Hello,
This is about fortune package, but I think that might be related also to
base R, so I am sending to package maintainer and R-devel list.
I have the following in my .Rprofile to break monotony of code writing
library(utils)
library(fortunes)
fortune()
detach("package:fortunes")
so I get a fortune every time I start R. It seems that this conflicts
with R CMD INSTALL in latest R-devel on Linux. Two things can happen:
1. R CMD INSTALL fails
----------------------------------------------------------------------
$ R-devel CMD INSTALL connectedness
* Installing to library '
My preference goes with the numbering scheme attributed to a tribe on some
island in the Pacific which consists of a 'factor' with four levels: 'one',
'two', 'three', and 'lots'. Hence, I'd go with 'lots of R users'.
-- Dirk Eddelbuettel (in a discussion about trying to estimate the
number of
R users)
R-help (April 2004)
/usr/local/R-devel/lib/R/library'
ERROR: cannot write to or create directory '
My preference goes with the numbering scheme attributed to a tribe on some
island in the Pacific which consists of a 'factor' with four levels: 'one',
'two', 'three', and 'lots'. Hence, I'd go with 'lots of R users'.
-- Dirk Eddelbuettel (in a discussion about trying to estimate the
number of
R users)
R-help (April 2004)
/usr/local/R-devel/lib/R/library'
2. R CMD INSTALL installs package in wrong place - see bellow
----------------------------------------------------------------------
$ R-devel CMD INSTALL connectedness
* Installing to library '
If you imagine that this pen is Trellis, then Lattice is not this pen.
-- Paul Murrell (on the difference of Lattice (which eventually was
called
grid) and Trellis)
DSC 2001, Wien (March 2001)
/usr/local/R-devel/lib/R/library'
* Installing *source* package 'connectedness' ...
** R
** data
** inst
cat: /home/ggorjan/programs/R/devel/r-ggorjan/: Is a directory
cat: If: No such file or directory
cat: you: No such file or directory
cat: imagine: No such file or directory
cat: that: No such file or directory
cat: this: No such file or directory
cat: pen: No such file or directory
cat: is: No such file or directory
cat: Trellis,: No such file or directory
cat: then: No such file or directory
cat: Lattice: No such file or directory
cat: is: No such file or directory
cat: not: No such file or directory
cat: this: No such file or directory
cat: pen.: No such file or directory
cat: Paul: No such file or directory
cat: Murrell: No such file or directory
cat: (on: No such file or directory
cat: the: No such file or directory
cat: difference: No such file or directory
cat: of: No such file or directory
cat: Lattice: No such file or directory
cat: (which: No such file or directory
cat: eventually: No such file or directory
cat: was: No such file or directory
cat: called: No such file or directory
cat: grid): No such file or directory
cat: and: No such file or directory
cat: Trellis): No such file or directory
cat: DSC: No such file or directory
cat: 2001,: No such file or directory
cat: Wien: No such file or directory
cat: (March: No such file or directory
cat: 2001): No such file or directory
cat: /usr/local/R-devel/lib/R/library/connectedness/R/connectedness: No
such file or directory
** help
>>> Building/Updating help pages for package 'connectedness'
Formats: text html latex example
connect text html latex
connectedness text html latex example
levelsBySubset text html latex example
plot.connectedness text html latex example
subset.connectedness text html latex example
** building package indices ...
* DONE (connectedness)
$ tree -d
.
|-- \012If you imagine that this pen is Trellis, then Lattice is not
this pen.\012 -- Paul Murrell (on the difference of Lattice (which
eventually was called\012 grid) and Trellis)\012 DSC 2001,
Wien (March 2001)\012\012
| `-- usr
| `-- local
| `-- R-devel
| `-- lib
| `-- R
| `-- library
| `-- connectedness
| |-- Meta
| |-- R
| |-- R-ex
| |-- data
| |-- doc
| |-- help
| |-- html
| |-- latex
| |-- man
| `-- unitTests
|-- connectedness
| |-- R
| |-- data
| |-- inst
| | |-- doc
| | `-- unitTests
| |-- man
| `-- tests
...
Looks like a bug to me.
Gregor
fortune() in .Rprofile conflicts with R CMD INSTALL
6 messages · Gregor Gorjanc, Seth Falcon, Kurt Hornik
Gregor Gorjanc <gregor.gorjanc at bfro.uni-lj.si> writes:
Hello,
This is about fortune package, but I think that might be related also to
base R, so I am sending to package maintainer and R-devel list.
I have the following in my .Rprofile to break monotony of code writing
library(utils)
library(fortunes)
fortune()
detach("package:fortunes")
The quick fix for you is, I believe,
if (interactive()) {
library(fortunes)
fortune()
detach("package:fortunes")
}
Whether something could be changed so that R's output doesn't confuse
itself and gcc when doing R CMD INSTALL, seems like it should be
possible.
+ seth
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
Seth Falcon <sfalcon <at> fhcrc.org> writes:
The quick fix for you is, I believe,
if (interactive()) {
library(fortunes)
fortune()
detach("package:fortunes")
}
Whether something could be changed so that R's output doesn't confuse
itself and gcc when doing R CMD INSTALL, seems like it should be
possible.
Yes, this solves my! problem. I do not know what is causing this behaviour. This did not happen with 2.4.1 Thank you Seth. Gregor
Gregor Gorjanc writes:
Seth Falcon <sfalcon <at> fhcrc.org> writes:
The quick fix for you is, I believe,
if (interactive()) {
library(fortunes)
fortune()
detach("package:fortunes")
}
Whether something could be changed so that R's output doesn't confuse
itself and gcc when doing R CMD INSTALL, seems like it should be
possible.
Yes, this solves my! problem. I do not know what is causing this behaviour.
Well, r-devel's src/scripts/INSTALL.in now has
if test -z "${lib}"; then
lib=`echo "cat(.libPaths()[1])" | \
R_DEFAULT_PACKAGES=NULL "${R_EXE}" --no-save --slave`
message "Installing to library '$lib'"
so we need to find a way to "just get" the result of cat(.libPaths()[1])
into $lib as intended.
One idea might be ensuring that this gets into the last line on its own,
and then taking $lib as the last line of what we got ...
Best
-k
This did not happen with 2.4.1
Thank you Seth.
Gregor
______________________________________________ R-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Kurt Hornik writes:
Gregor Gorjanc writes:
Seth Falcon <sfalcon <at> fhcrc.org> writes:
The quick fix for you is, I believe,
if (interactive()) {
library(fortunes)
fortune()
detach("package:fortunes")
}
Whether something could be changed so that R's output doesn't confuse
itself and gcc when doing R CMD INSTALL, seems like it should be
possible.
Yes, this solves my! problem. I do not know what is causing this behaviour.
Well, r-devel's src/scripts/INSTALL.in now has
if test -z "${lib}"; then
lib=`echo "cat(.libPaths()[1])" | \
R_DEFAULT_PACKAGES=NULL "${R_EXE}" --no-save --slave`
message "Installing to library '$lib'"
so we need to find a way to "just get" the result of cat(.libPaths()[1]) into $lib as intended.
One idea might be ensuring that this gets into the last line on its own, and then taking $lib as the last line of what we got ...
I think I found (and committed) a solution for this. Best -k
3 days later
Kurt Hornik wrote:
Kurt Hornik writes:
>> Well, r-devel's src/scripts/INSTALL.in now has
if test -z "${lib}"; then
lib=`echo "cat(.libPaths()[1])" | \
R_DEFAULT_PACKAGES=NULL "${R_EXE}" --no-save --slave`
message "Installing to library '$lib'"
so we need to find a way to "just get" the result of cat(.libPaths()[1]) into $lib as intended.
One idea might be ensuring that this gets into the last line on its own, and then taking $lib as the last line of what we got ...
I think I found (and committed) a solution for this.
Yep, looks OK now. Thanks, Gregor