Re: [R] Package installation help: Stuck at "** byte-compile and prepare package for lazy loading"
You can define the environment variable R_DONT_USE_TK (to any value) to
avoid this hang caused by code in the tkrplot package. You do not have to
have an X server running if R_DONT_USE_TK is set. This will avoid
potential hangs while installing the 23 packages that depend on tkrplot.
tools::package_dependencies("tkrplot", reverse=TRUE, recursive=TRUE)
$tkrplot
[1] "adoption" "baggingbwsel" "biplotbootGUI"
[4] "cncaGUI""ConvergenceConcepts""fisheyeR"
[7] "forensim" "GGEBiplotGUI" "GUIDE"
[10] "idendr0""InterfaceqPCR" "multibiplotGUI"
[13] "RclusTool" "RcmdrPlugin.FuzzyClust"
"RcmdrPlugin.PcaRobust"
[16] "rriskDistributions" "RVideoPoker""SyNet"
[19] "tsgui" "uHMM" "GGEBiplots"
[22] "decisionSupport""geneticae"
E.g.,
> install.packages("forensim", type="source",
INSTALL_opts="--no-byte-compile")
Installing package into ‘/home/bill/R-devel/R-build/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/forensim_4.3.tar.gz'
Content type 'application/x-gzip' length 84232 bytes (82 KB)
==
downloaded 82 KB
* installing *source* package ‘forensim’ ...
** package ‘forensim’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/home/bill/R-devel/R-build/include" -DNDEBUG -I/usr/local/include
-fpic -g -c auxilary.c -o auxilary.o
gcc -I"/home/bill/R-devel/R-build/include" -DNDEBUG -I/usr/local/include
-fpic -g -c recursFinal.c -o recursFinal.o
gcc -shared -L/usr/local/lib -o forensim.so auxilary.o recursFinal.o
installing to
/home/bill/R-devel/R-build/site-library/00LOCK-forensim/00new/forensim/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation
path
* DONE (forensim)
The downloaded source packages are in
‘/tmp/Rtmp0jqhj9/downloaded_packages’
The relevant code is in tkrplot/src/tcltkimg.c:
EXPORT(int,Rplot_Init)(interp)
Tcl_Interp *interp;
{
/* Added to allow CRAN to disable Tk initialization */
#if !defined(Win32) && !defined(HAVE_AQUA)
if (getenv("R_DONT_USE_TK") != NULL)
return 0;
#endif
-Bill
On Thu, Sep 30, 2021 at 9:35 AM Brodie, Kent wrote:
> Bill-- BINGO.You have found the answer. After some testing on
> one of my environments where it was always hanging, connecting to the same
> server with an X-Sever running on my workstation did indeed allow the
> package to be installed.
>
>
>
> **GOOD LORD THAT’S RIDICULOUS** But at least I know.And why it
> doesn’t error out without X running, who knows.
>
>
>
> After a ton more research, I ALSO discovered that there IS a timeout thing
> I can make use of, should I decide to continue just building things and
> ignoring the X-Server requirement for this (and probably some other?)
> packages.
>
>
>
> Before executing R and installing things, set this:
>
>
>
> export _R_INSTALL_PACKAGES_ELAPSED_TIMEOUT_=500
>
>
>
> (value is seconds). So, the previously-hanging R CMD INSTALL inside of
> the install.packages call will eventually die, and then move on to the next
> package.
>
> This is buried in the documentation but- it’s there and I confirmed it
> works.My example above times out a package install at 5 minutes.
>
>
>
> While knowing the X requirement is a huge win (thanks again!), I will
> probably stick with just using the timeout thing for what I’m trying to
> accomplish.Installing EVERYTHING from cran will take forever, and more
> than likely my VPN connection to my data center will be disconnected (thank
> you internal IT department) before it finishes.They have some sort of
> internal “you’ve been connected too long” timer that disconnects things
> overnight. Grr.
>
>
>
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Package installation help: Stuck at "** byte-compile and prepare package for lazy loading"
I tried this a second time, but with --no-byte-compile, and it hung with a slightly different traceback (gdb) where #0 0x7f95bc4c6689 in __fxstat64 () from /usr/lib/x86_64-linux-gnu/libc.so.6 #1 0x7f95bc497050 in opendir () from /usr/lib/x86_64-linux-gnu/libc.so.6 #2 0x7f95b935f1e0 in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so #3 0x7f95b9311242 in Tcl_FSMatchInDirectory () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so #4 0x7f95b92f3e2b in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so #5 0x7f95b92f34c5 in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so #6 0x7f95b92f29d8 in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so #7 0x7f95b92565f2 in TclNRRunCallbacks () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so #8 0x7f95b932bcd9 in Tcl_PkgRequireProc () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so #9 0x7f95b932bb06 in Tcl_PkgRequireEx () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so #10 0x7f95b96bdbe8 in Rplot_Init (interp=0x5625117460d0) at tcltkimg.c:465 and when I killed the R subprocess doing the lazyload prep I got a quasi-infinite stream of error messages: ... error reading package index file /home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_aquablue/pkgIndex.tcl: too many nested evaluations (infinite loop?) error reading package index file /home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl: too many nested evaluations (infinite loop?) error reading package index file /home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl: too many nested evaluations (infinite loop?) error reading package index file /home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl: can't find package tile error reading package index file /home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_aquablue/pkgIndex.tcl: too many nested evaluations (infinite loop?) error reading package index file /home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl: too many nested evaluations (infinite loop?) error reading package index file /home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl: too many nested evaluations (infinite loop?) error reading package index file /home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl: can't find package tile error reading package index file /home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl: can't find package tile error reading package index file /home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_clearlooks/pkgIndex.tcl: can't find package tile error reading package index file /home/bill/R-devel/R-build/site-library/tcltk2/tklibs/ttktheme_radiance/pkgIndex.tcl: can't find package tile ... -Bill On Thu, Sep 30, 2021 at 9:00 AM Bill Dunlap wrote: > I just tried installing forensim on R-devel/Ubuntu 20.04/WSL-2.0 without > an X server (hence DISPLAY was not set). Loading tktcl gives a warning > that Tk is not available because DISPLAY is not set. The installation hung > after the byte-compile message: > installing to > /home/bill/R-devel/R-build/site-library/00LOCK-tkrplot/00new/tkrplot/libs > ** R > ** byte-compile and prepare package for lazy loading > Warning message: > no DISPLAY variable so Tk is not available > ** help > *** installing help indices > ** building package indices > ** testing if installed package can be loaded from temporary location > Warning: no DISPLAY variable so Tk is not available > Warning: loading Rplot failed > ** checking absolute paths in shared objects and dynamic libraries > ** testing if installed package can be loaded from final location > Warning: no DISPLAY variable so Tk is not available > Warning: loading Rplot failed > ** testing if installed package keeps a record of temporary installation > path > * DONE (tkrplot) > * installing *source* package ‘forensim’ ... > ** package ‘forensim’ successfully unpacked and MD5 sums checked > ** using staged installation > ** libs > gcc -I"/home/bill/R-devel/R-build/include" -DNDEBUG -I/usr/local/include > -fpic -g -c auxilary.c -o auxilary.o > gcc -I"/home/bill/R-devel/R-build/include" -DNDEBUG -I/usr/local/include > -fpic -g -c recursFinal.c -o recursFinal.o > gcc -shared -L/usr/local/lib -o forensim.so auxilary.o recursFinal.o > installing to > /home/bill/R-devel/R-build/site-library/00LOCK-forensim/00new/forensim/libs > ** R > ** data > ** inst > ** byte-compile and prepare package for lazy loading > [hang] > > gdb gives a traceback that I think indicates that the package is trying to > plot something via tcltk at this point: > > Attaching to process 9310 > [New LWP 9315] > [Thread debugging using libthread_db enabled] > Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1". > 0x7fe20a50f560 in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so > (gdb) where > #0
Re: [R] Package installation help: Stuck at "** byte-compile and prepare package for lazy loading"
Bill-- BINGO.You have found the answer. After some testing on one of my environments where it was always hanging, connecting to the same server with an X-Sever running on my workstation did indeed allow the package to be installed. **GOOD LORD THAT’S RIDICULOUS** But at least I know.And why it doesn’t error out without X running, who knows. After a ton more research, I ALSO discovered that there IS a timeout thing I can make use of, should I decide to continue just building things and ignoring the X-Server requirement for this (and probably some other?) packages. Before executing R and installing things, set this: export _R_INSTALL_PACKAGES_ELAPSED_TIMEOUT_=500 (value is seconds). So, the previously-hanging R CMD INSTALL inside of the install.packages call will eventually die, and then move on to the next package. This is buried in the documentation but- it’s there and I confirmed it works. My example above times out a package install at 5 minutes. While knowing the X requirement is a huge win (thanks again!), I will probably stick with just using the timeout thing for what I’m trying to accomplish. Installing EVERYTHING from cran will take forever, and more than likely my VPN connection to my data center will be disconnected (thank you internal IT department) before it finishes.They have some sort of internal “you’ve been connected too long” timer that disconnects things overnight. Grr. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Package installation help: Stuck at "** byte-compile and prepare package for lazy loading"
This is a microcosm of why installing "all CRAN" packages is a bad idea. Now extend this to the other 5% of 16000+ packages that will have unclear requirements, and when you have all those installed try to update just one of the packages because one of your users has learned of a bug in that package and the cascade starts again. Then listen as another user complains that one of the dependencies updated in the first update broke something they were working on. User libraries. Project libraries (with renv). Do anything to go as fast as possible in the opposite direction from the concept presumed by this task... "universal usability". Or go help with CRAN because you are just the kind of selfless masochist that they need to keep it going and you will need a team to keep up with it. (Obligatory thanks extended here to the CRAN team.) On September 30, 2021 9:00:35 AM PDT, Bill Dunlap wrote: >I just tried installing forensim on R-devel/Ubuntu 20.04/WSL-2.0 without an >X server (hence DISPLAY was not set). Loading tktcl gives a warning that >Tk is not available because DISPLAY is not set. The installation hung >after the byte-compile message: >installing to >/home/bill/R-devel/R-build/site-library/00LOCK-tkrplot/00new/tkrplot/libs >** R >** byte-compile and prepare package for lazy loading >Warning message: >no DISPLAY variable so Tk is not available >** help >*** installing help indices >** building package indices >** testing if installed package can be loaded from temporary location >Warning: no DISPLAY variable so Tk is not available >Warning: loading Rplot failed >** checking absolute paths in shared objects and dynamic libraries >** testing if installed package can be loaded from final location >Warning: no DISPLAY variable so Tk is not available >Warning: loading Rplot failed >** testing if installed package keeps a record of temporary installation >path >* DONE (tkrplot) >* installing *source* package ‘forensim’ ... >** package ‘forensim’ successfully unpacked and MD5 sums checked >** using staged installation >** libs >gcc -I"/home/bill/R-devel/R-build/include" -DNDEBUG -I/usr/local/include > -fpic -g -c auxilary.c -o auxilary.o >gcc -I"/home/bill/R-devel/R-build/include" -DNDEBUG -I/usr/local/include > -fpic -g -c recursFinal.c -o recursFinal.o >gcc -shared -L/usr/local/lib -o forensim.so auxilary.o recursFinal.o >installing to >/home/bill/R-devel/R-build/site-library/00LOCK-forensim/00new/forensim/libs >** R >** data >** inst >** byte-compile and prepare package for lazy loading >[hang] > >gdb gives a traceback that I think indicates that the package is trying to >plot something via tcltk at this point: > >Attaching to process 9310 >[New LWP 9315] >[Thread debugging using libthread_db enabled] >Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1". >0x7fe20a50f560 in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so >(gdb) where >#0 0x7fe20a50f560 in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so >#1 0x7fe20a50f5f2 in TclNRRunCallbacks () from >/usr/lib/x86_64-linux-gnu/libtcl8.6.so >#2 0x7fe20a5e4cd9 in Tcl_PkgRequireProc () from >/usr/lib/x86_64-linux-gnu/libtcl8.6.so >#3 0x7fe20a5e4b06 in Tcl_PkgRequireEx () from >/usr/lib/x86_64-linux-gnu/libtcl8.6.so >#4 0x7fe20a976be8 in Rplot_Init (interp=0x55ae6437a6c0) at >tcltkimg.c:465 >#5 0x7fe20a5d1ee3 in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so >#6 0x7fe20a50f5f2 in TclNRRunCallbacks () from >/usr/lib/x86_64-linux-gnu/libtcl8.6.so >#7 0x7fe20b04d7f0 in dotTclObjv (args=0x55ae6489d210) at >/mnt/c/R/R-svn/trunk/src/library/tcltk/src/tcltk.c:250 >#8 0x55ae611cd5a8 in do_External (call=0x55ae6440a270, >op=0x55ae61fe1338, args=0x55ae6489d210, env=0x55ae6489d3d0) >at /mnt/c/R/R-svn/trunk/src/main/dotcode.c:576 >#9 0x55ae6122a0b3 in bcEval (body=0x55ae6440a190, rho=0x55ae6489d3d0, >useCache=TRUE) >at /mnt/c/R/R-svn/trunk/src/main/eval.c:7128 >#10 0x55ae6121644a in Rf_eval (e=0x55ae6440a190, rho=0x55ae6489d3d0) at >/mnt/c/R/R-svn/trunk/src/main/eval.c:740 >#11 0x55ae61215fda in forcePromise (e=0x55ae6489d398) at >/mnt/c/R/R-svn/trunk/src/main/eval.c:568 >#12 0x55ae61220b80 in FORCE_PROMISE (value=0x55ae6489d398, >symbol=0x55ae62282a08, rho=0x55ae6489d248, >keepmiss=FALSE) at /mnt/c/R/R-svn/trunk/src/main/eval.c:5149 >#13 0x55ae61220d2f in getvar (symbol=0x55ae62282a08, >rho=0x55ae6489d248, dd=FALSE, keepmiss=FALSE, >vcache=0x7fe20b2ec1f0, sidx=1) at >/mnt/c/R/R-svn/trunk/src/main/eval.c:5190 > >Henrik, can you reproduce this if you undefine DISPLAY? > >-Bill > > > > >On Wed, Sep 29, 2021 at 7:48 PM Henrik Bengtsson >wrote: > >> I just tried on an up-to-date CentOS 7 with R 4.1.1 built from source >> using gcc 8.3.1 (from SCL devtoolset-8; so not the default gcc 4.8.5), >> and it works there. If of any help, here's the output when installing >> to user's personal package library: >> >> > chooseCRANmirror(ind = 1) >> >
Re: [R] Package installation help: Stuck at "** byte-compile and prepare package for lazy loading"
I just tried installing forensim on R-devel/Ubuntu 20.04/WSL-2.0 without an
X server (hence DISPLAY was not set). Loading tktcl gives a warning that
Tk is not available because DISPLAY is not set. The installation hung
after the byte-compile message:
installing to
/home/bill/R-devel/R-build/site-library/00LOCK-tkrplot/00new/tkrplot/libs
** R
** byte-compile and prepare package for lazy loading
Warning message:
no DISPLAY variable so Tk is not available
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Warning: no DISPLAY variable so Tk is not available
Warning: loading Rplot failed
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: no DISPLAY variable so Tk is not available
Warning: loading Rplot failed
** testing if installed package keeps a record of temporary installation
path
* DONE (tkrplot)
* installing *source* package ‘forensim’ ...
** package ‘forensim’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/home/bill/R-devel/R-build/include" -DNDEBUG -I/usr/local/include
-fpic -g -c auxilary.c -o auxilary.o
gcc -I"/home/bill/R-devel/R-build/include" -DNDEBUG -I/usr/local/include
-fpic -g -c recursFinal.c -o recursFinal.o
gcc -shared -L/usr/local/lib -o forensim.so auxilary.o recursFinal.o
installing to
/home/bill/R-devel/R-build/site-library/00LOCK-forensim/00new/forensim/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
[hang]
gdb gives a traceback that I think indicates that the package is trying to
plot something via tcltk at this point:
Attaching to process 9310
[New LWP 9315]
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
0x7fe20a50f560 in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so
(gdb) where
#0 0x7fe20a50f560 in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so
#1 0x7fe20a50f5f2 in TclNRRunCallbacks () from
/usr/lib/x86_64-linux-gnu/libtcl8.6.so
#2 0x7fe20a5e4cd9 in Tcl_PkgRequireProc () from
/usr/lib/x86_64-linux-gnu/libtcl8.6.so
#3 0x7fe20a5e4b06 in Tcl_PkgRequireEx () from
/usr/lib/x86_64-linux-gnu/libtcl8.6.so
#4 0x7fe20a976be8 in Rplot_Init (interp=0x55ae6437a6c0) at
tcltkimg.c:465
#5 0x7fe20a5d1ee3 in ?? () from /usr/lib/x86_64-linux-gnu/libtcl8.6.so
#6 0x7fe20a50f5f2 in TclNRRunCallbacks () from
/usr/lib/x86_64-linux-gnu/libtcl8.6.so
#7 0x7fe20b04d7f0 in dotTclObjv (args=0x55ae6489d210) at
/mnt/c/R/R-svn/trunk/src/library/tcltk/src/tcltk.c:250
#8 0x55ae611cd5a8 in do_External (call=0x55ae6440a270,
op=0x55ae61fe1338, args=0x55ae6489d210, env=0x55ae6489d3d0)
at /mnt/c/R/R-svn/trunk/src/main/dotcode.c:576
#9 0x55ae6122a0b3 in bcEval (body=0x55ae6440a190, rho=0x55ae6489d3d0,
useCache=TRUE)
at /mnt/c/R/R-svn/trunk/src/main/eval.c:7128
#10 0x55ae6121644a in Rf_eval (e=0x55ae6440a190, rho=0x55ae6489d3d0) at
/mnt/c/R/R-svn/trunk/src/main/eval.c:740
#11 0x55ae61215fda in forcePromise (e=0x55ae6489d398) at
/mnt/c/R/R-svn/trunk/src/main/eval.c:568
#12 0x55ae61220b80 in FORCE_PROMISE (value=0x55ae6489d398,
symbol=0x55ae62282a08, rho=0x55ae6489d248,
keepmiss=FALSE) at /mnt/c/R/R-svn/trunk/src/main/eval.c:5149
#13 0x55ae61220d2f in getvar (symbol=0x55ae62282a08,
rho=0x55ae6489d248, dd=FALSE, keepmiss=FALSE,
vcache=0x7fe20b2ec1f0, sidx=1) at
/mnt/c/R/R-svn/trunk/src/main/eval.c:5190
Henrik, can you reproduce this if you undefine DISPLAY?
-Bill
On Wed, Sep 29, 2021 at 7:48 PM Henrik Bengtsson
wrote:
> I just tried on an up-to-date CentOS 7 with R 4.1.1 built from source
> using gcc 8.3.1 (from SCL devtoolset-8; so not the default gcc 4.8.5),
> and it works there. If of any help, here's the output when installing
> to user's personal package library:
>
> > chooseCRANmirror(ind = 1)
> > install.packages("forensim")
> Installing package into
> ‘/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8’
> (as ‘lib’ is unspecified)
> trying URL 'https://cloud.r-project.org/src/contrib/forensim_4.3.tar.gz'
> Content type 'application/x-gzip' length 84232 bytes (82 KB)
> ==
> downloaded 82 KB
>
> * installing *source* package ‘forensim’ ...
> ** package ‘forensim’ successfully unpacked and MD5 sums checked
> ** using staged installation
> ** libs
> gcc -I"/software/c4/cbi/software/R-4.1.1-gcc8/lib64/R/include"
> -DNDEBUG -I/usr/local/include -fpic -g -O2 -c auxilary.c -o
> auxilary.o
> gcc -I"/software/c4/cbi/software/R-4.1.1-gcc8/lib64/R/include"
> -DNDEBUG -I/usr/local/include -fpic -g -O2 -c recursFinal.c -o
> recursFinal.o
> gcc -shared -L/software/c4/cbi/software/R-4.1.1-gcc8/lib64/R/lib
> -L/usr/local/lib64 -o forensim.so auxilary.o recursFinal.o
> -L/software/c4/cbi/software/R-4.1.1-gcc8/lib64/R/lib -lR
> installing
Re: [R] Package installation help: Stuck at "** byte-compile and prepare package for lazy loading"
(As I said, I'll try anything!) OK, so I went ahead to get the scl devtoolset, and rebuilt R 4.1.1 with the same exact gcc you used. But- same result for me. Hung at the byte-compile step when installing that one package, no error, no messages, no logs. > -Original Message- > From: Henrik Bengtsson > Sent: Wednesday, September 29, 2021 9:43 PM > To: Brodie, Kent > Cc: r-help@r-project.org > Subject: Re: [R] Package installation help: Stuck at "** byte-compile and > prepare package for lazy loading" > > ATTENTION: This email originated from a sender outside of MCW. Use caution > when clicking on links or opening attachments. > > > I just tried on an up-to-date CentOS 7 with R 4.1.1 built from source using > gcc > 8.3.1 (from SCL devtoolset-8; so not the default gcc 4.8.5), and it works > there. > If of any help, here's the output when installing to user's personal package > library: > __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Package installation help: Stuck at "** byte-compile and prepare package for lazy loading"
I just tried on an up-to-date CentOS 7 with R 4.1.1 built from source
using gcc 8.3.1 (from SCL devtoolset-8; so not the default gcc 4.8.5),
and it works there. If of any help, here's the output when installing
to user's personal package library:
> chooseCRANmirror(ind = 1)
> install.packages("forensim")
Installing package into
‘/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/forensim_4.3.tar.gz'
Content type 'application/x-gzip' length 84232 bytes (82 KB)
==
downloaded 82 KB
* installing *source* package ‘forensim’ ...
** package ‘forensim’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/software/c4/cbi/software/R-4.1.1-gcc8/lib64/R/include"
-DNDEBUG -I/usr/local/include -fpic -g -O2 -c auxilary.c -o
auxilary.o
gcc -I"/software/c4/cbi/software/R-4.1.1-gcc8/lib64/R/include"
-DNDEBUG -I/usr/local/include -fpic -g -O2 -c recursFinal.c -o
recursFinal.o
gcc -shared -L/software/c4/cbi/software/R-4.1.1-gcc8/lib64/R/lib
-L/usr/local/lib64 -o forensim.so auxilary.o recursFinal.o
-L/software/c4/cbi/software/R-4.1.1-gcc8/lib64/R/lib -lR
installing to
/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/00LOCK-forensim/00new/forensim/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (forensim)
The downloaded source packages are in
‘/scratch/henrik/RtmpYFlQyS/downloaded_packages’
You could also try to install it via 'R CMD INSTALL' and try with
different options disabled to maybe narrow in on what's going on.
My $.02
/Henrik
On Wed, Sep 29, 2021 at 6:37 PM Brodie, Kent via R-help
wrote:
>
> Hey everyone! So, I've been asked by one of our researchers to install "all"
> cran packages on one of our servers.Yeah, it's a bit much (and clearly,
> not everything will install correctly due to various missing tidbits), but it
> will go a long way to having to constantly respond to install requests of
> various packages. OK, fine.
>
> Anyway, I have tried this, and things proceed nicely for several hours until
> the process gets completely and absolutely stuck. I have tried several
> things, for example trying newer versions of R, and even repeating the
> process on a CentOS 8 server instead of where my stuff is now (CentOS 7).
>
> While re-trying one of my newer attempts at this, I decided to focus on the
> very first place where it hangs. It dies on package "forensim".It's a
> slightly older package, and I don't see anything particularly special about
> it.The text below is where it hangs.The install "R" process doing
> this is whizzing at 100%, but no progress, no output, no errors. Nothing in
> the system logs.
>
> On new "R" installs, with either operating system (CentOS 7, CentOS 8) and
> even different versions of "R" (up to including 4.1.1), I get the same result
> when just attempting to install this ONE package.(and my guess, there's
> more packages out there that may bite me the same way).
>
> I am seeking any recommendations on how I can get past this? A debug
> option? A timeout of sorts so things will move along to the next package
> when attempting to install a ton, or...? I'm of course willing to try
> anything. It's stupidly frustrating.I'd be OK if it errored out and
> moved on. But it... hangs.
>
> Here's the latter part of the install attempt of this one package. This
> latest attempt has been stuck on that last line now for 5 hours and counting.
>
> * DONE (tkrplot)
> Making 'packages.html' ... done
> * installing *source* package 'forensim' ...
> ** package 'forensim' successfully unpacked and MD5 sums checked
> ** using staged installation
> ** libs
> gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -g
> -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2
> -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong
> -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1
> -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic
> -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c
> auxilary.c -o auxilary.o
> gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fpic -O2 -g
> -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2
> -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong
> -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1
> -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic
>
Re: [R] Package installation for 4.1 on windows.
Dear Duncan, Thank you. Indeed I did had the R_LIBS_USER env. variable defined. Best regards Witold On Mon, 7 Jun 2021 at 17:48, Duncan Murdoch wrote: > > On 07/06/2021 10:37 a.m., Witold E Wolski wrote: > > Hello, > > > > I just installed R 4.1 and now trying to update install some packages. > > > > R version 4.1.0 (2021-05-18) -- "Camp Pontanezen" > > Copyright (C) 2021 The R Foundation for Statistical Computing > > > > But when installing packages I read: > > > > Installing packages into ‘C:/Users/wolski/Documents/R/win-library/4.0’ > > > > Should not be a win-library/4.1. package directory be used by default? > > > > I suspect something in your local setup specifies that directory. The > usual place to install is the directory where R was installed; it only > switches to the user home directory if that fails, or the user requests it. > > Duncan Murdoch -- Witold Eryk Wolski __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Package installation for 4.1 on windows.
On 07/06/2021 10:37 a.m., Witold E Wolski wrote: Hello, I just installed R 4.1 and now trying to update install some packages. R version 4.1.0 (2021-05-18) -- "Camp Pontanezen" Copyright (C) 2021 The R Foundation for Statistical Computing But when installing packages I read: Installing packages into ‘C:/Users/wolski/Documents/R/win-library/4.0’ Should not be a win-library/4.1. package directory be used by default? I suspect something in your local setup specifies that directory. The usual place to install is the directory where R was installed; it only switches to the user home directory if that fails, or the user requests it. Duncan Murdoch __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Package installation problem
Hi John, This is a bit off-topic for this mailing list as your issue is a linux, specifically Fedora, issue, and not R. I don't use Fedora but I did a quick Google search on fedora missing package .pc file and that came back with a lot of hits. This one in particular should be a good place to start. It gives some explanation as to when installation will result in a .pc file (seems to relate to -dev versions). https://stackoverflow.com/questions/33050517/supply-pc-file-for-pkg-config HTH, Eric On Fri, May 29, 2020 at 8:03 AM John via R-help wrote: > > I'm not certain just what this problem is. Trying to install the > "curl" package, which "tseries" wants results in the following error: > > > Package libcurl was not found in the pkg-config search path. > Perhaps you should add the directory containing `libcurl.pc' > to the PKG_CONFIG_PATH environment variable > Package 'libcurl', required by 'virtual:world', not found > Package libcurl was not found in the pkg-config search path. > Perhaps you should add the directory containing `libcurl.pc' > to the PKG_CONFIG_PATH environment variable > Package 'libcurl', required by 'virtual:world', not found > Using PKG_CFLAGS= > Using PKG_LIBS=-lcurl > - ANTICONF ERROR --- > Configuration failed because libcurl was not found. Try installing: > * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc) > * rpm: libcurl-devel (Fedora, CentOS, RHEL) > * csw: libcurl_dev (Solaris) > If libcurl is already installed, check that 'pkg-config' is in your > PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config > is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: > R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' > > ERROR: configuration failed for package ‘curl’ > * removing ‘/home/john/R/x86_64-redhat-linux-gnu-library/3.6/curl’ > Warning in install.packages : > installation of package ‘curl’ had non-zero exit status > > > However, libcurl is installed, installed. What does seem to missing is > "libcurl.pc". The ../pkgconfig directory contains a number of > different *.pc files, but not that one. I'm asking here first because > someone else may have already encountered and solved this. I'm running > Fedora 32 with kde on a 4 X AMD system. I just updated Fedora. > > JWDougherty > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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 -- To UNSUBSCRIBE and more, see 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] Package installation problem
On Fri, 29 May 2020 08:47:35 +0300 Eric Berger wrote: > Hi John, > This is a bit off-topic for this mailing list as your issue is a > linux, specifically Fedora, issue, and not R. > I don't use Fedora but I did a quick Google search on > > fedora missing package .pc file > > and that came back with a lot of hits. This one in particular should > be a good place to start. > It gives some explanation as to when installation will result in a .pc > file (seems to relate to -dev versions). > > https://stackoverflow.com/questions/33050517/supply-pc-file-for-pkg-config > > HTH, > Eric > Thanks Eric. I wasn't sure where the hick-up was (R or Fedora). The library the error message said couldn't be found was right where it belonged. The first thing I did was check that the *devel file was in the lib64 directory, and it was. The pc file was the only vagrant, and it was not on the system at all. I'm going to try to get sense out of Fedora about this because with "devel" files it should have been. When I reinstalled this latest time from the command line, the "pc" file was placed just as it should have been. The threads on stackoverflow are four years old, so this has been around in one form or another for a while. Again, thanks, JWDougherty __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Package installation problem
On Fri, 29 May 2020 18:36:39 +0200 Martin Møller Skarbiniks Pedersen wrote: > sudo dnf install libcurl-devel Martin, I was going to say I had already done that more than once, using both the command line and the new "dnfdragora" package manager, but then decided, "what the heck. I'll try again." This time the *.pc file appeared where it belonged. So, thank you. Evidently, I tweaked the right thing, whatever it was, right before I gave up and wrote my request, thinking that if FC32 broke my tseries installation, it would have broken others. As usual the r-list is quicker, and much more helpful. I'll pass this along to Fedora, since there seems to be a problem of some kind. libcurl-devel was already installed on my system, the first thing I ckecked. It was just the *.pc file that was the problem. Thanks, JWDougherty __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Package installation problem
On Fri, 29 May 2020 at 07:03, John via R-help wrote: > I'm not certain just what this problem is. Trying to install the > "curl" package, which "tseries" wants results in the following error: > > > Package libcurl was not found in the pkg-config search path. > Perhaps you should add the directory containing `libcurl.pc' > Just run: sudo dnf install libcurl-devel Regards Martin [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Package installation problem
The library alone is not enough... you have to have the development headers for compiling code against the library. On May 28, 2020 10:03:18 PM PDT, John via R-help wrote: >I'm not certain just what this problem is. Trying to install the >"curl" package, which "tseries" wants results in the following error: > > >Package libcurl was not found in the pkg-config search path. >Perhaps you should add the directory containing `libcurl.pc' >to the PKG_CONFIG_PATH environment variable >Package 'libcurl', required by 'virtual:world', not found >Package libcurl was not found in the pkg-config search path. >Perhaps you should add the directory containing `libcurl.pc' >to the PKG_CONFIG_PATH environment variable >Package 'libcurl', required by 'virtual:world', not found >Using PKG_CFLAGS= >Using PKG_LIBS=-lcurl >- ANTICONF ERROR --- >Configuration failed because libcurl was not found. Try installing: > * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc) > * rpm: libcurl-devel (Fedora, CentOS, RHEL) > * csw: libcurl_dev (Solaris) >If libcurl is already installed, check that 'pkg-config' is in your >PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config >is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: >R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' > >ERROR: configuration failed for package ‘curl’ >* removing ‘/home/john/R/x86_64-redhat-linux-gnu-library/3.6/curl’ >Warning in install.packages : > installation of package ‘curl’ had non-zero exit status > > >However, libcurl is installed, installed. What does seem to missing is >"libcurl.pc". The ../pkgconfig directory contains a number of >different *.pc files, but not that one. I'm asking here first because >someone else may have already encountered and solved this. I'm running >Fedora 32 with kde on a 4 X AMD system. I just updated Fedora. > >JWDougherty > >__ >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >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. -- Sent from my phone. Please excuse my brevity. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Package installation
On 09/07/2018 6:18 AM, Steven Yen wrote: I have had trouble installing packages (e.g., car, aod) in some computers (such as computers in the student lab) but no problem in my own laptop. Installation typically goes through, but after I got out and back in R (and RStudios), the error message says "packages xxx not available". That is, earlier installation of the packages did not stay (despite the successful installation message). I went back as far as R3.0.3 and there is no problem. Does this tell anyone what may be going on? Thanks. The most common package installation problem in Windows is using different permissions to install R and the packages. Typically R is installed as administrator, but the packages are not. This means the packages can't be installed to the system library, so they get installed in a user's personal library, and the user probably may need to set .libPaths() explicitly to see them. To check for this, print .libPaths() just after installing the packages, and again when starting a new session. If the printed list of paths is different, you'll have problems. Duncan Murdoch __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] package installation
There is the directory that the compressed file gets downloaded (Temp), and
there is another directory where the the extracted files are "installed"
("library"). You can read all about this in the "R Administration and
Installation Manual" that comes with R.
The message about the download directory occurs when the library cannot be
written to. I am aware of two issues that can interfere with that step on
Windows:
A) You have multiple copies of R open on Windows with existing packages open.
Install packages with only one copy of R open.
B) You ran R or the setup program with Administrator privileges at some point,
and some or all of the packages in your user library (usually
C:\Users\Yourname\Documents\R\win-library) have abnormal permissions. Cleaning
up such a mess usually involves using Administrator privileges to completely
remove C:\Users\Yourname\Documents\R\ and then starting R and installing all
your packages again.
--
Sent from my phone. Please excuse my brevity.
On March 6, 2018 12:57:17 AM PST, Kabouch Nourdine via R-help
wrote:
>Hi, When installing packages is there any preferable path.
>In my case I got this message in R consol:The downloaded binary
>packages are in C: ~\ Temp \ RtmpQLTD5e \ downloaded_packages
>this is a temporary files that I delete every time.
>Is it possible to install packages in a specefic folder.
> [[alternative HTML version deleted]]
>
>__
>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>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 -- To UNSUBSCRIBE and more, see
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] package installation
Hi If you installed through install.packages you could specify lib see help page lib character vector giving the library directories where to install the packages. Recycled as needed. If missing, defaults to the first element of .libPaths(). But I believe you hardly need to do it. You probably do not know how to handle different locations for different packages and if you scatter packages within your computer you could have problems with invoking them. Cheers Petr > -Original Message- > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Kabouch > Nourdine via R-help > Sent: Tuesday, March 6, 2018 9:57 AM > To: r-help@r-project.org > Subject: [R] package installation > > Hi, When installing packages is there any preferable path. > In my case I got this message in R consol:The downloaded binary packages are > in C: ~\ Temp \ RtmpQLTD5e \ downloaded_packages this is a temporary > files that I delete every time. > Is it possible to install packages in a specefic folder. > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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. Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny pouze jeho adresátům. Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze svého systému. Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat. Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či zpožděním přenosu e-mailu. V případě, že je tento e-mail součástí obchodního jednání: - vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu. - a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce s dodatkem či odchylkou. - trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným dosažením shody na všech jejích náležitostech. - odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi či osobě jím zastoupené známá. This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients. If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system. If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner. The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email. In case that this e-mail forms part of business dealings: - the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning. - if the e-mail contains an offer, the recipient is entitled to immediately accept such offer; The sender of this e-mail (offer) excludes any acceptance of the offer on the part of the recipient containing any amendment or variation. - the sender insists on that the respective contract is concluded only upon an express mutual agreement on all its aspects. - the sender of this e-mail informs that he/she is not authorized to enter into any contracts on behalf of the company except for cases in which he/she is expressly authorized to do so in writing, and such authorization or power of attorney is submitted to the recipient or the person represented by the recipient, or the existence of such authorization is known to the recipient of the person represented by the recipient. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Package Installation: Repository for 3.2.1
On Oct 5, 2015, at 1:36 AM, Jutta Wrage wrote: > Hi! > > Guess, I got in trouble somehow now. > Not sure whether this question is placed well in this list. Do I have to ask > my question in R-SIG-MAC? > > Installed R version: 3.2.1 for OS X up to 10.8 > > I did update the package list from within R application and installed some > new package versions. > > Now I get a warning: > > Warnmeldung: > Paket ‘knitr’ wurde unter R Version 3.2.2 erstellt > 3.2.2 is only available for OS X up from 10.9 > > 1. Which URL do I have to put in preferences to get only packages for my > Computer? > 2. How do I repair things now? - If needed It's only a warning. There's no simple method for getting binary packages for older R versions. Generally packages built with a minor version upgrade will still work with one version back (but I have no experience doing that with knitr). You can build older packages from the source files in the Archives if needed. Things might become more problematic in the future if you stay with OSX version 10.8, because I don't know if the dual SnowLeppard and Mavericks forks will continue to be maintained. It was announced very recently that the build machine was now running El Capitan, i.e. OSX 10.11 You should ask Mac specific questions on R-SIG-Mac. > >> library() > tells me everything is in > ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library’ > > Jutta > David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] package installation failure virtualisation environment
On 2014-10-15 09:13, Sven E. Templer wrote: did you check the connection in R via for example: head(readLines(http://cran.r-project.org/web/licenses/GPL-3;)) which should yield: [1] GNU GENERAL PUBLIC LICENSE [2]Version 3, 29 June 2007 [3] [4] Copyright (C) 2007 Free Software Foundation, Inc. http://fsf.org/ [5] Everyone is permitted to copy and distribute verbatim copies [6] of this license document, but changing it is not allowed. Yes, this result is seen. __ 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] package installation failure virtualisation environment
On 2014-10-15 15:36, William Dunlap wrote: Have you looked at recent entries in the system log files in /var/log, especially /var/log/kern.log? No such log file exist and other files in the directory do not make reference to R and any general errors (e.g. internet access). __ 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] package installation failure virtualisation environment
The log files may not have the name of the process (R), but only its process number. A good way to look at the log files in /var/log is to cause your 'Kill' problem then use 'ls -lstA' or 'ls -lstrA' in /var/log to see which ones changed recently. Bill Dunlap TIBCO Software wdunlap tibco.com On Thu, Oct 16, 2014 at 2:03 AM, r...@openmailbox.org wrote: On 2014-10-15 15:36, William Dunlap wrote: Have you looked at recent entries in the system log files in /var/log, especially /var/log/kern.log? No such log file exist and other files in the directory do not make reference to R and any general errors (e.g. internet access). __ 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] package installation failure virtualisation environment
On 2014-10-14 15:40, Sven E. Templer wrote: Prevent graphic menues with: options(menu.graphics = FALSE) Same response after a pause: 'Killed' or and define repositories: options(repos = c(CRAN = http://cran.r-project.org;)) Same response after a pause: 'Killed' __ 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] package installation failure virtualisation environment
did you check the connection in R via for example: head(readLines(http://cran.r-project.org/web/licenses/GPL-3;)) which should yield: [1] GNU GENERAL PUBLIC LICENSE [2]Version 3, 29 June 2007 [3] [4] Copyright (C) 2007 Free Software Foundation, Inc. http://fsf.org/ [5] Everyone is permitted to copy and distribute verbatim copies [6] of this license document, but changing it is not allowed. On 15 October 2014 10:51, r...@openmailbox.org wrote: On 2014-10-14 15:40, Sven E. Templer wrote: Prevent graphic menues with: options(menu.graphics = FALSE) Same response after a pause: 'Killed' or and define repositories: options(repos = c(CRAN = http://cran.r-project.org;)) Same response after a pause: 'Killed' __ 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] package installation failure virtualisation environment
Have you looked at recent entries in the system log files in /var/log, especially /var/log/kern.log? Bill Dunlap TIBCO Software wdunlap tibco.com On Wed, Oct 15, 2014 at 1:51 AM, r...@openmailbox.org wrote: On 2014-10-14 15:40, Sven E. Templer wrote: Prevent graphic menues with: options(menu.graphics = FALSE) Same response after a pause: 'Killed' or and define repositories: options(repos = c(CRAN = http://cran.r-project.org;)) Same response after a pause: 'Killed' __ 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 provide commented, minimal, self-contained, reproducible code.
Re: [R] package installation failure virtualisation environment
Prevent graphic menues with: options(menu.graphics = FALSE) or and define repositories: options(repos = c(CRAN = http://cran.r-project.org;)) On 14 October 2014 17:00, r...@openmailbox.org wrote: Subscribers, A version of R is installed in a virtual machine, which has complete internet access via the host. The following error occurs when a package is selected: install.packages([packagename], dependencies=TRUE) --- Please select a CRAN mirror for use in this session --- Killed The error also occurs with: install.packages() The process is killed as shown previously (but not the R session), after selection of a package in the Tcl/tk dialogue window. The error occurs both as root and normal user. Any suggestions please to solve? R.version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 3 minor 1.1 year 2014 month 07 day10 svn rev66115 language R version.string R version 3.1.1 (2014-07-10) nickname Sock it to Me __ 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 provide commented, minimal, self-contained, reproducible code.
Re: [R] Package installation and path.package
On 09/09/2013 02:09, David Winsemius wrote: On Sep 8, 2013, at 8:00 AM, Simon Zehnder wrote: Dear R-Users and R-Devels, I am writing right now my own package that makes use of 'tempfile' and there within with 'path.package'. When I install it, I get the error: Error in path.package(mypackage) : none of the packages are loaded. I understand the error, but I would like to have a workaround. How can I give the path to the package I am actually installing without getting this error? (We do not have the code so this is speculation.) Your packages should be assumed to be available in one of the directories in .libPaths() Not until the package is fully installed. We do have no idea what is going on here ... and R-devel seems the appropriate list. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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] Package installation and path.package
I am following your suggestion and move this discussion to the R-devel list. Best Simon On Sep 9, 2013, at 7:58 AM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On 09/09/2013 02:09, David Winsemius wrote: On Sep 8, 2013, at 8:00 AM, Simon Zehnder wrote: Dear R-Users and R-Devels, I am writing right now my own package that makes use of 'tempfile' and there within with 'path.package'. When I install it, I get the error: Error in path.package(mypackage) : none of the packages are loaded. I understand the error, but I would like to have a workaround. How can I give the path to the package I am actually installing without getting this error? (We do not have the code so this is speculation.) Your packages should be assumed to be available in one of the directories in .libPaths() Not until the package is fully installed. We do have no idea what is going on here ... and R-devel seems the appropriate list. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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] Package installation and path.package
On Sep 8, 2013, at 8:00 AM, Simon Zehnder wrote: Dear R-Users and R-Devels, I am writing right now my own package that makes use of 'tempfile' and there within with 'path.package'. When I install it, I get the error: Error in path.package(mypackage) : none of the packages are loaded. I understand the error, but I would like to have a workaround. How can I give the path to the package I am actually installing without getting this error? (We do not have the code so this is speculation.) Your packages should be assumed to be available in one of the directories in .libPaths() -- David Winsemius Alameda, CA, USA __ 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] package installation error in Mac OS X
Hi, Did you install the Xcode Developer Tools on your machine? HTH, Pascal Le 04/02/2013 03:14, londonphd a écrit : Hi, I installed R in Mac OS X, and trying to installa package. R is not allowing me to install the meboot package. Below is the exact message I got from R: installation of package ‘meboot’ had non-zero exit status trying URL 'http://cran.ma.imperial.ac.uk/src/contrib/meboot_1.1-5.tar.gz' Content type 'application/x-gzip' length 411681 bytes (402 Kb) opened URL == downloaded 402 Kb * installing *source* package ‘meboot’ ... ** package ‘meboot’ successfully unpacked and MD5 sums checked ** libs *** arch - i386 sh: make: command not found ERROR: compilation failed for package ‘meboot’ * removing ‘/Users/ravshonbek/Library/R/2.15/library/meboot’ The downloaded source packages are in ‘/private/var/folders/c7/jrjv78_x6f53l3sw_w715gk0gn/T/RtmphnbWao/downloaded_packages’ Can anyone please shed some light on it? Thank you -- View this message in context: http://r.789695.n4.nabble.com/package-installation-error-in-Mac-OS-X-tp4657422.html Sent from the R help mailing list archive at Nabble.com. __ 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 provide commented, minimal, self-contained, reproducible code.
Re: [R] package installation problem.
Easiest answer would be to update to a more recent version of R: I'm not sure binaries are available for 2.10.z anymore. Cheers, M On Thu, Sep 13, 2012 at 12:35 PM, bokaha guy bokah...@yahoo.fr wrote: Dear friends from the R-community, I am djipie, bokaha and live in Germany. I am a student and user of R. During the installation of the package Metrics I had a pronlem as shown below: install.packages(Metrics) Warnung in install.packages(Metrics) : Argument 'lib' fehlt: nutze 'C:\Users\Guyso\Documents/R/win-library/2.10' --- Bitte einen CRAN Spiegel für diese Sitzung auswählen --- Warnung: kann nicht auf den Index für das Repository http://ftp.yalwa.org/cran/bin/windows/contrib/2.10 zugreifen Warnung: kann nicht auf den Index für das Repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.10 zugreifen Warnmeldung: In getDependencies(pkgs, dependencies, available, lib) : package ‘Metrics’ is not available For your help I thank you in advance. Friendly greetings Djipie,bokaha [[alternative HTML version deleted]] __ 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 provide commented, minimal, self-contained, reproducible code.
Re: [R] package installation problem.
On 13.09.2012 17:14, R. Michael Weylandt wrote: Easiest answer would be to update to a more recent version of R: I'm not sure binaries are available for 2.10.z anymore. R-2.10.x is no longer supported, but binaries that were built years ago for that version of R are still available on CRAN mirrors. The mirror selected is just not working, hence use another mirror. The other message shows that the CRAN extras repository does not provide binaries for such outdated versions of R. Anyway, upgrading is highly recommended. Best, Uwe Ligges Cheers, M On Thu, Sep 13, 2012 at 12:35 PM, bokaha guy bokah...@yahoo.fr wrote: Dear friends from the R-community, I am djipie, bokaha and live in Germany. I am a student and user of R. During the installation of the package Metrics I had a pronlem as shown below: install.packages(Metrics) Warnung in install.packages(Metrics) : Argument 'lib' fehlt: nutze 'C:\Users\Guyso\Documents/R/win-library/2.10' --- Bitte einen CRAN Spiegel für diese Sitzung auswählen --- Warnung: kann nicht auf den Index für das Repository http://ftp.yalwa.org/cran/bin/windows/contrib/2.10 zugreifen Warnung: kann nicht auf den Index für das Repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.10 zugreifen Warnmeldung: In getDependencies(pkgs, dependencies, available, lib) : package ‘Metrics’ is not available For your help I thank you in advance. Friendly greetings Djipie,bokaha [[alternative HTML version deleted]] __ 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 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 provide commented, minimal, self-contained, reproducible code.
Re: [R] Package installation errors
On 06.09.2012 20:58, Santosh wrote: Dear Rxperts.. I am trying to install a few packages in R (version 2.14.2) on a *64-bit Window 7* workstation. Some of the errors are posted below.. Both 32-bit and 64-bit versions of R were installed. I did not get errors while installing packages through *32-bit R*, except that it could not update some of the packages (already installed with 64-bit R) *A*) When I start *64-bit R (2.14.2)* Loading required package: tcltk Loading required package: R2HTML Error in structure(.External(dotTcl, ..., PACKAGE = tcltk), class = tclObj) : [tcl] invalid command name dde. In addition: Warning message: In tclRequire(dde, warn = TRUE) : Tcl package 'dde' not found options(repos='http://cran.stat.ucla.edu') install.packages(dde,dependencies=T) Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ‘dde’ is not available (for R version 2.14.2) *B)* While installing rJava from *64-bit R (2.14.2)* install.packages(rJava,repos='http://cran.stat.ucla.edu') trying URL ' http://cran.stat.ucla.edu/bin/windows/contrib/2.14/rJava_0.9-3.zip' Content type 'application/zip' length 745867 bytes (728 Kb) opened URL downloaded 728 Kb package ‘rJava’ successfully unpacked and MD5 sums checked The downloaded packages are in C:\Users\santosh\AppData\Local\Temp\RtmpsJ5HoF\downloaded_packages library(rJava) Error : .onLoad failed in loadNamespace() for 'rJava', details: call: fun(libname, pkgname) error: JAVA_HOME cannot be determined from the Registry Error: package/namespace load failed for ‘rJava’ *B*) While installing XML *64-bit R (2.14.2)* install.packages(XML,repos='http://www.omegahat.org/R') Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ‘XML’ is not available (for R version 2.14.2) XML: This is because Omegahat does not host a binary version for R-2.14.x for Windows. Use the version from CRAN extras. Using *64-bit R (2.14.2), *I could not install other packages like xlsx that depend on rJava. Installing the latest JRE has not seemed to help. You need a 64-bit version of Java for rJava running on a 64-bit R, I guess you only have a 32-bit Java installed. Uwe Ligges Any suggestions/solutions are most welcome Thanks and regards, Santosh [[alternative HTML version deleted]] __ 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 provide commented, minimal, self-contained, reproducible code.
Re: [R] package installation error in unix
Hello,
There is a mistake. Type
install.packages(hdf5)
instead of
installed.packages(hdf5)
in order to install a package.
Best Regards,
Passcal
Le 19/07/2012 17:02, uday a écrit :
Hi,
Recently I have installed R in my Linux operating system , after
installation I was trying to install some packages and I was getting error
installed.packages(hdf5)
{ Package LibPath Version Priority Depends
Imports LinkingTo Suggests Enhances OS_type
License Archs Built}
this is first time that I am using R in Linux, could somebody please tell me
how to fix this error .
I am using R version 2.14.1 (2011-12-22)
Thank you
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Re: [R] package installation error in unix
Hi
Thanks for reply
after usinginstall.packages(hdf5)
I get error
{Installing package(s) into ‘/home/uday/R/x86_64-pc-linux-gnu-library/2.14’
(as ‘lib’ is unspecified)
trying URL
'http://cran.revolutionanalytics.com/src/contrib/hdf5_1.6.9.tar.gz'
Content type 'application/x-gzip' length 50870 bytes (49 Kb)
opened URL
==
downloaded 49 Kb
* installing *source* package ‘hdf5’ ...
** package ‘hdf5’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for library containing inflate... -lz
checking for library containing H5open... no
configure: error: Can't find HDF5
ERROR: configuration failed for package ‘hdf5’
* removing ‘/home/uday/R/x86_64-pc-linux-gnu-library/2.14/hdf5’
Warning in install.packages :
installation of package ‘hdf5’ had non-zero exit status
The downloaded packages are in
‘/tmp/Rtmp7Ot3Yl/downloaded_packages’ }
So what is this non-zero exit status ?
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Re: [R] package installation error in unix
The error message is here: configure: error: Can't find HDF5
The hdf5 package is an interface to the HDF5 library, so you need to
install hdf5 and hdf5-devel through your package manager (yum or
apt-get or whatever you use to install things on your linux distro).
Or you can get it straight from the source:
http://www.hdfgroup.org/HDF5/release/obtain5.html
Sarah
On Thu, Jul 19, 2012 at 8:14 AM, uday uday_143...@hotmail.com wrote:
Hi
Thanks for reply
after usinginstall.packages(hdf5)
I get error
{Installing package(s) into ‘/home/uday/R/x86_64-pc-linux-gnu-library/2.14’
(as ‘lib’ is unspecified)
trying URL
'http://cran.revolutionanalytics.com/src/contrib/hdf5_1.6.9.tar.gz'
Content type 'application/x-gzip' length 50870 bytes (49 Kb)
opened URL
==
downloaded 49 Kb
* installing *source* package ‘hdf5’ ...
** package ‘hdf5’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for library containing inflate... -lz
checking for library containing H5open... no
configure: error: Can't find HDF5
ERROR: configuration failed for package ‘hdf5’
* removing ‘/home/uday/R/x86_64-pc-linux-gnu-library/2.14/hdf5’
Warning in install.packages :
installation of package ‘hdf5’ had non-zero exit status
The downloaded packages are in
‘/tmp/Rtmp7Ot3Yl/downloaded_packages’ }
So what is this non-zero exit status ?
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--
Sarah Goslee
http://www.stringpage.com
http://www.sarahgoslee.com
http://www.functionaldiversity.org
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Re: [R] Package Installation in osx
This was garbled en route, but (a) Your R is far too old: please update as the posting guide asked of you. (You seem to be using a pre-release of 2.11.0.) (b) You need to set DISPLAY, as the message says. It usually is set at a Mac OS X console, so perhaps you need to ask on R-sig-mac about that. On Mon, 22 Aug 2011, Ehsan Karim wrote: Dear List: Wondering how to get around the following problem: any suggestions are welcome. Cheers, Ehsan install.packages(geepack)Warning in install.packages(geepack) : argument 'lib' is missing: using '/home/grad/student/Library/R/2.11/library'--- Please select a CRAN mirror for use in this session ---Loading Tcl/Tk interface ... doneError in structure(.External(dotTclObjv, objv, PACKAGE = tcltk), class = tclObj) : [tcl] invalid command name toplevel.In addition: Warning message:In fun(...) : no display name and no $DISPLAY environment variable R.Version()$platform[1] x86_64-apple-darwin9.8.0$arch[1] x86_64$os[1] darwin9.8.0$system[1] x86_64, darwin9.8.0$status[1] Under development (unstable)$major[1] 2$minor[1] 11.0$year[1] 2010$month[1] 03$day[1] 14$`svn rev`[1] 51276$language[1] R$version.string[1] R version 2.11.0 Under development (unstable) (2010-03-14 r51276) __ 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. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ 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] Package Installation
On Mon, 21 Mar 2011, Bogaso Christofer wrote: Dear all, can somebody guide me how to install the package RQuantLib, for which windows binary is not available. I have tried installing it with R CMD INSTALL in my windows vista machine (I have Rtools installed), however it stopped due to an error saying: compilation failed for package 'RQuantLib'. And what did the package maintainer say when you asked (see the posting guide)? You'll need to work on the C++ code in the package and its dependent library QuantLib. There is a good reason why a Windows binary is not available Actually, I did at some point in 2010 make a x64 binary package by cross-compiling, but as this is C++ you need an exact match between the cross-compiler and the native libraries, and in the 32-bit case the cross-compilers available were not compatible enough. What is should do right to install this package? Use a more capable OS. i.e. one with POSIX 1003 tools and C libraries. [[alternative HTML version deleted]] PLEASE do follow the posting guide No HTML in postings 'at a minimum' information Consult the package maintainer R-devel is the list for discussion of compiler 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 provide commented, minimal, self-contained, reproducible code.
Re: [R] Package Installation
On Sun, Mar 20, 2011 at 2:42 PM, Bogaso Christofer bogaso.christo...@gmail.com wrote: Dear all, can somebody guide me how to install the package RQuantLib, for which windows binary is not available. I have tried installing it with R CMD INSTALL in my windows vista machine (I have Rtools installed), however it stopped due to an error saying: compilation failed for package 'RQuantLib'. What is should do right to install this package? I wrote about how to build RQuantLib on Windows on my blog: http://blog.fosstrading.com/2010/12/build-rquantlib-on-32-bit-windows.html Thanks and regards, [[alternative HTML version deleted]] __ 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. -- Joshua Ulrich | FOSS Trading: www.fosstrading.com __ 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] package installation for Windows 7
Now that I have installed R outside Program files to get past the
permissions problem, there are packages I can only access from certain
working directories:
setwd(U:/Calc/zTemp) # U: points to a USB hard drive
library(splines) # ok
library(locfdr)
Error in library(locfdr) : there is no package called 'locfdr'
setwd(C:/Users/dbickel/Documents)
library(locfdr) # ok
The same error occurs whether or not I run R as administrator. Is there a
work around or better solution?
David
On 08/07/2010 9:46 AM, David Bickel wrote:
Thanks, Joris. Your suggestion solved the problem without requiring me to
run R as an administrator.
Best regards,
David
On 08/07/2010 8:45 AM, Joris Meys wrote:
Hi,
I am running Windows 7 and R 2.11.1, and everything is installing just
fine for me. Did you install R in the Program Files folder? If so,
uninstall and try to re-install R in another folder (e.g.
c:\R\R2.11.1\ like on my computer). I noticed in the past that the
access control of Windows treats the Program Files folder different
compared to other folders.
Cheers
Joris
On Thu, Jul 8, 2010 at 1:15 PM, Dave Bickel
davidbickel.com+re...@gmail.com davidbickel.com+re...@gmail.com wrote:
Neither biocLite nor the GUI menus can install packages on my system. Here
is relevant output:
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 11.1
year 2010
month 05
day 31
svn rev 52157
language R
version.string R version 2.11.1 (2010-05-31)
source(http://bioconductor.org/biocLite.R;http://bioconductor.org/biocLite.R)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
biocLite(ALL)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] ALL
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;http://bioconductor.org/biocLite.R)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining biocinstall
2: In safeSource() : Redefining biocinstallPkgGroups
3: In safeSource() : Redefining biocinstallRepos
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
library(Biobase)
Error in library(Biobase) : there is no package called 'Biobase'
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;http://bioconductor.org/biocLite.R)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining biocinstall
2: In safeSource() : Redefining biocinstallPkgGroups
3: In safeSource() : Redefining biocinstallRepos
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
utils:::menuInstallLocal() # Install package(s) from local zip files...
Error in if (ok) { : missing value where TRUE/FALSE needed
utils:::menuInstallPkgs() # Install package(s)...
--- Please select a CRAN mirror for use in this session ---
Error in if (ok) { : missing value where TRUE/FALSE needed
I would appreciate any assistance.
David
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
Re: [R] package installation for Windows 7
David Bickel wrote:
Now that I have installed R outside Program files to get past the
permissions problem, there are packages I can only access from certain
working directories:
setwd(U:/Calc/zTemp) # U: points to a USB hard drive
library(splines) # ok
library(locfdr)
Error in library(locfdr) : there is no package called 'locfdr'
setwd(C:/Users/dbickel/Documents)
library(locfdr) # ok
The same error occurs whether or not I run R as administrator. Is there a
work around or better solution?
What does .libPaths() look like? I would guess you've got something like
a relative path in there, which is probably a bad idea, for exactly the
reason you're seeing.
Duncan Murdoch
David
On 08/07/2010 9:46 AM, David Bickel wrote:
Thanks, Joris. Your suggestion solved the problem without requiring me to
run R as an administrator.
Best regards,
David
On 08/07/2010 8:45 AM, Joris Meys wrote:
Hi,
I am running Windows 7 and R 2.11.1, and everything is installing just
fine for me. Did you install R in the Program Files folder? If so,
uninstall and try to re-install R in another folder (e.g.
c:\R\R2.11.1\ like on my computer). I noticed in the past that the
access control of Windows treats the Program Files folder different
compared to other folders.
Cheers
Joris
On Thu, Jul 8, 2010 at 1:15 PM, Dave Bickel
davidbickel.com+re...@gmail.com davidbickel.com+re...@gmail.com wrote:
Neither biocLite nor the GUI menus can install packages on my system. Here
is relevant output:
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 11.1
year 2010
month 05
day 31
svn rev 52157
language R
version.string R version 2.11.1 (2010-05-31)
source(http://bioconductor.org/biocLite.R;http://bioconductor.org/biocLite.R)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
biocLite(ALL)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] ALL
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;http://bioconductor.org/biocLite.R)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
library(Biobase)
Error in library(Biobase) : there is no package called 'Biobase'
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;http://bioconductor.org/biocLite.R)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
utils:::menuInstallLocal() # Install package(s) from local zip files...
Error in if (ok) { : missing value where TRUE/FALSE needed
utils:::menuInstallPkgs() # Install package(s)...
--- Please select a CRAN mirror for use in this session ---
Error in if (ok) { : missing value where TRUE/FALSE needed
I would appreciate any assistance.
David
Re: [R] package installation for Windows 7
Thank you, Prof. Murdoch. I have this:
.libPaths()
[1] \\Users\\dbickel/R/win-library/2.11 C:/R/R-2.11.1/library
Since the following naive line in the profile failed, I just moved the
new packages to the same directory as the default packages.
.libPaths(c(C:/Users/dbickel/R/win-library/2.11/, .libPaths()))
Best regards,
David
On 10/07/2010 8:43 AM, Duncan Murdoch wrote:
David Bickel wrote:
Now that I have installed R outside Program files to get past the
permissions problem, there are packages I can only access from certain
working directories:
setwd(U:/Calc/zTemp) # U: points to a USB hard drive
library(splines) # ok
library(locfdr)
Error in library(locfdr) : there is no package called 'locfdr'
setwd(C:/Users/dbickel/Documents)
library(locfdr) # ok
The same error occurs whether or not I run R as administrator. Is
there a
work around or better solution?
What does .libPaths() look like? I would guess you've got something
like a relative path in there, which is probably a bad idea, for
exactly the reason you're seeing.
Duncan Murdoch
David
On 08/07/2010 9:46 AM, David Bickel wrote:
Thanks, Joris. Your suggestion solved the problem without requiring
me to
run R as an administrator.
Best regards,
David
On 08/07/2010 8:45 AM, Joris Meys wrote:
Hi,
I am running Windows 7 and R 2.11.1, and everything is installing just
fine for me. Did you install R in the Program Files folder? If so,
uninstall and try to re-install R in another folder (e.g.
c:\R\R2.11.1\ like on my computer). I noticed in the past that the
access control of Windows treats the Program Files folder different
compared to other folders.
Cheers
Joris
On Thu, Jul 8, 2010 at 1:15 PM, Dave Bickel
davidbickel.com+re...@gmail.com davidbickel.com+re...@gmail.com
wrote:
Neither biocLite nor the GUI menus can install packages on my system.
Here
is relevant output:
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 11.1
year 2010
month 05
day 31
svn rev 52157
language R
version.string R version 2.11.1 (2010-05-31)
source(http://bioconductor.org/biocLite.R;http://bioconductor.org/biocLite.R)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
biocLite(ALL)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] ALL
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;http://bioconductor.org/biocLite.R)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
library(Biobase)
Error in library(Biobase) : there is no package called 'Biobase'
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;http://bioconductor.org/biocLite.R)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value
Re: [R] package installation for Windows 7
On 10/07/2010 10:37 AM, David Bickel wrote:
Thank you, Prof. Murdoch. I have this:
.libPaths()
[1] \\Users\\dbickel/R/win-library/2.11 C:/R/R-2.11.1/library
That first path doesn't look like it would work in Windows: it has no
drive letter, so its meaning will depend on the driver letter of the
current working directory. Effectively it's a relative path.
Duncan Murdoch
Since the following naive line in the profile failed, I just moved the
new packages to the same directory as the default packages.
.libPaths(c(C:/Users/dbickel/R/win-library/2.11/, .libPaths()))
Best regards,
David
On 10/07/2010 8:43 AM, Duncan Murdoch wrote:
David Bickel wrote:
Now that I have installed R outside Program files to get past the
permissions problem, there are packages I can only access from certain
working directories:
setwd(U:/Calc/zTemp) # U: points to a USB hard drive
library(splines) # ok
library(locfdr)
Error in library(locfdr) : there is no package called 'locfdr'
setwd(C:/Users/dbickel/Documents)
library(locfdr) # ok
The same error occurs whether or not I run R as administrator. Is
there a
work around or better solution?
What does .libPaths() look like? I would guess you've got something
like a relative path in there, which is probably a bad idea, for
exactly the reason you're seeing.
Duncan Murdoch
David
On 08/07/2010 9:46 AM, David Bickel wrote:
Thanks, Joris. Your suggestion solved the problem without requiring
me to
run R as an administrator.
Best regards,
David
On 08/07/2010 8:45 AM, Joris Meys wrote:
Hi,
I am running Windows 7 and R 2.11.1, and everything is installing just
fine for me. Did you install R in the Program Files folder? If so,
uninstall and try to re-install R in another folder (e.g.
c:\R\R2.11.1\ like on my computer). I noticed in the past that the
access control of Windows treats the Program Files folder different
compared to other folders.
Cheers
Joris
On Thu, Jul 8, 2010 at 1:15 PM, Dave Bickel
davidbickel.com+re...@gmail.com davidbickel.com+re...@gmail.com
wrote:
Neither biocLite nor the GUI menus can install packages on my system.
Here
is relevant output:
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 11.1
year 2010
month 05
day 31
svn rev 52157
language R
version.string R version 2.11.1 (2010-05-31)
source(http://bioconductor.org/biocLite.R;http://bioconductor.org/biocLite.R)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
biocLite(ALL)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] ALL
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;http://bioconductor.org/biocLite.R)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
library(Biobase)
Error in library(Biobase) : there is no package called 'Biobase'
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;http://bioconductor.org/biocLite.R)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining
Re: [R] package installation for Windows 7
Hi,
I am running Windows 7 and R 2.11.1, and everything is installing just
fine for me. Did you install R in the Program Files folder? If so,
uninstall and try to re-install R in another folder (e.g.
c:\R\R2.11.1\ like on my computer). I noticed in the past that the
access control of Windows treats the Program Files folder different
compared to other folders.
Cheers
Joris
On Thu, Jul 8, 2010 at 1:15 PM, Dave Bickel
davidbickel.com+re...@gmail.com wrote:
Neither biocLite nor the GUI menus can install packages on my system. Here
is relevant output:
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 11.1
year 2010
month 05
day 31
svn rev 52157
language R
version.string R version 2.11.1 (2010-05-31)
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
biocLite(ALL)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] ALL
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
library(Biobase)
Error in library(Biobase) : there is no package called 'Biobase'
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
utils:::menuInstallLocal() # Install package(s) from local zip files...
Error in if (ok) { : missing value where TRUE/FALSE needed
utils:::menuInstallPkgs() # Install package(s)...
--- Please select a CRAN mirror for use in this session ---
Error in if (ok) { : missing value where TRUE/FALSE needed
I would appreciate any assistance.
David
--
David R. Bickel, PhD
Associate Professor
Ottawa Institute of Systems Biology
Biochem., Micro. and I. Department
Mathematics and Statistics Department
University of Ottawa
451 Smyth Road
Ottawa, Ontario K1H 8M5
http://www.statomics.com
Office Tel: (613) 562-5800 ext. 8670
Office Fax: (613) 562-5185
Office Room: RGN 4510F (Follow the signs to the elevator, and take it to the
fourth floor. Turn left and go all the way to the end of the hall, and enter
the door to the OISB area.)
Lab Tel.: (613) 562-5800 ext. 8304
Lab Room: RGN 4501T
__
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.
--
Joris Meys
Statistical consultant
Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control
tel : +32 9
Re: [R] package installation for Windows 7
On 08/07/2010 7:15 AM, Dave Bickel wrote:
Neither biocLite nor the GUI menus can install packages on my system.
This is probably a permissions problem. Are you running R as an
administrator when you try the install? If not, you won't be able to
install to the default location, but you should be able to set up your
own library somewhere else, and install there.
The error message should be fixed; we shouldn't give
Error in if (ok) { : missing value where TRUE/FALSE needed
but I doubt if that's the source of your problem.
BTW, in future Bioconductor questions should go to their list. In this
case it looks as though it's not a BioC problem, but that just means
there's no need to list all the biocLite.R material at the start: short
simple bug reports are easier to deal with.
Duncan Murdoch
Here is relevant output:
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 11.1
year 2010
month 05
day 31
svn rev 52157
language R
version.string R version 2.11.1 (2010-05-31)
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
biocLite(ALL)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] ALL
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
library(Biobase)
Error in library(Biobase) : there is no package called 'Biobase'
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
utils:::menuInstallLocal() # Install package(s) from local zip
files...
Error in if (ok) { : missing value where TRUE/FALSE needed
utils:::menuInstallPkgs() # Install package(s)...
--- Please select a CRAN mirror for use in this session ---
Error in if (ok) { : missing value where TRUE/FALSE needed
I would appreciate any assistance.
David
__
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] package installation for Windows 7
As far as my experience goes, there is no need whatsoever to run R as
an administrator for installation of any package, including
BioConductor, provided you stay away from the Program Files folder.
Cheers
Joris
On Thu, Jul 8, 2010 at 2:55 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote:
On 08/07/2010 7:15 AM, Dave Bickel wrote:
Neither biocLite nor the GUI menus can install packages on my system.
This is probably a permissions problem. Are you running R as an
administrator when you try the install? If not, you won't be able to
install to the default location, but you should be able to set up your own
library somewhere else, and install there.
The error message should be fixed; we shouldn't give
Error in if (ok) { : missing value where TRUE/FALSE needed
but I doubt if that's the source of your problem.
BTW, in future Bioconductor questions should go to their list. In this case
it looks as though it's not a BioC problem, but that just means there's no
need to list all the biocLite.R material at the start: short simple bug
reports are easier to deal with.
Duncan Murdoch
Here is relevant output:
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 11.1
year 2010
month 05
day 31
svn rev 52157
language R
version.string R version 2.11.1 (2010-05-31)
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
biocLite(ALL)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] ALL
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
library(Biobase)
Error in library(Biobase) : there is no package called 'Biobase'
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
utils:::menuInstallLocal() # Install package(s) from local zip
files...
Error in if (ok) { : missing value where TRUE/FALSE needed
utils:::menuInstallPkgs() # Install package(s)...
--- Please select a CRAN mirror for use in this session ---
Error in if (ok) { : missing value where TRUE/FALSE needed
I would appreciate any assistance.
David
__
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.
--
Joris Meys
Statistical consultant
Ghent University
Faculty of Bioscience Engineering
Department of Applied
Re: [R] package installation for Windows 7
On 08/07/2010 9:26 AM, David Bickel wrote:
Yes, the User into which I logged in before launching RGui is an
Administrator. Correct, the problem is not limited to Bioconductor packages.
On Windows 7, it's not enough to have the user be an administrator, you
need to run programs specifically with administrative rights. You do
this by right clicking on the icon, and choosing Run as administrator.
Duncan Murdoch
David
On 08/07/2010 8:55 AM, Duncan Murdoch wrote:
On 08/07/2010 7:15 AM, Dave Bickel wrote:
Neither biocLite nor the GUI menus can install packages on my system.
This is probably a permissions problem. Are you running R as an
administrator when you try the install? If not, you won't be able to
install to the default location, but you should be able to set up your
own library somewhere else, and install there.
The error message should be fixed; we shouldn't give
Error in if (ok) { : missing value where TRUE/FALSE needed
but I doubt if that's the source of your problem.
BTW, in future Bioconductor questions should go to their list. In
this case it looks as though it's not a BioC problem, but that just
means there's no need to list all the biocLite.R material at the
start: short simple bug reports are easier to deal with.
Duncan Murdoch
Here is relevant output:
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 11.1
year 2010
month 05
day 31
svn rev 52157
language R
version.string R version 2.11.1 (2010-05-31)
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
biocLite(ALL)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] ALL
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
library(Biobase)
Error in library(Biobase) : there is no package called 'Biobase'
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
utils:::menuInstallLocal() # Install package(s) from local zip
files...
Error in if (ok) { : missing value where TRUE/FALSE needed
utils:::menuInstallPkgs() # Install package(s)...
--- Please select a CRAN mirror for use in this session ---
Error in if (ok) { : missing value where TRUE/FALSE needed
I would appreciate any assistance.
David
__
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
Re: [R] package installation for Windows 7
Yes, the User into which I logged in before launching RGui is an
Administrator. Correct, the problem is not limited to Bioconductor packages.
David
On 08/07/2010 8:55 AM, Duncan Murdoch wrote:
On 08/07/2010 7:15 AM, Dave Bickel wrote:
Neither biocLite nor the GUI menus can install packages on my system.
This is probably a permissions problem. Are you running R as an
administrator when you try the install? If not, you won't be able to
install to the default location, but you should be able to set up your
own library somewhere else, and install there.
The error message should be fixed; we shouldn't give
Error in if (ok) { : missing value where TRUE/FALSE needed
but I doubt if that's the source of your problem.
BTW, in future Bioconductor questions should go to their list. In
this case it looks as though it's not a BioC problem, but that just
means there's no need to list all the biocLite.R material at the
start: short simple bug reports are easier to deal with.
Duncan Murdoch
Here is relevant output:
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 11.1
year 2010
month 05
day 31
svn rev 52157
language R
version.string R version 2.11.1 (2010-05-31)
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
biocLite(ALL)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] ALL
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
library(Biobase)
Error in library(Biobase) : there is no package called 'Biobase'
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
utils:::menuInstallLocal() # Install package(s) from local zip
files...
Error in if (ok) { : missing value where TRUE/FALSE needed
utils:::menuInstallPkgs() # Install package(s)...
--- Please select a CRAN mirror for use in this session ---
Error in if (ok) { : missing value where TRUE/FALSE needed
I would appreciate any assistance.
David
__
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] package installation for Windows 7
Yes, the User into which I logged in before launching RGui is an
Administrator. Correct, the problem is not limited to Bioconductor packages.
David
On 08/07/2010 8:55 AM, Duncan Murdoch wrote:
On 08/07/2010 7:15 AM, Dave Bickel wrote:
Neither biocLite nor the GUI menus can install packages on my system.
This is probably a permissions problem. Are you running R as an
administrator when you try the install? If not, you won't be able to
install to the default location, but you should be able to set up your
own library somewhere else, and install there.
The error message should be fixed; we shouldn't give
Error in if (ok) { : missing value where TRUE/FALSE needed
but I doubt if that's the source of your problem.
BTW, in future Bioconductor questions should go to their list. In
this case it looks as though it's not a BioC problem, but that just
means there's no need to list all the biocLite.R material at the
start: short simple bug reports are easier to deal with.
Duncan Murdoch
Here is relevant output:
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 11.1
year 2010
month 05
day 31
svn rev 52157
language R
version.string R version 2.11.1 (2010-05-31)
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
biocLite(ALL)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] ALL
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
library(Biobase)
Error in library(Biobase) : there is no package called 'Biobase'
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
utils:::menuInstallLocal() # Install package(s) from local zip
files...
Error in if (ok) { : missing value where TRUE/FALSE needed
utils:::menuInstallPkgs() # Install package(s)...
--- Please select a CRAN mirror for use in this session ---
Error in if (ok) { : missing value where TRUE/FALSE needed
I would appreciate any assistance.
David
--
David R. Bickel, PhD
Associate Professor
Ottawa Institute of Systems Biology
Biochem., Micro. and I. Department
Mathematics and Statistics Department
University of Ottawa
451 Smyth Road
Ottawa, Ontario K1H 8M5
http://www.statomics.com
dbic...@uottawa.ca
Office Tel: (613) 562-5800 ext. 8670
Office Fax: (613) 562-5185
Office Room: RGN 4510F (Follow the signs to the elevator, and take it to
the fourth floor. Turn left and go all the way to the end of the hall,
and enter the door to the OISB area.)
Lab Tel.: (613) 562-5800 ext. 8304
Lab Room: RGN 4501T
Re: [R] package installation for Windows 7
Thanks, Joris. Your suggestion solved the problem without requiring me
to run R as an administrator.
Best regards,
David
On 08/07/2010 8:45 AM, Joris Meys wrote:
Hi,
I am running Windows 7 and R 2.11.1, and everything is installing just
fine for me. Did you install R in the Program Files folder? If so,
uninstall and try to re-install R in another folder (e.g.
c:\R\R2.11.1\ like on my computer). I noticed in the past that the
access control of Windows treats the Program Files folder different
compared to other folders.
Cheers
Joris
On Thu, Jul 8, 2010 at 1:15 PM, Dave Bickel
davidbickel.com+re...@gmail.com wrote:
Neither biocLite nor the GUI menus can install packages on my system. Here
is relevant output:
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 11.1
year 2010
month 05
day 31
svn rev 52157
language R
version.string R version 2.11.1 (2010-05-31)
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
biocLite(ALL)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] ALL
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
biocLite()
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] affy affydata affyPLM affyQCReport
[5] annaffy annotate Biobase biomaRt
[9] Biostrings DynDoc gcrma genefilter
[13] geneplotter GenomicRanges hgu95av2.db limma
[17] marray multtest vsn xtable
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
library(Biobase)
Error in library(Biobase) : there is no package called 'Biobase'
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
source(http://bioconductor.org/biocLite.R;)
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
biocLite(Biobase)
Using R version 2.11.1, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] Biobase
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11'
Error in if (ok) { : missing value where TRUE/FALSE needed
utils:::menuInstallLocal() # Install package(s) from local zip files...
Error in if (ok) { : missing value where TRUE/FALSE needed
utils:::menuInstallPkgs() # Install package(s)...
--- Please select a CRAN mirror for use in this session ---
Error in if (ok) { : missing value where TRUE/FALSE needed
I would appreciate any assistance.
David
--
David R. Bickel, PhD
Associate Professor
Ottawa Institute of Systems Biology
Biochem., Micro. and I. Department
Mathematics and Statistics Department
University of Ottawa
451 Smyth Road
Ottawa, Ontario K1H 8M5
http://www.statomics.com
Office Tel: (613) 562-5800 ext. 8670
Office Fax: (613) 562-5185
Office Room: RGN 4510F (Follow the signs to the elevator, and take it to the
fourth floor. Turn left and go all the way to the end of the hall, and enter
the door to the OISB area.)
Lab Tel.: (613) 562-5800 ext. 8304
Lab Room: RGN 4501T
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
Re: [R] package installation for Windows 7
On Thu, Jul 8, 2010 at 3:39 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 08/07/2010 9:26 AM, David Bickel wrote: Yes, the User into which I logged in before launching RGui is an Administrator. Correct, the problem is not limited to Bioconductor packages. On Windows 7, it's not enough to have the user be an administrator, you need to run programs specifically with administrative rights. You do this by right clicking on the icon, and choosing Run as administrator. Reason for this is that Program Files is a protected directory, and changes can only be done by programs that get administrator rights (which is not the same as running a program in an administrator account). Without those administrator rights, R cannot access the default folder for the packages, as that one is also included in the Program Files. Also changing the Rprofile.site becomes a hassle, as so many other tweaks. Actually, the only programs getting there are Microsoft related applications. If there's no strict need to place a program there, I stay away from that folder as far as possible. Vista has the same problem by the way, and obviously the same solutions. Cheers Joris -- Joris Meys Statistical consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php __ 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] package installation from source
Hi Duncan Murdoch murd...@stats.uwo.ca napsal dne 16.10.2009 17:01:59: On 10/16/2009 9:31 AM, Petr PIKAL wrote: Dear all I noticed from NEWS 2.11.0,dev SIGNIFICANT USER-VISIBLE CHANGES o Packages must have been installed under R 2.10.0 or later, as the current help system is the only one now supported. So I tried to follow instructions in manual, Duncan Murdoch presentation and help pages to prepare and accomplish installation of a set of functions I use. However in R 2.11.0dev and too in R 2.10.0dev I was not able to finish it. snip install.packages(D:/temp/fun, repos=NULL, type=source) sh nenˇ n zvem vnitýnˇho ani vnŘjçˇho pýˇkazu, spustiteln‚ho programu nebo d vkov‚ho souboru. Warning message: In install.packages(D:/temp/fun, repos = NULL, type = source) : installation of package 'D:/temp/fun' had non-zero exit status which basically tells that sh is not a name of command, exe or bat file. There should be a sh.exe in d:\programy\Rtools\bin if that's where you installed the Rtools. Are you sure you have the path set the way you Yes there is it list.files(D:/programy/Rtools/bin) [1] basename.exe cat.execmp.exe snip 40] sh.exe sort.exe tar.exe [43] texindex.exe touch.exe tr.exe [46] uniq.exe unzip.exe wc.exe [49] zip.exe think you do? Remember that PATH is an environment variable, and environment variable settings are local: so setting the PATH in a CMD window has no effect on R or any other command window. You need to use Hm. It is a problem. I do not have admin rights. Therefore I set PATH in the command window and used the same window to issue R CMD INSTALL fun, but it gave me the same error message as above. the Control Panel to set the default system path, and then restart any process that needs to see it. As I can not change system wide PATH I tried to set user PATH. This resulted in modified PATH value but the required values for installation was at the end and I got the same error. As I am not sure if our IT guys change the system path for me (permanently) I would like to know if there is some workaround like few years before with make, make install etc. Maybe more complicated but without need to fiddle with PATH value. Thank you and best regards Petr Duncan Murdoch The same I get when I try to run D:\temp R CMD INSTALL fun Please can you give me any suggestion for making installation work. I remember when going from 1.9 to 2.0 versions it was also necessary to install my bunch of functions, however at that time I need to use something like make, make install or so and gather all necessary programs myself. Best regards Petr __ 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 provide commented, minimal, self-contained, reproducible code.
Re: [R] package installation from source
Petr PIKAL wrote: Hi Duncan Murdoch murd...@stats.uwo.ca napsal dne 16.10.2009 17:01:59: On 10/16/2009 9:31 AM, Petr PIKAL wrote: Dear all I noticed from NEWS 2.11.0,dev SIGNIFICANT USER-VISIBLE CHANGES o Packages must have been installed under R 2.10.0 or later, as the current help system is the only one now supported. So I tried to follow instructions in manual, Duncan Murdoch presentation and help pages to prepare and accomplish installation of a set of functions I use. However in R 2.11.0dev and too in R 2.10.0dev I was not able to finish it. snip install.packages(D:/temp/fun, repos=NULL, type=source) sh nenˇ n zvem vnitýnˇho ani vnŘjçˇho pýˇkazu, spustiteln‚ho programu nebo d vkov‚ho souboru. Warning message: In install.packages(D:/temp/fun, repos = NULL, type = source) : installation of package 'D:/temp/fun' had non-zero exit status which basically tells that sh is not a name of command, exe or bat file. There should be a sh.exe in d:\programy\Rtools\bin if that's where you installed the Rtools. Are you sure you have the path set the way you Yes there is it list.files(D:/programy/Rtools/bin) [1] basename.exe cat.execmp.exe snip 40] sh.exe sort.exe tar.exe [43] texindex.exe touch.exe tr.exe [46] uniq.exe unzip.exe wc.exe [49] zip.exe think you do? Remember that PATH is an environment variable, and environment variable settings are local: so setting the PATH in a CMD window has no effect on R or any other command window. You need to use Hm. It is a problem. I do not have admin rights. Therefore I set PATH in the command window and used the same window to issue R CMD INSTALL fun, but it gave me the same error message as above. That should have worked. Just to confirm, try running R from that shell (using either Rgui or R), and then print Sys.getenv(PATH) and make sure it shows what you expected. the Control Panel to set the default system path, and then restart any process that needs to see it. As I can not change system wide PATH I tried to set user PATH. This resulted in modified PATH value but the required values for installation was at the end and I got the same error. Yes, I believe Windows always puts the user PATH after the system one. As I am not sure if our IT guys change the system path for me (permanently) I would like to know if there is some workaround like few years before with make, make install etc. Maybe more complicated but without need to fiddle with PATH value. I think you'll need to fiddle with the PATH, but maybe not at the system level. I would do what you did (setting it in the command window). You just need to figure out what went wrong. Duncan Murdoch Thank you and best regards Petr Duncan Murdoch The same I get when I try to run D:\temp R CMD INSTALL fun Please can you give me any suggestion for making installation work. I remember when going from 1.9 to 2.0 versions it was also necessary to install my bunch of functions, however at that time I need to use something like make, make install or so and gather all necessary programs myself. Best regards Petr __ 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 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 provide commented, minimal, self-contained, reproducible code.
Re: [R] package installation from source
On 10/19/2009 7:59 AM, Petr PIKAL wrote: Hi r-help-boun...@r-project.org napsal dne 19.10.2009 12:24:47: Petr PIKAL wrote: Hi Duncan Murdoch murd...@stats.uwo.ca napsal dne 16.10.2009 17:01:59: On 10/16/2009 9:31 AM, Petr PIKAL wrote: Dear all I noticed from NEWS 2.11.0,dev SIGNIFICANT USER-VISIBLE CHANGES o Packages must have been installed under R 2.10.0 or later, as the current help system is the only one now supported. So I tried to follow instructions in manual, Duncan Murdoch presentation and help pages to prepare and accomplish installation of a set of functions I use. However in R 2.11.0dev and too in R 2.10.0dev I was not able to finish it. snip That should have worked. Just to confirm, try running R from that shell (using either Rgui or R), and then print Sys.getenv(PATH) and make sure it shows what you expected. It seems like the path is set but system does not accepts it. Rgui does not start until I switch to its bin directory. Sys.getenv than shows correct path. See attached pictures. I believe the problem is the spaces that you have in your PATH. (You have spaces after the semi-colons, before the D:\ beginning of several entries.) If you remove those it should work. Duncan Murdoch __ 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] package installation from source
Hi Up! I finally get it work. For the record: 1. problem - spaces in path definition 2. problem - customised Rprofile.site which throws error when trying to load some packages After starting with all customised values disabled R CMD INSTALL worked as charm. Thank you very much, it is a long time I dealed with DOS and path setting. However now I will remember forever - no spaces -. Best regards Petr Duncan Murdoch murd...@stats.uwo.ca napsal dne 19.10.2009 14:18:23: On 10/19/2009 7:59 AM, Petr PIKAL wrote: Hi r-help-boun...@r-project.org napsal dne 19.10.2009 12:24:47: Petr PIKAL wrote: Hi Duncan Murdoch murd...@stats.uwo.ca napsal dne 16.10.2009 17:01:59: On 10/16/2009 9:31 AM, Petr PIKAL wrote: Dear all I noticed from NEWS 2.11.0,dev SIGNIFICANT USER-VISIBLE CHANGES o Packages must have been installed under R 2.10.0 or later, as the current help system is the only one now supported. So I tried to follow instructions in manual, Duncan Murdoch presentation and help pages to prepare and accomplish installation of a set of functions I use. However in R 2.11.0dev and too in R 2.10.0dev I was not able to finish it. snip That should have worked. Just to confirm, try running R from that shell (using either Rgui or R), and then print Sys.getenv(PATH) and make sure it shows what you expected. It seems like the path is set but system does not accepts it. Rgui does not start until I switch to its bin directory. Sys.getenv than shows correct path. See attached pictures. I believe the problem is the spaces that you have in your PATH. (You have spaces after the semi-colons, before the D:\ beginning of several entries.) If you remove those it should work. Duncan Murdoch __ 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] package installation from source
On 10/16/2009 9:31 AM, Petr PIKAL wrote: Dear all I noticed from NEWS 2.11.0,dev SIGNIFICANT USER-VISIBLE CHANGES o Packages must have been installed under R 2.10.0 or later, as the current help system is the only one now supported. So I tried to follow instructions in manual, Duncan Murdoch presentation and help pages to prepare and accomplish installation of a set of functions I use. However in R 2.11.0dev and too in R 2.10.0dev I was not able to finish it. I installed Rtools210 I opened commander window and or R program with --vanilla option. I coppied all my functions and data to R and run package.skeleton package.skeleton(list=ls(), name=fun) Creating directories ... Creating DESCRIPTION ... Creating Read-and-delete-me ... Saving functions and data ... Making help files ... Done. Further steps are described in './fun/Read-and-delete-me'. Package structure seems to be ok list.files(D:/temp/fun, recursive=TRUE) [1] data/modely1.rda data/modely2.rda data/modely3.rda [4] data/stand.rda DESCRIPTION man/addLine.Rd [7] man/azce.Rd man/bayerf.h.Rd man/bayerf.Rd snip [112] R/tridy.RR/trigrid.R R/truehist.R [115] R/voda.tlak.RR/vodiv2rozkl.R R/warmcold.R [118] R/weighted.mean.RR/weighted.var.R R/write.excel.R [121] Read-and-delete-me I changed PATH by PATH = D:\programy\Rtools\bin; D:\programy\Rtools\perl\bin; D:\programy\Rtools\MinGW\bin; D:\programy\R-2.10.0dev\bin; %PATH% When I try to do install.packages(D:/temp/fun, repos=NULL, type=source) sh nenˇ n zvem vnitýnˇho ani vnŘjçˇho pýˇkazu, spustiteln‚ho programu nebo d vkov‚ho souboru. Warning message: In install.packages(D:/temp/fun, repos = NULL, type = source) : installation of package 'D:/temp/fun' had non-zero exit status which basically tells that sh is not a name of command, exe or bat file. There should be a sh.exe in d:\programy\Rtools\bin if that's where you installed the Rtools. Are you sure you have the path set the way you think you do? Remember that PATH is an environment variable, and environment variable settings are local: so setting the PATH in a CMD window has no effect on R or any other command window. You need to use the Control Panel to set the default system path, and then restart any process that needs to see it. Duncan Murdoch The same I get when I try to run D:\temp R CMD INSTALL fun Please can you give me any suggestion for making installation work. I remember when going from 1.9 to 2.0 versions it was also necessary to install my bunch of functions, however at that time I need to use something like make, make install or so and gather all necessary programs myself. Best regards Petr __ 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 provide commented, minimal, self-contained, reproducible code.
Re: [R] package installation error
Héctor Villalobos wrote: Hi, This also happens in 2.9.1 and 2.9.2. My personal solution is to look under ' C:\Program Files\R\R-2.9.0\library' for a bizarre-named directory (starts with an 'f' and has numbers and letters mixed) , which contains the package directory (in this case 'robustbase') and move it up one level (like the other packages). This is annoying, but so far is the only solutions I have found. I haven't been able to reproduce this, so all I can do is guess at the cause, but it looks as though a directory rename failed. One cause for that would be that some application (like a virus checker, or file indexer, or some other background process) has a file open within the directory. You could try disabling all such programs (though it's not easy in Windows, there are lots of ways to start them) and see if that helps. Duncan Murdoch On 31 Aug 2009 at 9:32, Duncan Murdoch wrote: On 31/08/2009 8:53 AM, Haynes, Maurice (NIH/NICHD) [E] wrote: On Sun April 19, you posted the following on R-help: After installing 2.9.0 I tried loading packages, but keep getting the following error. package 'robustbase' successfully unpacked and MD5 sums checked Error in normalizePath(path) : path[1]=C:\Program Files\R\R-2.9.0\library/robustbase: The system cannot find the file specified I have had the same problem for months. Have you found a solution? There have been two patch releases since 2.9.0. Have you tried 2.9.2? Duncan Murdoch __ 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. -- Héctor Villalobos hvill...@ipn.mx CICIMAR - IPN A.P. 592. Col. Centro La Paz, Baja California Sur, MÉXICO. 23000 Tels. (+52 612) 122 53 44; 123 46 58; 123 47 34 ext. 82425 Fax. (+52 612) 122 53 22 __ 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] package installation error
Hi, Thank you for your responses. Héctor, I had also discovered the solution you suggested. However, when I install files from a list (such as pckg.list), failure in the installation of one package in the list results in none of the packages later in the list being installed. After moving the 'problem' package up one level and deleting the empty temporary directory, the name and name attribute of the problem package must be removed from the list before loading the list and calling the function install.packages() again. With multiple failures in the list of packages, that can get tedious. Duncan, I suspect you are correct that a file within the directory for the 'failed' package may have been locked by an antivirus program or some other background process so that the package directory cannot be renamed. However, although I am able to disable the virus check of files on my home desktop and laptop (which I will do in the future), I have no control over such applications as the enterprise-wide antivirus program in my office desktop. (I have administrative rights only on my local machine.) Could the internal function normalizePath() be rewritten so that before it attempts to convert the path of a package directory to a subdirectory of the library directory it checks whether it has access to the file and pauses until it has access or for some reasonably short time? Please excuse me if I have just displayed ignorance or arrogance. I suspect, however, that there are more than a few users of R who have these problems and cannot control all the background applications on their machine. Again, thank you both. Maurice -Original Message- From: Duncan Murdoch [mailto:murd...@stats.uwo.ca] Sent: Wednesday, September 02, 2009 6:32 AM To: Héctor Villalobos Cc: Haynes, Maurice (NIH/NICHD) [E]; r-help@r-project.org Subject: Re: [R] package installation error Héctor Villalobos wrote: Hi, This also happens in 2.9.1 and 2.9.2. My personal solution is to look under ' C:\Program Files\R\R-2.9.0\library' for a bizarre-named directory (starts with an 'f' and has numbers and letters mixed) , which contains the package directory (in this case 'robustbase') and move it up one level (like the other packages). This is annoying, but so far is the only solutions I have found. I haven't been able to reproduce this, so all I can do is guess at the cause, but it looks as though a directory rename failed. One cause for that would be that some application (like a virus checker, or file indexer, or some other background process) has a file open within the directory. You could try disabling all such programs (though it's not easy in Windows, there are lots of ways to start them) and see if that helps. Duncan Murdoch On 31 Aug 2009 at 9:32, Duncan Murdoch wrote: On 31/08/2009 8:53 AM, Haynes, Maurice (NIH/NICHD) [E] wrote: On Sun April 19, you posted the following on R-help: After installing 2.9.0 I tried loading packages, but keep getting the following error. package 'robustbase' successfully unpacked and MD5 sums checked Error in normalizePath(path) : path[1]=C:\Program Files\R\R-2.9.0\library/robustbase: The system cannot find the file specified I have had the same problem for months. Have you found a solution? There have been two patch releases since 2.9.0. Have you tried 2.9.2? Duncan Murdoch __ 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. -- Héctor Villalobos hvill...@ipn.mx CICIMAR - IPN A.P. 592. Col. Centro La Paz, Baja California Sur, MÉXICO. 23000 Tels. (+52 612) 122 53 44; 123 46 58; 123 47 34 ext. 82425 Fax. (+52 612) 122 53 22 __ 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] package installation error
Hi, This also happens in 2.9.1 and 2.9.2. My personal solution is to look under 'C:\Program Files\R\R-2.9.0\library' for a bizarre-named directory (starts with an 'f' and has numbers and letters mixed) , which contains the package directory (in this case 'robustbase') and move it up one level (like the other packages). This is annoying, but so far is the only solutions I have found. On 31 Aug 2009 at 9:32, Duncan Murdoch wrote: On 31/08/2009 8:53 AM, Haynes, Maurice (NIH/NICHD) [E] wrote: On Sun April 19, you posted the following on R-help: After installing 2.9.0 I tried loading packages, but keep getting the following error. package 'robustbase' successfully unpacked and MD5 sums checked Error in normalizePath(path) : path[1]=C:\Program Files\R\R-2.9.0\library/robustbase: The system cannot find the file specified I have had the same problem for months. Have you found a solution? There have been two patch releases since 2.9.0. Have you tried 2.9.2? Duncan Murdoch __ 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. -- Héctor Villalobos hvill...@ipn.mx CICIMAR - IPN A.P. 592. Col. Centro La Paz, Baja California Sur, MÉXICO. 23000 Tels. (+52 612) 122 53 44; 123 46 58; 123 47 34 ext. 82425 Fax. (+52 612) 122 53 22 [[alternative HTML version deleted]] __ 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] package installation error
On Sun April 19, you posted the following on R-help: After installing 2.9.0 I tried loading packages, but keep getting the following error. package 'robustbase' successfully unpacked and MD5 sums checked Error in normalizePath(path) : path[1]=C:\Program Files\R\R-2.9.0\library/robustbase: The system cannot find the file specified I have had the same problem for months. Have you found a solution? Maurice O. Maurice Haynes, Ph.D. Statistician, Child and Family Research Section Laboratory for Comparative Ethology Eunice Kennedy Shriver National Institute of Child Health and Human Development NIH, DHHS 6705 Rockledge Drive, Suite 8030 Bethesda, Maryland 20892 Phone: 301-496-8180 E-mail: mh1...@nih.govmailto:mh1...@nih.gov [[alternative HTML version deleted]] __ 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] package installation error
On 31/08/2009 8:53 AM, Haynes, Maurice (NIH/NICHD) [E] wrote: On Sun April 19, you posted the following on R-help: After installing 2.9.0 I tried loading packages, but keep getting the following error. package 'robustbase' successfully unpacked and MD5 sums checked Error in normalizePath(path) : path[1]=C:\Program Files\R\R-2.9.0\library/robustbase: The system cannot find the file specified I have had the same problem for months. Have you found a solution? There have been two patch releases since 2.9.0. Have you tried 2.9.2? Duncan Murdoch __ 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] package installation error
No, this is on Windows-Xp. From: Erin Hodgess erinm.hodg...@gmail.com To: Joseph P. Gray jpg...@uwm.edu Sent: Sun, 19 Apr 2009 19:17:34 -0500 (CDT) Subject: Re: [R] package installation error Hi Pat! Are you using Windows Vista by any chance, please? If so, try running as administrator. It might help. Sincerely, Erin On Sun, Apr 19, 2009 at 6:38 PM, Joseph P Gray jpg...@uwm.edu wrote: After installing 2.9.0 I tried loading packages, but keep getting the following error. package 'robustbase' successfully unpacked and MD5 sums checked Error in normalizePath(path) : path[1]=C:\Program Files\R\R-2.9.0\library/robustbase: The system cannot find the file specified I've tried loading various packages with the same result. Thanks for any help. Pat Gray Department of Anthropology University of Wisconsin-Milwaukee PO Box 413 Milwaukee, WI 53201-0413 414-229-4822 jpg...@uwm.edu __ 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. -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: erinm.hodg...@gmail.com __ 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] Package installation failed
Dear Uwe and folks, I had connections to CRAN daily and won't have problems for most packages, but only some does. Installed directory is: C:\Documents and Settings\R\library\downloaded_packages I do not have set library path except the R default. I tried to download lme4 and packages that unable to install, but still same error message came up. error in normalizePath(path) : path[1]: no such file to load Any help would be greatly appreciated. Odette On Fri, Jan 23, 2009 at 7:15 PM, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: Odette Gaston wrote: Hi Uwe and all, Error message was: error in normalizePath(path) : path[1]: no such file to load Hmmm, what does traceback() tell you at that point? Have you had a cionnection to CRAN and has something been downloaded? If so, to which directory? Where is R installed? Do you have set some library path other than the R default? Uwe Ligges Many thanks, Odette On Fri, Jan 23, 2009 at 1:22 AM, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: Odette Gaston wrote: Hi folks, I am currently having the problem with using R 2.8.1 that I cannot install some of packages from CRAN or local drive and somebody may be able to help me. ex) faraway package and lme4 package. I have downloaded them in my hard drive as local, but still R was unable to find the package (message showed up as no such file). I could download most packages, but not all what I want. I showed my PC to R experts around and nobody had ideas. I've re-installed newest R and updated packages hundred times, but still same message came up. So, what is the error message when you try, e.g. install.packages(lme4) ? Uwe Ligges My working environment is: OS: XP Windows R2.8.1 Any suggestions would be appreciated. Thanks a lot, Odette [[alternative HTML version deleted]] __ 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.htmlhttp://www.r-project.org/posting-guide.html http://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ 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] Package installation failed
Odette Gaston wrote: Hi Uwe and all, Error message was: error in normalizePath(path) : path[1]: no such file to load Hmmm, what does traceback() tell you at that point? Have you had a cionnection to CRAN and has something been downloaded? If so, to which directory? Where is R installed? Do you have set some library path other than the R default? Uwe Ligges Many thanks, Odette On Fri, Jan 23, 2009 at 1:22 AM, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: Odette Gaston wrote: Hi folks, I am currently having the problem with using R 2.8.1 that I cannot install some of packages from CRAN or local drive and somebody may be able to help me. ex) faraway package and lme4 package. I have downloaded them in my hard drive as local, but still R was unable to find the package (message showed up as no such file). I could download most packages, but not all what I want. I showed my PC to R experts around and nobody had ideas. I've re-installed newest R and updated packages hundred times, but still same message came up. So, what is the error message when you try, e.g. install.packages(lme4) ? Uwe Ligges My working environment is: OS: XP Windows R2.8.1 Any suggestions would be appreciated. Thanks a lot, Odette [[alternative HTML version deleted]] __ 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.htmlhttp://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 provide commented, minimal, self-contained, reproducible code.
Re: [R] Package installation failed
Odette Gaston wrote: Hi folks, I am currently having the problem with using R 2.8.1 that I cannot install some of packages from CRAN or local drive and somebody may be able to help me. ex) faraway package and lme4 package. I have downloaded them in my hard drive as local, but still R was unable to find the package (message showed up as no such file). I could download most packages, but not all what I want. I showed my PC to R experts around and nobody had ideas. I've re-installed newest R and updated packages hundred times, but still same message came up. So, what is the error message when you try, e.g. install.packages(lme4) ? Uwe Ligges My working environment is: OS: XP Windows R2.8.1 Any suggestions would be appreciated. Thanks a lot, Odette [[alternative HTML version deleted]] __ 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 provide commented, minimal, self-contained, reproducible code.
Re: [R] Package installation failed
Hi Uwe and all, Error message was: error in normalizePath(path) : path[1]: no such file to load Many thanks, Odette On Fri, Jan 23, 2009 at 1:22 AM, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: Odette Gaston wrote: Hi folks, I am currently having the problem with using R 2.8.1 that I cannot install some of packages from CRAN or local drive and somebody may be able to help me. ex) faraway package and lme4 package. I have downloaded them in my hard drive as local, but still R was unable to find the package (message showed up as no such file). I could download most packages, but not all what I want. I showed my PC to R experts around and nobody had ideas. I've re-installed newest R and updated packages hundred times, but still same message came up. So, what is the error message when you try, e.g. install.packages(lme4) ? Uwe Ligges My working environment is: OS: XP Windows R2.8.1 Any suggestions would be appreciated. Thanks a lot, Odette [[alternative HTML version deleted]] __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ 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] Package installation
Why don't you post your message in the Bioconductor list? People there will be able to help you better. Best regards, Carlos J. Gil Bellosta http://www.datanalytics.com On Wed, 2008-12-31 at 08:00 -0500, jianying...@med.unc.edu wrote: Dear all, I tried to install bioconductor package using biocLite(). I got warning that c:/program file/R../library is not writable. In any rate, after the downloading/installing, I looked for packages like affy gcrma etc. but I did not seem them in the library folder. However, when I try to load the library, it worked. Does anybody have any experience? Where are those packages installed? P.S. I am using window vista Thanks. Jianying - Original Message - From: Carlos J. Gil Bellosta c...@datanalytics.com Date: Wednesday, December 31, 2008 6:30 am Subject: Re: [R] Paste in a FOR loop To: Michael Pearmain mpearm...@google.com Cc: r-help@r-project.org ?eval Carlos J. Gil Bellosta http://www.datanalytics.com __ 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. [[alternative HTML version deleted]] __ 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 provide commented, minimal, self-contained, reproducible code.
Re: [R] Package installation in Windows
On Tue, 9 Sep 2008, [EMAIL PROTECTED] wrote: As a sys admin, how do I install packages so that there is one common library for all users of the MS Windows computer, instead of the default individual location for each user? I've done this for Linux. The same way. You set R_LIBS_SITE in etc/Renviron.site. See ?.Library.site . This was discussed on this list with the last couple of weeks, so please do check the archives. Thanks, in advance, for your help. Mike -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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] Package installation in Windows - Urgent!
Thanks for your response. However, I need more guidance. 1) I searched the archives of this list back to June 1. I found no discussion on this subject as I examined all the subject titles for the string [Ww]in. 2) I tried (what I understand) to be you suggestion. I created etc/Renviron.site: R_LIBS_SITE=C:\Program Files\R\R-2.7.2\library:C:\Program Files\R\R-2.7.2\Packages 3) As a test, downloading a package resulted in it being stored in: C:\Documents and Settings\[USER]\Local Settings\Temp\RtmpO7pcpi\downloaded_packages 4) From the documantation of Renviron: Unix versions of R have a file 'R_HOME/etc/Renviron' which is read very early in the start-up processing. It contains environment variables set by R in the configure process, and is *not used on R for Windows*. I seek your guidance, for I quickly need to deploy R and selected contributed packages on several classroom computers. Mike On Wed, Sep 10, 2008 at 2:02 AM, Prof Brian Ripley [EMAIL PROTECTED] wrote: On Tue, 9 Sep 2008, [EMAIL PROTECTED] wrote: As a sys admin, how do I install packages so that there is one common library for all users of the MS Windows computer, instead of the default individual location for each user? I've done this for Linux. The same way. You set R_LIBS_SITE in etc/Renviron.site. See ?.Library.site This was discussed on this list with the last couple of weeks, so please do check the archives. Thanks, in advance, for your help. Mike -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 [[alternative HTML version deleted]] __ 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] Package Installation produces linux/limits.h: No such file or directory error when installing the lpSolve package
Hi, I too had this same problem but it got resolved by installing two packages : 1. kernel-headers 2. kernel-devel I hope this helps in your case. Regards Sharwan Joe_K wrote: Dear Friends, I am trying to install a few packages in R and am receiving error messages. Since the error messages are different, I am posting them separately. The second error is with the installation of lpSolve. The core error message is: In file included from /usr/include/bits/posix1_lim.h:153, from /usr/include/limits.h:145, from /usr/lib64/gcc/x86_64-suse-linux/4.2.1/include/limits.h:122, from /usr/lib64/gcc/x86_64-suse-linux/4.2.1/include/syslimits.h:7, from /usr/lib64/gcc/x86_64-suse-linux/4.2.1/include/limits.h:11, from colamd.c:677: /usr/include/bits/local_lim.h:36:26 error: linux/limits.h: No such file or directory make: *** [colamd.o] Error 1 ERROR: compilation failed for package 'lpSolve' The first things that I tried was to figure out where linux/limits.h was. I discovered that there are seven versions of limits.h on the system and they are not identical. /usr/include/limits.h /usr/src/linux-2.6.22.13-0.3/Documentation/i2c/chips/limits.h /usr/include/c++/4.2.1/tr1/limits.h /usr/lib64/qt4/demos/qtdemo/xml/limits.h /usr/src/linux-2.6.22.13-0.3/include/linux/limits.h /usr/src/linux-2.6.22.13-0.3/include/asm-arm/limits.h /usr/src/linux-2.6.22.13-0.3/include/asm-arm26/limits.h Only one has linux immediately preceding it in the path: /usr/src/linux-2.6.22.13-0.3/include/linux/limits.h I assume that /usr/include/bits/local_lim.h is trying to use a relative path. The only line in local_lim.h with limits.h in it is: #include linux/limits.h So, I tried modifying the line to read: #include /usr/src/linux-2.6.22.13-0.3/include/linux/limits.h That did not work, so I changed it back again. I guess my theory about it looking for a relative path was wrong. Since then, I have been Googling the issue all weekend and have found similar errors, but not exactly the same. Some are suggesting changing kernel headers and other files. Since the context of these other posts are dissimilar, I figured it best not to mess with kernel headers or some of the other radical solutions offered. There was one suggestion in a post to install glibc-headers, however, I cannot seem to find that for Suse 10.3. Is it something included in another package? Is it something that is now obsolete? CAN ANYONE HELP ME DEBUG THIS? I am running R version 2.6.1 (2007-11-26) on Suse Linux 10.3 64-bit x86_64 on a Boxx Technologies computer with a TYAN Thunder K8WE S2895 Motherboard with 4Gb Ram and 2 dual CPUs (total of 4 CPUs). The CPUs are AMD Opteron. Hard Disk Usage is 4 150 Gb SATA drives array with a Com3 9550SX Controller set at RAID 5. The full error message received from Rkward upon the package installation attempt was: R version 2.6.1 (2007-11-26) Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 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. options (repos=c (CRAN=http://lib.stat.cmu.edu/R/CRAN;)) install.packages (pkgs=c (lpSolve), lib=/home/joe/R/x86_64-unknown-linux-gnu-library/2.6, destdir=/home/joe/.rkward/package_archive, dependencies=TRUE) trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/lpSolve_5.5.8.tar.gz' Content type 'application/x-gzip' length 449804 bytes (439 Kb) opened URL downloaded 439 Kb /home/joe/R/x86_64-unknown-linux-gnu-library/2.6 * Installing *source* package 'lpSolve' ... ** libs gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/lib64/R/include -I . -DINTEGERTIME -DPARSER_LP -DBUILDING_FOR_R -DYY_NEVER_INTERACTIVE -DUSRDLL -DCLOCKTIME -DRoleIsExternalInvEngine -DINVERSE_ACTIVE=INVERSE_LUSOL -DINLINE=static -DParanoia -I/usr/local/include-fpic -g -O2 -c colamd.c -o colamd.o In file included from /usr/include/bits/posix1_lim.h:153, from /usr/include/limits.h:145, from /usr/lib64/gcc/x86_64-suse-linux/4.2.1/include/limits.h:122, from /usr/lib64/gcc/x86_64-suse-linux/4.2.1/include/syslimits.h:7, from
