/home_impala/ lrwxrwxrwx 1 root root21 Jan 27 08:13 home_lynx2 - /net/lynx2/home_lynx2/ lrwxrwxrwx 1 root root 5 Mar 30 04:25 lib - lib64/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ -rw-r--r-- 1 root root 1797418 May 14 14:22 login.log drwx-- 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 4 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 270 root root 0 May 14 14:21 proc/ drwx-- 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ -rw-r--r-- 1 root root 162191459 Jan 13 2011 stage3-amd64-20110113.tar.bz2 dr-xr-xr-x 12 root root 0 May 14 14:21 sys/ drwxrwxrwt 16 root root 1648 May 17 17:14 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ Then I did as root: R source(http://bioconductor.org/biocLite.R;) biocLite(vsn) Save workspace image? [y/n/c]: n root@caiman:/root(15)# ll / total 93 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ drwx-- 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 2 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 272 root root 0 May 14 14:21 proc/ drwx-- 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ dr-xr-xr-x 12 root root 0 May 17 17:38 sys/ drwxrwxrwt 19 root root 1752 May 17 18:33 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ I.e., all not directory files in / disappeared. This happens on two systems. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and
