[Rd] as.matrix.data.frame( Date ) -> character
Hello,
Is this intended:
> m <- data.frame( date = seq.Date( as.Date("2000-01-01"),
as.Date("2000-01-05"), by = "day" ) )
> sapply( m, typeof )
date
"double"
> as.matrix( m )
date
[1,] "2000-01-01"
[2,] "2000-01-02"
[3,] "2000-01-03"
[4,] "2000-01-04"
[5,] "2000-01-05"
> typeof( as.matrix( m ) )
[1] "character"
In particular :
> m <- data.frame( date = seq.Date( as.Date("2000-01-01"), by = "day",
length.out = 50 ), x = rnorm(50) )
> loess( x ~ date, data= m)
Error: NA/NaN/Inf in foreign function call (arg 2)
In addition: Warning message:
NAs introduced by coercion
> loess( x ~ as.double(date), data= m)
Call:
loess(formula = x ~ as.double(date), data = m)
Number of Observations: 50
Equivalent Number of Parameters: 4.42
Residual Standard Error: 0.9712
Replacing this line in loess :
x <- as.matrix(x)
by this :
x <- tryCatch( do.call( cbind, lapply( x, as.double ) ), error =
function(e){
stop( "predictors must all be numeric" )
} )
does the trick for me.
Romain
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|- http://tr.im/BcPw : celebrating R commit #5
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[Rd] Possible bug in the Rd parser?
Dear list,
I got an automatic email complaining than some of my packages didn't
pass 'R CMD check' for R-2.10.0 alpha anymore. Both of them make use of
the "cases" LaTeX environment.
Inspecting the log outputs I got:
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Misplaced alignment tab character &.
I noticed that the Rd parser changed quite recently and that '#', '_'
and '&' must not be escaped according to "Writing R extensions".
However, the problematic .Rd portion seems (to me) OK
\deqn{\theta(h) =
\begin{cases}
u_\beta \left(\mu + \frac{\nu(h)}{\Gamma(1 - \xi)}
\right),&\xi \neq 0\\
\exp\left(\frac{\nu(h)}{\sigma}\right),&\xi = 0
\end{cases}
}{u_beta (mu + nu(h) / Gamma(1 - \xi)), if \xi < 1,
exp(nu(h)/sigma), otherwise}
Removing the alignment tab character '&' solves the issue but doesn't
produce the expected LaTeX output. Do I miss something with the new Rd
parser requirements?
I'm not 100% sure but it also seems like that "\\' symbol isn't
interpreted as a break line - in the "cases" environment at least. This
might be one reason why the alignment tab '&' is misplaced.
Best,
Mathieu
--
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Ecole Polytechnique Fédérale de Lausanne
STAT-IMA-FSB-EPFL, Station 8
CH-1015 Lausanne Switzerland
http://stat.epfl.ch/
Tel: + 41 (0)21 693 7907
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[Rd] installing any package fails using 'install.packages()' (PR#13993)
Dear all,
I installed my R-2.9.2 on my ubuntu version 9.04 successfully using the
command
sudo apt-get install r-base-dev
The problem is that I cannot install any package.
See my details below:
> install.packages("epicalc")
Warning in install.packages("epicalc") :
argument 'lib' is missing: using
'/home/lmramba/R/i486-pc-linux-gnu-library/2.9'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
Error in read.dcf(file = tmpf) : Line starting ' ...' is malformed!
>
> install.packages("lattice")
Warning in install.packages("lattice") :
argument 'lib' is missing: using
'/home/lmramba/R/i486-pc-linux-gnu-library/2.9'
Error in read.dcf(file = tmpf) : Line starting ' ...' is malformed!
>
> sessionInfo()
R version 2.9.2 (2009-08-24)
i486-pc-linux-gnu
locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tcltk_2.9.2 tools_2.9.2
>
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[Rd] Errors in installing package "rJava" on Ubuntu (PR#13992)
*Hello,
I have had this serious problem while trying to install package rJava. It is
a requirement by the package JGR and it cannot be downloaded due to the
error indicated below.
I have googled and looked at the FAQ but no solution yet.
Please advise.
Kind regards,
Lazarus
> install.packages("rJava")*
Warning in install.packages("rJava") :
argument 'lib' is missing: using
'/home/lmramba/R/i486-pc-linux-gnu-library/2.9'
*Error in read.dcf(file = tmpf) : Line starting ' ...' is malformed!*
>
*> install.packages("JGR")*
Warning in install.packages("JGR") :
argument 'lib' is missing: using
'/home/lmramba/R/i486-pc-linux-gnu-library/2.9'
*Error in read.dcf(file = tmpf) : Line starting ' ...' is malformed!
*
*> sessionInfo()*
R version 2.9.2 (2009-08-24)
i486-pc-linux-gnu
locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tcltk_2.9.2 tools_2.9.2
>
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[Rd] rJava downloads but cannot load, when I run R as root (PR#13994)
> library(rJava)
Error in library(rJava) : there is no package called 'rJava'
> install.packages("rJava")
Warning in install.packages("rJava") :
argument 'lib' is missing: using '/usr/local/lib/R/site-library'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://cran.uk.r-project.org/src/contrib/rJava_0.7-0.tar.gz'
Content type 'application/x-gzip' length 249486 bytes (243 Kb)
opened URL
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
downloaded 243 Kb
* Installing *source* package =91rJava=92 ...
checking for gcc... gcc -std=3Dgnu99
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 -std=3Dgnu99 accepts -g... yes
checking for gcc -std=3Dgnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=3Dgnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether gcc -std=3Dgnu99 supports static inline...
yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver: '/usr/bin/jar'
compiler: '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags : ''
java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/i386/server
-L/usr/lib/jvm/java-6-openjdk/jre/lib/i386
-L/usr/lib/jvm/java-6-openjdk/jre/../lib/i386 -L
-L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm'
configure: error: One or more Java configuration variables are not set.
Make sure R is configured with full Java support (including JDK). Run
R CMD javareconf
as root to add Java support to R.
If you don't have root privileges, run
R CMD javareconf -e
to set all Java-related variables and then install rJava.
ERROR: configuration failed for package =91rJava=92
* Removing =91/usr/local/lib/R/site-library/rJava=92
The downloaded packages are in
=91/tmp/RtmpOjM9hY/downloaded_packages=92
Warning message:
In install.packages("rJava") :
installation of package 'rJava' had non-zero exit status
>
I went ahead and did this:
r...@lmramba-laptop:/home/lmramba# R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.6.0_0
Java home path : /usr/lib/jvm/java-6-openjdk/jre
Java compiler: /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Java library path:
$(JAVA_HOME)/lib/i386/server:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386=
::/usr/java/packages/lib/i386:/lib:/usr/lib
JNI linker flags : -L$(JAVA_HOME)/lib/i386/server -L$(JAVA_HOME)/lib/i386
-L$(JAVA_HOME)/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib
-L/usr/lib -ljvm
JNI cpp flags:
Updating Java configuration in /etc/R
Done.
But still installing rJava fails
Plz help
Regards,
Lazarus
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[Rd] Setting a mirror "permanently" on R on ubuntu (PR#13995)
Dear all,
I seem to have many problems as I run R on my ubuntu system.
want to set a mirror so that anytime I use the command "install.packages",
it does not ask me for which mirror to use but go direct.
This is because of the error I keep on getting below and I dont know how to
solve it.
Please help.
Kind regards,
Lazarus
> library(epicalc)
Loading required package: foreign
Loading required package: survival
Loading required package: splines
> install.packages("lattice")
Warning in install.packages("lattice") :
argument 'lib' is missing: using
'/home/lmramba/R/i486-pc-linux-gnu-library/2.9'
Error in contrib.url(repos, type) :
trying to use CRAN without setting a mirror
Calls: install.packages -> grep -> contrib.url
Execution halted
Exited: 256
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Re: [Rd] Errors in installing package "rJava" on Ubuntu (PR#13992)
On 10 October 2009 at 04:15, lmra...@gmail.com wrote:
| *Hello,
| I have had this serious problem while trying to install package rJava. It is
| a requirement by the package JGR and it cannot be downloaded due to the
| error indicated below.
a) Problems with packages should go to the maintainer, not the lists. So
this one is for Simon.
b) That said, also wrong list.
Debian and Ubuntu questions go to the r-sig-debian list.
| I have googled and looked at the FAQ but no solution yet.
|
| Please advise.
| Kind regards,
| Lazarus
|
| > install.packages("rJava")*
c) "Wrong" (in the 'you are making your life to complicated' sense) as
$ sudo apt-get install r-cran-rjava
works:
e...@joe:~$ sudo apt-get install r-cran-rjava
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following NEW packages will be installed:
r-cran-rjava
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 225kB of archives.
After this operation, 836kB of additional disk space will be used.
Get:1 http://archive.ubuntu.com jaunty/universe r-cran-rjava 0.6-2-1 [225kB]
Fetched 225kB in 1s (146kB/s)
Selecting previously deselected package r-cran-rjava.
(Reading database ... 397686 files and directories currently installed.)
Unpacking r-cran-rjava (from .../r-cran-rjava_0.6-2-1_i386.deb) ...
Setting up r-cran-rjava (0.6-2-1) ...
e...@joe:~$
Having this installed should provide the base for installed RWeka, JGR,
... and other users of rJava.
So in sum: not a bug in R and you just created extra work for R Core to
maintain the bug database.
Dirk
| Warning in install.packages("rJava") :
| argument 'lib' is missing: using
| '/home/lmramba/R/i486-pc-linux-gnu-library/2.9'
| *Error in read.dcf(file = tmpf) : Line starting ' ...' is malformed!*
| >
| *> install.packages("JGR")*
| Warning in install.packages("JGR") :
| argument 'lib' is missing: using
| '/home/lmramba/R/i486-pc-linux-gnu-library/2.9'
| *Error in read.dcf(file = tmpf) : Line starting ' ...' is malformed!
| *
| *> sessionInfo()*
| R version 2.9.2 (2009-08-24)
| i486-pc-linux-gnu
|
| locale:
|
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
|
| attached base packages:
| [1] stats graphics grDevices utils datasets methods base
|
| loaded via a namespace (and not attached):
| [1] tcltk_2.9.2 tools_2.9.2
| >
|
| [[alternative HTML version deleted]]
|
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Re: [Rd] installing any package fails using 'install.packages()' (PR#13993)
On 10 October 2009 at 05:25, lmra...@gmail.com wrote:
| Dear all,
| I installed my R-2.9.2 on my ubuntu version 9.04 successfully using the
| command
|
|sudo apt-get install r-base-dev
|
| The problem is that I cannot install any package.
Huh? This has _nothing_ to do with the error below.
| See my details below:
|
|
|
| > install.packages("epicalc")
| Warning in install.packages("epicalc") :
| argument 'lib' is missing: using
| '/home/lmramba/R/i486-pc-linux-gnu-library/2.9'
This is suspicuous.
If you used the Ubuntu package, it would use /usr/local/lib/R/site-library by
default. So if you have a locally built version *you* need to figure out
what you broke there.
| --- Please select a CRAN mirror for use in this session ---
| Loading Tcl/Tk interface ... done
| Error in read.dcf(file = tmpf) : Line starting ' ...' is malformed!
| >
| > install.packages("lattice")
| Warning in install.packages("lattice") :
| argument 'lib' is missing: using
| '/home/lmramba/R/i486-pc-linux-gnu-library/2.9'
| Error in read.dcf(file = tmpf) : Line starting ' ...' is malformed!
No idea but you busted there. But it looks suspiciously like a local error on
your end.
Set an explicit argument for the repos, e.g. via ~/.Rprofile
options("repos"="http://cran.us.r-project.org";)## US mirror
(as I am in the US, adapt accordingly for a close mirror for you) to avoid
the tcl/tk query.
That, again, works like a charm here on Ubuntu 9.10:
R> install.packages("epicalc")
Warning in install.packages("epicalc") :
argument 'lib' is missing: using '/usr/local/lib/R/site-library'
trying URL 'http://cran.us.r-project.org/src/contrib/epicalc_2.9.2.5.tar.gz'
Content type 'application/x-gzip' length 201849 bytes (197 Kb)
opened URL
==
downloaded 197 Kb
* Installing *source* package ‘epicalc’ ...
** R
** data
** demo
** preparing package for lazy loading
Loading required package: splines
** help
*** installing help indices
>>> Building/Updating help pages for package 'epicalc'
Formats: text html latex example
ANCdata texthtmllatex
[...]
use texthtmllatex example
zap texthtmllatex example
** building package indices ...
* DONE (epicalc)
The downloaded packages are in
‘/tmp/RtmpydkfiZ/downloaded_packages’
R>
If you install into /usr/local/lib/R/site-library, I recommend making that
directory's group mode one of the ones you have and set it to group-write. I
typically make myself member of group 'staff' (or 'admin').
Again, in sum: not a bug in R and you just created extra work for R Core to
maintain the bug database.
Dirk
| > sessionInfo()
| R version 2.9.2 (2009-08-24)
| i486-pc-linux-gnu
|
| locale:
|
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
|
| attached base packages:
| [1] stats graphics grDevices utils datasets methods base
|
| loaded via a namespace (and not attached):
| [1] tcltk_2.9.2 tools_2.9.2
| >
|
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|
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Re: [Rd] rJava downloads but cannot load, when I run R as root (PR#13994)
On 10 October 2009 at 05:40, lmra...@gmail.com wrote:
| > library(rJava)
| Error in library(rJava) : there is no package called 'rJava'
| > install.packages("rJava")
| Warning in install.packages("rJava") :
| argument 'lib' is missing: using '/usr/local/lib/R/site-library'
| --- Please select a CRAN mirror for use in this session ---
| Loading Tcl/Tk interface ... done
| trying URL 'http://cran.uk.r-project.org/src/contrib/rJava_0.7-0.tar.gz'
| Content type 'application/x-gzip' length 249486 bytes (243 Kb)
| opened URL
| =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
| =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
| downloaded 243 Kb
|
| * Installing *source* package =91rJava=92 ...
| checking for gcc... gcc -std=3Dgnu99
| checking for C compiler default output file name... a.out
[...]
| configure: checking whether gcc -std=3Dgnu99 supports static inline...
| yes
| checking Java support in R... present:
| interpreter : '/usr/bin/java'
| archiver: '/usr/bin/jar'
| compiler: '/usr/bin/javac'
| header prep.: '/usr/bin/javah'
| cpp flags : ''
| java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/i386/server
| -L/usr/lib/jvm/java-6-openjdk/jre/lib/i386
| -L/usr/lib/jvm/java-6-openjdk/jre/../lib/i386 -L
| -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm'
| configure: error: One or more Java configuration variables are not set.
| Make sure R is configured with full Java support (including JDK). Run
| R CMD javareconf
| as root to add Java support to R.
R tells you your Java setup is not right. This *is* difficult, which is why I
have offered to maintain and provide the rJava in Debian / Ubuntu as
r-cran-rjava.
As demonstrated to you two emails ago, it also works. I would use that.
Otherwise, fix your Java setup first as R told you to here.
|
| If you don't have root privileges, run
| R CMD javareconf -e
| to set all Java-related variables and then install rJava.
|
| ERROR: configuration failed for package =91rJava=92
| * Removing =91/usr/local/lib/R/site-library/rJava=92
|
| The downloaded packages are in
| =91/tmp/RtmpOjM9hY/downloaded_packages=92
| Warning message:
| In install.packages("rJava") :
| installation of package 'rJava' had non-zero exit status
| >
|
|
| I went ahead and did this:
|
| r...@lmramba-laptop:/home/lmramba# R CMD javareconf
| Java interpreter : /usr/bin/java
| Java version : 1.6.0_0
| Java home path : /usr/lib/jvm/java-6-openjdk/jre
| Java compiler: /usr/bin/javac
| Java headers gen.: /usr/bin/javah
| Java archive tool: /usr/bin/jar
| Java library path:
| $(JAVA_HOME)/lib/i386/server:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386=
| ::/usr/java/packages/lib/i386:/lib:/usr/lib
| JNI linker flags : -L$(JAVA_HOME)/lib/i386/server -L$(JAVA_HOME)/lib/i386
| -L$(JAVA_HOME)/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib
| -L/usr/lib -ljvm
| JNI cpp flags:
| Updating Java configuration in /etc/R
| Done.
|
|
| But still installing rJava fails
As before: not a bug in R and you just created extra work for R Core to
maintain the bug database.
Dirk
| Plz help
|
| Regards,
| Lazarus
|
| [[alternative HTML version deleted]]
|
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Re: [Rd] rJava downloads but cannot load, (PR#13997)
On 10 October 2009 at 05:40, lmra...@gmail.com wrote:
| > library(rJava)
| Error in library(rJava) : there is no package called 'rJava'
| > install.packages("rJava")
| Warning in install.packages("rJava") :
| argument 'lib' is missing: using '/usr/local/lib/R/site-library'
| --- Please select a CRAN mirror for use in this session ---
| Loading Tcl/Tk interface ... done
| trying URL 'http://cran.uk.r-project.org/src/contrib/rJava_0.7-0.tar.gz'
| Content type 'application/x-gzip' length 249486 bytes (243 Kb)
| opened URL
| =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
| =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
| downloaded 243 Kb
|
| * Installing *source* package =91rJava=92 ...
| checking for gcc... gcc -std=3Dgnu99
| checking for C compiler default output file name... a.out
[...]
| configure: checking whether gcc -std=3Dgnu99 supports static inline...
| yes
| checking Java support in R... present:
| interpreter : '/usr/bin/java'
| archiver: '/usr/bin/jar'
| compiler: '/usr/bin/javac'
| header prep.: '/usr/bin/javah'
| cpp flags : ''
| java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/i386/server
| -L/usr/lib/jvm/java-6-openjdk/jre/lib/i386
| -L/usr/lib/jvm/java-6-openjdk/jre/../lib/i386 -L
| -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm'
| configure: error: One or more Java configuration variables are not set.
| Make sure R is configured with full Java support (including JDK). Run
| R CMD javareconf
| as root to add Java support to R.
R tells you your Java setup is not right. This *is* difficult, which is why I
have offered to maintain and provide the rJava in Debian / Ubuntu as
r-cran-rjava.
As demonstrated to you two emails ago, it also works. I would use that.
Otherwise, fix your Java setup first as R told you to here.
|
| If you don't have root privileges, run
| R CMD javareconf -e
| to set all Java-related variables and then install rJava.
|
| ERROR: configuration failed for package =91rJava=92
| * Removing =91/usr/local/lib/R/site-library/rJava=92
|
| The downloaded packages are in
| =91/tmp/RtmpOjM9hY/downloaded_packages=92
| Warning message:
| In install.packages("rJava") :
| installation of package 'rJava' had non-zero exit status
| >
|
|
| I went ahead and did this:
|
| r...@lmramba-laptop:/home/lmramba# R CMD javareconf
| Java interpreter : /usr/bin/java
| Java version : 1.6.0_0
| Java home path : /usr/lib/jvm/java-6-openjdk/jre
| Java compiler: /usr/bin/javac
| Java headers gen.: /usr/bin/javah
| Java archive tool: /usr/bin/jar
| Java library path:
| $(JAVA_HOME)/lib/i386/server:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386=
| ::/usr/java/packages/lib/i386:/lib:/usr/lib
| JNI linker flags : -L$(JAVA_HOME)/lib/i386/server -L$(JAVA_HOME)/lib/i386
| -L$(JAVA_HOME)/../lib/i386 -L -L/usr/java/packages/lib/i386 -L/lib
| -L/usr/lib -ljvm
| JNI cpp flags:
| Updating Java configuration in /etc/R
| Done.
|
|
| But still installing rJava fails
As before: not a bug in R and you just created extra work for R Core to
maintain the bug database.
Dirk
| Plz help
|
| Regards,
| Lazarus
|
| [[alternative HTML version deleted]]
|
| __
| R-devel@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel
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Re: [Rd] Setting a mirror "permanently" on R on ubuntu (PR#13995)
On 10 October 2009 at 05:55, lmra...@gmail.com wrote:
| Dear all,
|
| I seem to have many problems as I run R on my ubuntu system.
| want to set a mirror so that anytime I use the command "install.packages",
| it does not ask me for which mirror to use but go direct.
| This is because of the error I keep on getting below and I dont know how to
| solve it.
Can you _please stop abusing the bug tracking system_ by asking these
beginner questions?
This is answered, inter alia, in
help(install.packages) # telling you about option("repos")
help(options)# telling you about the repos option
help(Startup)# telling you about R's inits
as well as the different manuals.
Also, see one of the emails I just sent you for the concrete example:
e...@joe:~$ cat .Rprofile
options("width"=160)
#options("pdfviewer"="kpdf")
# as in AER by Zeileis and Kleiber
options(prompt="R> ", digits=4, show.signif.stars=FALSE)
options("repos"="http://cran.us.r-project.org";)## US mirror
Lastly, *please* switch to r-sig-debian for help with your Debian / Ubuntu
system and stop abusing the r-devel list and the bug tracker.
Dirk
| Please help.
|
| Kind regards,
| Lazarus
|
|
| > library(epicalc)
| Loading required package: foreign
| Loading required package: survival
| Loading required package: splines
| > install.packages("lattice")
| Warning in install.packages("lattice") :
| argument 'lib' is missing: using
| '/home/lmramba/R/i486-pc-linux-gnu-library/2.9'
| Error in contrib.url(repos, type) :
| trying to use CRAN without setting a mirror
| Calls: install.packages -> grep -> contrib.url
| Execution halted
|
| Exited: 256
|
| [[alternative HTML version deleted]]
|
| __
| R-devel@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel
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Re: [Rd] installing any package fails using 'install.packages()' (PR#13996)
On 10 October 2009 at 05:25, lmra...@gmail.com wrote:
| Dear all,
| I installed my R-2.9.2 on my ubuntu version 9.04 successfully using=
the
| command
|=20
|sudo apt-get install r-base-dev
|=20
| The problem is that I cannot install any package.
Huh? This has _nothing_ to do with the error below.
=20
| See my details below:
|=20
|=20
|=20
| > install.packages("epicalc")
| Warning in install.packages("epicalc") :
| argument 'lib' is missing: using
| '/home/lmramba/R/i486-pc-linux-gnu-library/2.9'
This is suspicuous.=20
If you used the Ubuntu package, it would use /usr/local/lib/R/site-libr=
ary by
default. So if you have a locally built version *you* need to figure o=
ut
what you broke there.
| --- Please select a CRAN mirror for use in this session ---
| Loading Tcl/Tk interface ... done
| Error in read.dcf(file =3D tmpf) : Line starting ' ...' is malf=
ormed!
| >
| > install.packages("lattice")
| Warning in install.packages("lattice") :
| argument 'lib' is missing: using
| '/home/lmramba/R/i486-pc-linux-gnu-library/2.9'
| Error in read.dcf(file =3D tmpf) : Line starting ' ...' is malf=
ormed!
No idea but you busted there. But it looks suspiciously like a local er=
ror on
your end.
Set an explicit argument for the repos, e.g. via ~/.Rprofile
options("repos"=3D"http://cran.us.r-project.org";)## US mirror
(as I am in the US, adapt accordingly for a close mirror for you) to av=
oid
the tcl/tk query. =20
That, again, works like a charm here on Ubuntu 9.10:
R> install.packages("epicalc")
Warning in install.packages("epicalc") :
argument 'lib' is missing: using '/usr/local/lib/R/site-library'
trying URL 'http://cran.us.r-project.org/src/contrib/epicalc_2.9.2.5.ta=
r.gz'
Content type 'application/x-gzip' length 201849 bytes (197 Kb) =
=20
opened URL =
=20
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D =20
downloaded 197 Kb =
=20
* Installing *source* package =E2=80=98epicalc=E2=80=99 ...
** R =20
** data =20
** demo =20
** preparing package for lazy loading =20
Loading required package: splines =20
** help =20
*** installing help indices =20
>>> Building/Updating help pages for package 'epicalc'
Formats: text html latex example =20
ANCdata texthtmllatex
[...]
use texthtmllatex example
zap texthtmllatex example
** building package indices ...
* DONE (epicalc)
The downloaded packages are in
=E2=80=98/tmp/RtmpydkfiZ/downloaded_packages=E2=80=99
R>
If you install into /usr/local/lib/R/site-library, I recommend making t=
hat
directory's group mode one of the ones you have and set it to group-wri=
te. I
typically make myself member of group 'staff' (or 'admin').
Again, in sum: not a bug in R and you just created extra work for R Cor=
e to
maintain the bug database.
Dirk
| > sessionInfo()
| R version 2.9.2 (2009-08-24)
| i486-pc-linux-gnu
|=20
| locale:
| LC_CTYPE=3Den_GB.UTF-8;LC_NUMERIC=3DC;LC_TIME=3Den_GB.UTF-8;LC_COLLAT=
E=3Den_GB.UTF-8;LC_MONETARY=3DC;LC_MESSAGES=3Den_GB.UTF-8;LC_PAPER=3Den=
_GB.UTF-8;LC_NAME=3DC;LC_ADDRESS=3DC;LC_TELEPHONE=3DC;LC_MEASUREMENT=3D=
en_GB.UTF-8;LC_IDENTIFICATION=3DC
|=20
| attached base packages:
| [1] stats graphics grDevices utils datasets methods base
|=20
| loaded via a namespace (and not attached):
| [1] tcltk_2.9.2 tools_2.9.2
| >
|=20
| =09[[alternative HTML version deleted]]
|=20
| __
| R-devel@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel
--=20
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Re: [Rd] [R-SIG-Mac] rnorm.halton
Hi all, I need to transform classic 32bit Fortran code to 64bit Fortran code, see the discussion [R-SIG-Mac] rnorm.halton. But I'm clearly a beginner in Fortran... Does someone already do this for his package? From here, http://techpubs.sgi.com/library/tpl/cgi-bin/getdoc.cgi?coll=linux&db=bks&fname=/SGI_Developer/Porting_Guide/ch03.html , I identify the following changes (Fortran types) to the Fortran code: - INTEGER to INTEGER*8 - REAL*8 to REAL*16 The code I would like to change is available on R forge here : http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/pkg/randtoolbox/src/LowDiscrepancy.f?rev=4229&root=rmetrics&view=markup Another question I have is how do I tell the R code to use the 64bit version of my code on 64bit machine? In the current implementation, the file quasiRNG.R calls directly the Fortran code with .Fortran. How could I use the 64bit version directly in the R code? I suspect I need to have a quasiRNG.c file where I will use preprocessor statement that will select the good version of the function to call. Is that correct? Thanks in advance Christophe Le 15 sept. 2009 à 18:25, Anirban Mukherjee a écrit : Sorry, what I should have said was Halton numbers are quasi-random, and not pseudo-random. Quasi-random is the technically appropriate terminology. Halton sequences are low discrepancy: the subsequence looks/smells random. Hence, they are often used in quasi monte carlo simulations. To be precise, there is only 1 Halton sequence for a particular prime. Repeated calls to Halton should return the same numbers. The first column is the Halton sequence for 2. the second for 3, the third for 5 and so on using the first M primes (for M columns). (You can also scramble the sequence to avoid this.) I am using them to integrate over a multivariate normal space. If you take 1000 random draws, then sum f() over the draws is the expectation of f(). If f() is very non-linear (and/or multi-variate) then even with large N, its often hard to get a good integral. With quasi-random draws, the integration is better for the same N. (One uses the inverse distribution function.) For an example, you can look at Train's paper (page 4 and 5 have a good explanation) at: http://elsa.berkeley.edu/wp/train0899.pdf In the context of simulated maximum likelihood estimation, such integrals are very common. Of course true randomness has its own place/importance: its just that quasi-random numbers can be very useful in certain contexts. Regards, Anirban PS: qnorm(halton()) gets around the problem of the random deviates not working. On Tue, Sep 15, 2009 at 11:37 AM, David Winsemius wrote: On Sep 15, 2009, at 11:10 AM, Anirban Mukherjee wrote: Thanks everyone for your replies. Particularly David. The numbers are pseudo-random. Repeated calls should/would give the same output. As I said, this package is not one with which I have experience. It has _not_ however the case that repeated calls to (typical?) random number functions give the same output when called repeatedly: > rnorm(10) [1] -0.8740195 2.1827411 -0.1473012 -1.4406262 0.1820631 -1.3151244 -0.4813703 0.8177692 [9] 0.2076117 1.8697418 > rnorm(10) [1] -0.7725731 0.8696742 -0.4907099 0.1561859 0.5913528 -0.8441891 0.2285653 -0.1231755 [9] 0.5190459 -0.7803617 > rnorm(10) [1] -0.9585881 -0.0458582 1.1967342 0.6421980 -0.5290280 -1.0735112 0.6346301 0.2685760 [9] 1.5767800 1.0864515 > rnorm(10) [1] -0.60400852 -0.06611533 1.00787048 1.48289305 0.5465 -0.67630052 0.52664127 -0.36449997 [9] 0.88039397 0.56929333 I cannot imagine a situation where one would _want_ the output to be the same on repeated calls unless one reset a seed. Unless perhaps I am not understanding the meaning of "random" in the financial domain? -- David Currently, Halton works fine when used to just get the Halton sequence, but the random deviates call is not working in 64 bit R. For now, I will generate the numbers in 32 bit R, save them and then load them back in when using 64 bit R. The package maintainers can look at it if/when they get a chance and/or access to 64 bit R. Thanks! Best, Anirban On Tue, Sep 15, 2009 at 9:01 AM, David Winsemius wrote: I get very different output from the two versions of Mac OSX R as well. The 32 bit version puts out a histogram that has an expected, almost symmetric unimodal distribution. The 64 bit version created a bimodal distribution with one large mode near 0 and another smaller mode near 10E+37. Postcript output attached. -- Anirban Mukherjee | Assistant Professor, Marketing | LKCSB, SMU 5062 School of Business, 50 Stamford Road, Singapore 178899 | +65-6828-1932 ___ R-SIG-Mac mailing list r-sig-...@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac David Winsemius, MD Heritage Laboratories West Hartford, CT -- Anirban Mukherjee | Assistant Professor, Marketing
Re: [Rd] [R-SIG-Mac] rnorm.halton
Christophe, you're looking at the wrong docs -- normally there is nothing you need to change FORTRAN code when switching between 32-bit and 64-bit. There is no separate "64-bit code" or "32-bit code". None of the scalar types used by R in interfaces changes (int, double and INTEGER, REAL*8 are both the same). You only need to change your code if you make assumptions about the size of pointers which increases from 4 bytes to 8 bytes (and normally you should not be making those assumptions). I don't think you should touch any Fortran code. For the C code, the only thing that changes (beside pointer size) is "long" data types. If you use those in your code, you must be aware that the corresponding size change. I suspect that if you have a discrepancy in your 32/64-bit binaries then you either have a bug somewhere (Fortran or C) or your C code is not 64-bit clean (i.e. makes some 32-bit assumptions that are not true in 64-bit environment - check the use of "long" data types and pointers). Again, the solution is to fix the code to be clean, it will still be the same for both 32-bit and 64-bit. Cheers, Simon On Oct 10, 2009, at 12:04 PM, Christophe Dutang wrote: Hi all, I need to transform classic 32bit Fortran code to 64bit Fortran code, see the discussion [R-SIG-Mac] rnorm.halton. But I'm clearly a beginner in Fortran... Does someone already do this for his package? From here, http://techpubs.sgi.com/library/tpl/cgi-bin/getdoc.cgi?coll=linux&db=bks&fname=/SGI_Developer/Porting_Guide/ch03.html , I identify the following changes (Fortran types) to the Fortran code: - INTEGER to INTEGER*8 - REAL*8 to REAL*16 The code I would like to change is available on R forge here : http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/pkg/randtoolbox/src/LowDiscrepancy.f?rev=4229&root=rmetrics&view=markup Another question I have is how do I tell the R code to use the 64bit version of my code on 64bit machine? In the current implementation, the file quasiRNG.R calls directly the Fortran code with .Fortran. How could I use the 64bit version directly in the R code? I suspect I need to have a quasiRNG.c file where I will use preprocessor statement that will select the good version of the function to call. Is that correct? Thanks in advance Christophe Le 15 sept. 2009 à 18:25, Anirban Mukherjee a écrit : Sorry, what I should have said was Halton numbers are quasi-random, and not pseudo-random. Quasi-random is the technically appropriate terminology. Halton sequences are low discrepancy: the subsequence looks/smells random. Hence, they are often used in quasi monte carlo simulations. To be precise, there is only 1 Halton sequence for a particular prime. Repeated calls to Halton should return the same numbers. The first column is the Halton sequence for 2. the second for 3, the third for 5 and so on using the first M primes (for M columns). (You can also scramble the sequence to avoid this.) I am using them to integrate over a multivariate normal space. If you take 1000 random draws, then sum f() over the draws is the expectation of f(). If f() is very non-linear (and/or multi-variate) then even with large N, its often hard to get a good integral. With quasi- random draws, the integration is better for the same N. (One uses the inverse distribution function.) For an example, you can look at Train's paper (page 4 and 5 have a good explanation) at: http://elsa.berkeley.edu/wp/train0899.pdf In the context of simulated maximum likelihood estimation, such integrals are very common. Of course true randomness has its own place/importance: its just that quasi-random numbers can be very useful in certain contexts. Regards, Anirban PS: qnorm(halton()) gets around the problem of the random deviates not working. On Tue, Sep 15, 2009 at 11:37 AM, David Winsemius wrote: On Sep 15, 2009, at 11:10 AM, Anirban Mukherjee wrote: Thanks everyone for your replies. Particularly David. The numbers are pseudo-random. Repeated calls should/would give the same output. As I said, this package is not one with which I have experience. It has _not_ however the case that repeated calls to (typical?) random number functions give the same output when called repeatedly: > rnorm(10) [1] -0.8740195 2.1827411 -0.1473012 -1.4406262 0.1820631 -1.3151244 -0.4813703 0.8177692 [9] 0.2076117 1.8697418 > rnorm(10) [1] -0.7725731 0.8696742 -0.4907099 0.1561859 0.5913528 -0.8441891 0.2285653 -0.1231755 [9] 0.5190459 -0.7803617 > rnorm(10) [1] -0.9585881 -0.0458582 1.1967342 0.6421980 -0.5290280 -1.0735112 0.6346301 0.2685760 [9] 1.5767800 1.0864515 > rnorm(10) [1] -0.60400852 -0.06611533 1.00787048 1.48289305 0.5465 -0.67630052 0.52664127 -0.36449997 [9] 0.88039397 0.56929333 I cannot imagine a situation where one would _want_ the output to be the same on repeated calls unless one reset a seed. Unless perhaps I am not understanding
Re: [Rd] Possible bug in the Rd parser?
On 10/10/2009 8:07 AM, Mathieu Ribatet wrote:
Dear list,
I got an automatic email complaining than some of my packages didn't
pass 'R CMD check' for R-2.10.0 alpha anymore. Both of them make use of
the "cases" LaTeX environment.
Inspecting the log outputs I got:
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Misplaced alignment tab character &.
I noticed that the Rd parser changed quite recently and that '#', '_'
and '&' must not be escaped according to "Writing R extensions".
However, the problematic .Rd portion seems (to me) OK
\deqn{\theta(h) =
\begin{cases}
u_\beta \left(\mu + \frac{\nu(h)}{\Gamma(1 - \xi)}
\right),&\xi \neq 0\\
\exp\left(\frac{\nu(h)}{\sigma}\right),&\xi = 0
\end{cases}
}{u_beta (mu + nu(h) / Gamma(1 - \xi)), if \xi < 1,
exp(nu(h)/sigma), otherwise}
Removing the alignment tab character '&' solves the issue but doesn't
produce the expected LaTeX output. Do I miss something with the new Rd
parser requirements?
I think the new parser is working properly, but there is something wrong
with your LaTeX. When I paste that block into a test file and run it
through the 2.9 parser, the \\ gets converted to \bsl{}, and garbage
results. The new parser faithfully reproduces what you wrote, but for
some reason it's not legal LaTeX.
I suspect the problem is that the text is generated within a \deqn{}
macro, which is defined in Rd.sty. Something you're doing is not
allowed in that context.
It's helpful to run
Rcmd Rd2dvi --no-clean test.Rd
to be able to examine the LaTeX produced by R (which will be saved in a
temporary directory; the --no-clean tells R not to delete it at the end).
I don't know LaTeX well enough to tell you the best workaround for this,
but one option is to used the recently added \if or \ifelse and \out
macros instead of \deqn. Of course, that will make your Rd file
unusable in earlier versions, so it's not necessarily the best idea.
Duncan Murdoch
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Re: [Rd] [R-SIG-Mac] rnorm.halton
Christophe, I forgot to answer the second part of your e-mail -- see below. On Oct 10, 2009, at 12:04 PM, Christophe Dutang wrote: Hi all, I need to transform classic 32bit Fortran code to 64bit Fortran code, see the discussion [R-SIG-Mac] rnorm.halton. But I'm clearly a beginner in Fortran... Does someone already do this for his package? From here, http://techpubs.sgi.com/library/tpl/cgi-bin/getdoc.cgi?coll=linux&db=bks&fname=/SGI_Developer/Porting_Guide/ch03.html , I identify the following changes (Fortran types) to the Fortran code: - INTEGER to INTEGER*8 - REAL*8 to REAL*16 The code I would like to change is available on R forge here : http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/pkg/randtoolbox/src/LowDiscrepancy.f?rev=4229&root=rmetrics&view=markup Another question I have is how do I tell the R code to use the 64bit version of my code on 64bit machine? In the current implementation, the file quasiRNG.R calls directly the Fortran code with .Fortran. How could I use the 64bit version directly in the R code? You don't have a choice -- whether 32 or 64 bits are used is defined by R, because you cannot mix 32-bit and 64-bit code. So in 64-bit R your package will be compiled into 64-bit. In 32-bit R your package will be compiled in 32-bit. You can see which R you are using with 8 * .Machine$sizeof.pointer (Note: The Mac binaries we provide are multi-arch so they [the Leopard build] do in fact include both 32-bit and 64-bit -- which one gets started depends on the --arch flag, see R docs for details on multi- arch installations). Cheers, Simon I suspect I need to have a quasiRNG.c file where I will use preprocessor statement that will select the good version of the function to call. Is that correct? No (see previous e-mail). Thanks in advance Christophe Le 15 sept. 2009 à 18:25, Anirban Mukherjee a écrit : Sorry, what I should have said was Halton numbers are quasi-random, and not pseudo-random. Quasi-random is the technically appropriate terminology. Halton sequences are low discrepancy: the subsequence looks/smells random. Hence, they are often used in quasi monte carlo simulations. To be precise, there is only 1 Halton sequence for a particular prime. Repeated calls to Halton should return the same numbers. The first column is the Halton sequence for 2. the second for 3, the third for 5 and so on using the first M primes (for M columns). (You can also scramble the sequence to avoid this.) I am using them to integrate over a multivariate normal space. If you take 1000 random draws, then sum f() over the draws is the expectation of f(). If f() is very non-linear (and/or multi-variate) then even with large N, its often hard to get a good integral. With quasi- random draws, the integration is better for the same N. (One uses the inverse distribution function.) For an example, you can look at Train's paper (page 4 and 5 have a good explanation) at: http://elsa.berkeley.edu/wp/train0899.pdf In the context of simulated maximum likelihood estimation, such integrals are very common. Of course true randomness has its own place/importance: its just that quasi-random numbers can be very useful in certain contexts. Regards, Anirban PS: qnorm(halton()) gets around the problem of the random deviates not working. On Tue, Sep 15, 2009 at 11:37 AM, David Winsemius wrote: On Sep 15, 2009, at 11:10 AM, Anirban Mukherjee wrote: Thanks everyone for your replies. Particularly David. The numbers are pseudo-random. Repeated calls should/would give the same output. As I said, this package is not one with which I have experience. It has _not_ however the case that repeated calls to (typical?) random number functions give the same output when called repeatedly: > rnorm(10) [1] -0.8740195 2.1827411 -0.1473012 -1.4406262 0.1820631 -1.3151244 -0.4813703 0.8177692 [9] 0.2076117 1.8697418 > rnorm(10) [1] -0.7725731 0.8696742 -0.4907099 0.1561859 0.5913528 -0.8441891 0.2285653 -0.1231755 [9] 0.5190459 -0.7803617 > rnorm(10) [1] -0.9585881 -0.0458582 1.1967342 0.6421980 -0.5290280 -1.0735112 0.6346301 0.2685760 [9] 1.5767800 1.0864515 > rnorm(10) [1] -0.60400852 -0.06611533 1.00787048 1.48289305 0.5465 -0.67630052 0.52664127 -0.36449997 [9] 0.88039397 0.56929333 I cannot imagine a situation where one would _want_ the output to be the same on repeated calls unless one reset a seed. Unless perhaps I am not understanding the meaning of "random" in the financial domain? -- David Currently, Halton works fine when used to just get the Halton sequence, but the random deviates call is not working in 64 bit R. For now, I will generate the numbers in 32 bit R, save them and then load them back in when using 64 bit R. The package maintainers can look at it if/when they get a chance and/or access to 64 bit R. Thanks! Best, Anirban On Tue, Sep 15, 2009 at 9:01 AM, David Winsemius wrote: I get v
Re: [Rd] Possible bug in the Rd parser?
On 10/10/2009 8:07 AM, Mathieu Ribatet wrote:
Dear list,
I got an automatic email complaining than some of my packages didn't
pass 'R CMD check' for R-2.10.0 alpha anymore. Both of them make use of
the "cases" LaTeX environment.
Inspecting the log outputs I got:
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Misplaced alignment tab character &.
I noticed that the Rd parser changed quite recently and that '#', '_'
and '&' must not be escaped according to "Writing R extensions".
However, the problematic .Rd portion seems (to me) OK
\deqn{\theta(h) =
\begin{cases}
u_\beta \left(\mu + \frac{\nu(h)}{\Gamma(1 - \xi)}
\right),&\xi \neq 0\\
\exp\left(\frac{\nu(h)}{\sigma}\right),&\xi = 0
\end{cases}
}{u_beta (mu + nu(h) / Gamma(1 - \xi)), if \xi < 1,
exp(nu(h)/sigma), otherwise}
One more followup: the problem appears to be in the "cases"
environment. If I rewrite that block using "array" instead, things are
fine:
\deqn{\theta(h) =
\left\{\begin{array}{ll}
u_\beta \left(\mu + \frac{\nu(h)}{\Gamma(1 - \xi)}
\right),&\xi \neq 0\\
\exp\left(\frac{\nu(h)}{\sigma}\right),&\xi = 0
\end{array}\right.
}{u_beta (mu + nu(h) / Gamma(1 - \xi)), if \xi < 1,
exp(nu(h)/sigma), otherwise}
This makes me think it's a bug in the LaTeX package that provides
"cases", or a conflict with our Rd.sty file, but I don't know which.
Duncan Murdoch
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Re: [Rd] Possible bug in the Rd parser?
On 10/10/2009 2:25 PM, Duncan Murdoch wrote:
On 10/10/2009 8:07 AM, Mathieu Ribatet wrote:
Dear list,
I got an automatic email complaining than some of my packages didn't
pass 'R CMD check' for R-2.10.0 alpha anymore. Both of them make use of
the "cases" LaTeX environment.
Inspecting the log outputs I got:
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Misplaced alignment tab character &.
I noticed that the Rd parser changed quite recently and that '#', '_'
and '&' must not be escaped according to "Writing R extensions".
However, the problematic .Rd portion seems (to me) OK
\deqn{\theta(h) =
\begin{cases}
u_\beta \left(\mu + \frac{\nu(h)}{\Gamma(1 - \xi)}
\right),&\xi \neq 0\\
\exp\left(\frac{\nu(h)}{\sigma}\right),&\xi = 0
\end{cases}
}{u_beta (mu + nu(h) / Gamma(1 - \xi)), if \xi < 1,
exp(nu(h)/sigma), otherwise}
One more followup: the problem appears to be in the "cases"
environment. If I rewrite that block using "array" instead, things are
fine:
\deqn{\theta(h) =
\left\{\begin{array}{ll}
u_\beta \left(\mu + \frac{\nu(h)}{\Gamma(1 - \xi)}
\right),&\xi \neq 0\\
\exp\left(\frac{\nu(h)}{\sigma}\right),&\xi = 0
\end{array}\right.
}{u_beta (mu + nu(h) / Gamma(1 - \xi)), if \xi < 1,
exp(nu(h)/sigma), otherwise}
This makes me think it's a bug in the LaTeX package that provides
"cases", or a conflict with our Rd.sty file, but I don't know which.
And the final answer: the "cases" environment is in the amsmath
package, which is not used by R. You need to use regular LaTeX, not
fancy stuff like that. (There's a \cases macro in LaTex, which doesn't
know what to do with alignment tabs: that's why you got the error you did.)
Duncan Murdoch
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[Rd] Help with OCaml bindings for R interpreter.
Hello. I've made out a Debian package out of Maxence Guesdon's OCaml/R bindings: http://yziquel.homelinux.org/topos/debian-ocamlr.html http://yziquel.homelinux.org/debian/pool/main/o/ocaml-r/ The upstream software itself is on the following page: http://home.gna.org/ocaml-r/ This binding is dynamically linked to the /usr/lib/R/lib/libR.so and to the /usr/lib/libRmath.so libraries. Its purpose is to access R functionalities from OCaml programs. However, as it now stands, the binding is not fully functional: When an OCaml program is compiled with this binding, to generate, say, myprog.byte, it is necessary to run R CMD ./myprog.byte in order for the program to work as expected. I would therefore like to know how to *completely* embed the R interpreter inside my binding. Could anyone provide generic information on this topic, or point me to the right documentation? All the best, -- Guillaume Yziquel http://yziquel.homelinux.org/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Help with OCaml bindings for R interpreter.
On Oct 10, 2009, at 3:53 PM, Guillaume Yziquel wrote: Hello. I've made out a Debian package out of Maxence Guesdon's OCaml/R bindings: http://yziquel.homelinux.org/topos/debian-ocamlr.html http://yziquel.homelinux.org/debian/pool/main/o/ocaml-r/ The upstream software itself is on the following page: http://home.gna.org/ocaml-r/ This binding is dynamically linked to the /usr/lib/R/lib/libR.so and to the /usr/lib/libRmath.so libraries. Its purpose is to access R functionalities from OCaml programs. However, as it now stands, the binding is not fully functional: When an OCaml program is compiled with this binding, to generate, say, myprog.byte, it is necessary to run R CMD ./myprog.byte in order for the program to work as expected. I would therefore like to know how to *completely* embed the R interpreter inside my binding. It *is* completely embedded. R CMD simply sets up the correct environment for the current R. For a given, specific R installation you could re-create the environment in the executable (see R CMD sh -c set), but by definition it is specific for that installation so you'd have to compile that binary at install time. Cheers, Simon Could anyone provide generic information on this topic, or point me to the right documentation? All the best, -- Guillaume Yziquel http://yziquel.homelinux.org/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Help with OCaml bindings for R interpreter.
Simon Urbanek a écrit : On Oct 10, 2009, at 3:53 PM, Guillaume Yziquel wrote: However, as it now stands, the binding is not fully functional: When an OCaml program is compiled with this binding, to generate, say, myprog.byte, it is necessary to run R CMD ./myprog.byte in order for the program to work as expected. I would therefore like to know how to *completely* embed the R interpreter inside my binding. It *is* completely embedded. R CMD simply sets up the correct environment for the current R. OK. I just stumbled a minute or two ago on: http://cran.r-project.org/doc/manuals/R-exts.html#Embedding-R-under-Unix_002dalikes I now get it. For a given, specific R installation you could re-create the environment in the executable (see R CMD sh -c set), but by definition it is specific for that installation so you'd have to compile that binary at install time. OK. So it seems that there will be some more work needed in order to hide that completely to the OCaml end-user. Cheers, Simon Thanks a lot. -- Guillaume Yziquel http://yziquel.homelinux.org/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] isFALSE
Hello,
Just wondering why there is "isTRUE" and not "isFALSE".
Romain
--
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
|- http://tr.im/BcPw : celebrating R commit #5
|- http://tr.im/ztCu : RGG #158:161: examples of package IDPmisc
`- http://tr.im/yw8E : New R package : sos
Index: src/library/base/R/identical.R
===
--- src/library/base/R/identical.R (revision 50027)
+++ src/library/base/R/identical.R (working copy)
@@ -18,3 +18,5 @@
.Internal(identical(x,y, num.eq, single.NA, attrib.as.set))
isTRUE <- function(x) identical(TRUE, x)
+
+isFALSE <- function(x) identical(FALSE, x)
Index: src/library/base/man/Logic.Rd
===
--- src/library/base/man/Logic.Rd (revision 50027)
+++ src/library/base/man/Logic.Rd (working copy)
@@ -14,6 +14,7 @@
xor(x, y)
isTRUE(x)
+isFALSE(x)
}
\alias{!}
\alias{&}
@@ -23,6 +24,7 @@
\alias{xor}
\alias{Logic}
\alias{isTRUE}
+\alias{isFALSE}
\description{
These operators act on logical and number-like vectors.
}
@@ -48,7 +50,11 @@
\code{isTRUE(x)} is an abbreviation of \code{identical(TRUE, x)}, and
so is true if and only if \code{x} is a length-one logical vector with
no attributes (not even names).
-
+
+ \code{isFALSE(x)} is an abbreviation of \code{identical(FALSE, x)}, and
+ so is true if and only if \code{x} is a length-one logical vector with
+ no attributes (not even names).
+
Numeric and complex vectors will be coerced to logical values, with
zero being false and all non-zero values being true. Raw vectors are
handled without any coercion for \code{!}, \code{&}, \code{|} and
@@ -87,7 +93,7 @@
used. For arrays (and an array result) the dimensions and dimnames
are taken from first argument if it is an array, otherwise the second.
- For \code{||}, \code{&&} and \code{isTRUE}, a length-one logical vector.
+ For \code{||}, \code{&&}, \code{isFALSE} and \code{isTRUE}, a length-one
logical vector.
}
\section{S4 methods}{
\code{!}, \code{&} and \code{|} are S4 generics, the latter two part
Index: src/library/base/man/identical.Rd
===
--- src/library/base/man/identical.Rd (revision 50027)
+++ src/library/base/man/identical.Rd (working copy)
@@ -85,7 +85,8 @@
\seealso{
\code{\link{all.equal}} for descriptions of how two objects differ;
\link{Comparison} for operators that generate elementwise comparisons.
- \code{\link{isTRUE}} is a simple wrapper based on \code{identical}.
+ \code{\link{isTRUE}} and \code{\link{isFALSE}} are simple
+ wrappers based on \code{identical}.
}
\examples{
identical(1, NULL) ## FALSE -- don't try this with ==
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