| Summary: | dev-lang/R-3.1.0: biocLite("vsn") removes all files in / | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Juergen Rose <rose> |
| Component: | Current packages | Assignee: | Gentoo Linux bug wranglers <bug-wranglers> |
| Status: | RESOLVED INVALID | ||
| Severity: | normal | ||
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
(In reply to Juergen Rose from comment #0) > Then I did as root: > R > > source("http://bioconductor.org/biocLite.R") > > biocLite("vsn") You downloaded something from the web and executed it as root. (In reply to Jeroen Roovers from comment #1) > (In reply to Juergen Rose from comment #0) > > Then I did as root: > > R > > > source("http://bioconductor.org/biocLite.R") > > > biocLite("vsn") > > You downloaded something from the web and executed it as root. So far as I know, I have to do this, if I want to install R-packages for all users. At least if I install R-packages with install.package() as a normal user it is installed in the home directory of the user. (In reply to Juergen Rose from comment #2) > > > R > > > > source("http://bioconductor.org/biocLite.R") > > > > biocLite("vsn") > > > > You downloaded something from the web and executed it as root. > > So far as I know, I have to do this, if I want to install R-packages for all > users. At least if I install R-packages with install.package() as a normal > user it is installed in the home directory of the user. It's both beyond the control of Gentoo Linux and INVALID. |
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 root 11 Jan 22 2011 data -> data_caiman/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ lrwxrwxrwx 1 root root 23 Dec 29 13:43 data_impala -> /net/impala/data_impala/ lrwxrwxrwx 1 root root 21 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 root 11 Jan 23 2011 home -> home_caiman/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ lrwxrwxrwx 1 root root 23 Dec 29 13:43 home_impala -> /net/impala/home_impala/ lrwxrwxrwx 1 root root 21 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. Reproducible: Always