On 11-04-12 07:06 PM, Simon Urbanek wrote:
On Apr 12, 2011, at 8:53 PM, Hervé Pagès wrote:
Hi Uwe,
On 11-04-11 08:13 AM, Uwe Ligges wrote:
On 11.04.2011 02:47, Hervé Pagès wrote:
Hi,
More about the new --resave-data option
As mentioned previously here
https://stat.ethz.ch/pipermail/r
Hi Simon,
On 11-04-08 01:05 PM, Simon Urbanek wrote:
On Apr 8, 2011, at 2:55 PM, Hervé Pagès wrote:
Hi Duncan, Marc,
On 11-04-05 11:15 AM, Duncan Murdoch wrote:
On 05/04/2011 1:51 PM, Marc Carlson wrote:
Hi,
I have seen several packages that with the most recent version of R are
giving
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CMD build --keep-empty-dirs --no-resave-data
I hope the list of options/flags that we need to use to fix 'R CMD
build' (and make it consistent with R CMD INSTALL) is not going to
grow too much ;-)
Thanks,
H.
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, I'm not sure how
literally to take it).
Duncan Murdoch
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with duplicated name
'%s':,
nm),
.pretty_format(bad[[nm]]))
}))
Cheers,
H.
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that the See Also section points to rowSums and not
colSums, which adds to the confusion...
Cheers,
H.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
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the corresponding results.
I see. Thanks Simon.
I missed this:
levels: an optional vector of the values that ‘x’ might have taken.
The default is the unique set of values taken by
‘as.character(x)’, ...
Cheers,
H.
Cheers,
Simon
On Feb 23, 2011, at 2:55 PM, Hervé Pagès wrote
the
man page:
By definition the min/max of a numeric vector containing an ‘NaN’
is ‘NaN’, except that the min/max of any vector containing an ‘NA’
is ‘NA’ even if it also contains an ‘NaN’.
Cheers,
H.
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getting the full story:
foo(bar())
Error in bar() : bar() is broken
Error in foo(bar()) :
error in evaluating the argument 'x' in selecting a method for
function 'foo'
Could this behavior be restored?
Thanks,
H.
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(Value section).
Thanks,
H.
On 11/10/2010 01:13 PM, Hervé Pagès wrote:
Hi,
Today we've seen the following problem with the R-2.12 that we use
for our Windows builds:
installed.packages()
Error: subscript out of bounds
After some investigation we discovered that the cause of this failure
packages:
[1] stats graphics grDevices utils datasets methods base
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On 11/10/2010 05:02 AM, Prof Brian Ripley wrote:
On Tue, 9 Nov 2010, Hervé Pagès wrote:
Hi,
Found in ?eapply (in current R-devel):
\value{
A named (unless \code{USE.NAMES = FALSE}) list. Note that the order of
the components is arbitrary for hashed environments: currently
On 11/10/2010 10:38 AM, Hervé Pagès wrote:
On 11/10/2010 05:02 AM, Prof Brian Ripley wrote:
On Tue, 9 Nov 2010, Hervé Pagès wrote:
Hi,
Found in ?eapply (in current R-devel):
\value{
A named (unless \code{USE.NAMES = FALSE}) list. Note that the order of
the components is arbitrary for hashed
(desc[Built], ;)[[1L]][1L],
[ \t]+)[[1L]][2L]
Thanks,
H.
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hashed?
environments.
}
This looks like a typo.
Thanks,
H.
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still worth reporting the problem,
especially when it's a crash. Also AFAIK the posting guide says nothing
about me having to use the debugging tools or come up with a solution
before I report a problem.
Thanks again for the fix,
H.
On Thu, 28 Oct 2010, Hervé Pagès wrote:
Hi,
The following
understanding the
code.
Yes, exactly and
/Henrik
/Henrik
Thanks again for the fix,
H.
On Thu, 28 Oct 2010, Hervé Pagès wrote:
Hi,
The following code produces different kinds of problems depending
on which platform you run it:
x- as.list(1:20)
names(x)- paste(A, 1:20, sep=)
e- list2env(x
the 'envir' arg is supplied)
doesn't seem to have this problem.
Cheers,
H.
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E-mail: hpa...@fhcrc.org
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(once every 20 attempts or so) I get a segfault when
trying to open this url with url().
Cheers,
H.
On Thu, 21 Oct 2010, Hervé Pagès wrote:
Hi,
Trying to access files on the ftp server at ftp.ncbi.nih.gov
will either give a time out or sometimes even a segfault on Linux.
The 2 following
build a 32-bit library on a 64-bit
windows machine. But it doesn't look possible to build a 64-bit
library on a 32-bit windows machine?
Thanks,
--Michael
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E-mail: hpa...@fhcrc.org
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This problems seems to be solved in current R 2.12 RC. Thanks! H.
On 10/10/2010 10:47 PM, Hervé Pagès wrote:
Hi,
'R CMD build' (with R 2.12.0 RC) fails to clean the src/ folder
on Windows:
D:\biocbld\bbs-2.7-biocls meat/BUS/src
BUS.cpp BUS.h
D:\biocbld\bbs-2.7-biocR\bin\R CMD build meat\BUS
ztvf BUS_1.5.0.tar.gz --wildcards '*.o'
-rwxr--r-- biocbuild2/root 16503 2010-10-10 22:15 BUS/src/BUS.o
Packages with a Makefile in src/ don't seem to be affected.
This is with R 2.12.0 RC (2010-10-07 r53227).
Thanks,
H.
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This has been fixed in R-beta. Thanks! H.
On 10/01/2010 06:31 PM, Hervé Pagès wrote:
Hi,
The cleanup_pkg() function defined the big tools:::.build_packages()
function in tools/R/build.R is currently broken. When Makefiles are
used cleanup_pkg() doesn't clean anything because of the way
Hi,
On 09/30/2010 10:45 AM, Hervé Pagès wrote:
[...]
If that is not desirable, could the tools:::.build_packages() function
not put quotes around the value of the TAR environment variable (the
code does shQuote(TAR)), at least on Windows, so I can set this
variable to
tar --no-same-owner
thru the 'args' argument.
Cheers,
H.
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E-mail: hpa...@fhcrc.org
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() (only
the first doesn't put them) but that's another story.
Thanks!
H.
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E-mail: hpa...@fhcrc.org
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This has been addressed in current R-alpha, thanks! H.
On 09/29/2010 02:11 PM, Hervé Pagès wrote:
Hi,
I can confirm that most of those strange R CMD build/check errors
we observe on Windows are actually a consequence of the temp
Rscript file collision I reported yesterday here:
https
temp file now), so I'm going to report them in
a separate post.
Can the patch above be applied? Thanks!
H.
On 09/11/2010 11:10 PM, Hervé Pagès wrote:
Hi,
This is a follow up to:
https://stat.ethz.ch/pipermail/r-devel/2010-July/057921.html
The Bioconductor daily builds have been reporting a lot
It looks like this has been fixed in current R-alpha. Thanks! H.
On 09/28/2010 04:27 PM, Hervé Pagès wrote:
Hi,
Cosmetic. Starting R with e.g. --max-ppsize=-10 produces the following
warning:
WARNING: '-max-ppsize' value is negative: ignored
The name of the option displayed in the warning
the name of this option needs to be adjusted).
This is with current R-alpha.
Thanks!
H.
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E-mail: hpa
Rterm process needs to create at most 1 temp Rscript file
so maybe using rand() is not even needed.
Note that Unix is safe because tmpfile() is used there (file
src/unix/system.c).
Cheers,
H.
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-24 r52991) on Windows Server 2003 R2
(32-bit). The tar command used is from current Rtools212.
Cheers,
H.
On 09/15/2010 05:21 PM, Hervé Pagès wrote:
On 09/14/2010 11:23 AM, Hervé Pagès wrote:
Hi Uwe,
On 09/14/2010 04:49 AM, Uwe Ligges wrote:
...
Brian had some ideas that the problems
interactively.
Thanks!
H.
On 09/15/2010 09:54 PM, Hervé Pagès wrote:
Hi,
On both Unix and Windows there is a mechanism to add variables
to the environment when R is started. I noticed that, on Unix,
this mechanism is not used when R is started normally at the
command line but only when it's started
This fixed in current R-alpha (r52991) too. Thanks!
H.
On 09/15/2010 11:33 PM, Hervé Pagès wrote:
I think I found the problem. During the recent transition from
Perl-based to R-based 'R CMD check/build', the rcmdfn() function
in src/gnuwin32/front-ends/rcmdfn.c has been hacked quite a bit
variables that they used to see anymore. Only
a normal 'R' command still gets them.
Cheers,
H.
On 09/15/2010 04:55 PM, Hervé Pagès wrote:
Hi,
This is a follow-up to the problem reported here:
https://stat.ethz.ch/pipermail/r-devel/2010-September/058460.html
After I updated R-2.12 to 2010-09-13
= .,
compressed = NA, extras = NULL, verbose = FALSE,
tar = Sys.getenv(TAR))
Thanks!
H.
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.
Cheers,
H.
-k
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that the clean step runs too late.
But shouldn't 'R CMD check' run the clean step (if it runs it at all)
right after the 'R CMD INSTALL' step?
Cheers,
H.
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on a package for which the problem is gone so
I went ahead and started to sing victory... not so fast!
I'm gonna post with a new subject and give more details.
H.
On 09/14/2010 11:48 AM, Duncan Murdoch wrote:
On 14/09/2010 2:46 PM, Hervé Pagès wrote:
Duncan,
On 09/13/2010 11:47 AM, Duncan Murdoch
that is really puzzling is that if I cd to
adSplit/inst/doc and run 'R CMD make' then it works.
Any help/comment on this will be highly appreciated.
Thanks,
H.
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1100 Fairview
On 09/14/2010 11:23 AM, Hervé Pagès wrote:
Hi Uwe,
On 09/14/2010 04:49 AM, Uwe Ligges wrote:
...
Brian had some ideas that the problems are related to the shell that is
used. Is the problem still apparent in a very recent R-devel from few
days ago? I am just back from vacations and have
Sys.getenv('TEXINPUTS') | R
Fatal error: you must specify '--save', '--no-save' or '--vanilla'
What about --slave? Thanks!
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P.O. Box 19024
Seattle
Hi Uwe,
On 09/14/2010 04:49 AM, Uwe Ligges wrote:
On 12.09.2010 12:10, Hervé Pagès wrote:
Hi Peter,
On 09/12/2010 01:51 AM, Peter Dalgaard wrote:
On 09/12/2010 08:10 AM, Hervé Pagès wrote:
...
AFAICT those problems were never seen before (i.e. with R 2.12).
They show up randomly everyday
Duncan,
On 09/13/2010 11:47 AM, Duncan Murdoch wrote:
On 13/09/2010 2:38 PM, Hervé Pagès wrote:
[...]
Thanks for suggesting workarounds but don't you think there is a real
problem?
As I said, we don't use TEXINPUTS on Windows, we use the command line
version. I didn't write the code, so I
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only from 4MB to
4.3MB. Thus in principle I could upload both files to SVN for BioC 2.7,
and this should eliminate the warning message. What is your opinion?
I still don't understand why you want to have them in the source
tarball.
H.
Best regards
Christian
On 9/14/10 11:32 PM, Hervé Pagès
On 09/14/2010 03:30 PM, Duncan Murdoch wrote:
On 14/09/2010 6:08 PM, Hervé Pagès wrote:
On 09/14/2010 02:58 PM, cstrato wrote:
Dear Herve,
Thank you for your reply, however maybe I was not quite clear.
The files xpsDict.h and xpsDict.cxx are automatically created by the
ROOT framework during
On 09/13/2010 03:34 AM, Duncan Murdoch wrote:
Hervé Pagès wrote:
Hi Duncan,
On 09/12/2010 05:07 AM, Duncan Murdoch wrote:
On 12/09/2010 12:49 AM, Hervé Pagès wrote:
Hi Duncan,
On 09/11/2010 03:56 AM, Duncan Murdoch wrote:
On 11/09/2010 12:52 AM, Hervé Pagès wrote:
Hi,
I found
everyday
and any package seems to be a potential victim (I've not been able
to observe any obvious pattern so far).
Does anyone have any idea what could make 'R CMD build' and
'R CMD check' so confused/unreliable on Windows?
Thanks,
H.
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Hi Peter,
On 09/12/2010 01:51 AM, Peter Dalgaard wrote:
On 09/12/2010 08:10 AM, Hervé Pagès wrote:
...
AFAICT those problems were never seen before (i.e. with R 2.12).
They show up randomly everyday for a small number of packages
(between 10 and 20 out of 400). The set of victims changes
Hi Duncan,
On 09/12/2010 05:07 AM, Duncan Murdoch wrote:
On 12/09/2010 12:49 AM, Hervé Pagès wrote:
Hi Duncan,
On 09/11/2010 03:56 AM, Duncan Murdoch wrote:
On 11/09/2010 12:52 AM, Hervé Pagès wrote:
Hi,
I found the following problem with recent R-devel
(2010-08-26 r52817) on Windows (32
Hi Duncan,
On 09/11/2010 03:56 AM, Duncan Murdoch wrote:
On 11/09/2010 12:52 AM, Hervé Pagès wrote:
Hi,
I found the following problem with recent R-devel
(2010-08-26 r52817) on Windows (32-bit and 64-bit):
'R CMD build pkg' gets stalled during vignett
creation for packages that have
that be related
to the problem?
I don't see that problem on platforms other than Windows or
with R 2.12
Thanks,
H.
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not_matrix;
}
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(and not attached):
[1] tools_2.12.0
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E-mail: hpa...@fhcrc.org
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and R-2.12.0.
Thanks,
H.
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r52464).
Cheers,
H.
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E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667-1319
-buildsrc.html
Cheers,
H.
On 06/21/2010 12:20 PM, Hervé Pagès wrote:
Hi,
After updating R-2.12 on the Bioconductor build system about 1 week ago
(we update R every 4-6 weeks for our devel builds), we've started to see
something never seen before on Windows: for some BioC packages,
'R CMD build
Uwe Ligges wrote:
On 10.06.2010 23:16, Hervé Pagès wrote:
Hi,
The R-based version of R CMD build doesn't work for me on Windows:
E:\biocbld\bbs-2.7-biocR\bin\R CMD build meat\Biobase
* checking for file 'meat\Biobase/DESCRIPTION' ... OK
* preparing 'Biobase':
* checking DESCRIPTION meta
see anything like that on the check summaries for
CRAN packages:
http://cran.r-project.org/web/checks/check_summary.html
Maybe because CRAN only runs R CMD check which is still Perl-based?
Thanks,
H.
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Fred
/a
but latter in the file, the referred section is tagged with:
a name=g_t64_002dbit-Windows-builds/a
Thanks,
H.
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Thanks Martin. H.
Martin Maechler wrote:
HP == Hervé Pagès hpa...@fhcrc.org
on Thu, 03 Jun 2010 13:25:10 -0700 writes:
HP Hi,
HP I just realized that a named empty list is displayed the same
HP way as an empty list:
list(aa=2:5)[0]
HP list()
list()
HP list
=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
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.
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1100 Fairview Ave. N, M2-B876
P.O. Box 19024
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Follow up...
Hervé Pagès wrote:
Hi Matthew,
Matthew Dowle wrote:
Just to add some clarification, the suggestion wasn't motivated by
speeding up a length 3 vector being recycled 3.3 million times. But
its a good point that any change should not make that case slower. I
don't know how much
Hervé Pagès wrote:
[...]
Code:
===
#include stdio.h
#include string.h
#include stdlib.h
void memcpy_with_recycling_of_src(char *dest, size_t dest_nblocks,
const char *src, size_t src_nblocks
has a use for it other
than in as()? If you look at the code, you'll see that would simplify
it significantly, and even speed up selection somewhat. There's a change
I would be happy about!
That sounds all good to me.
Thanks,
H.
John
On 4/1/10 2:59 PM, Hervé Pagès wrote:
John Chambers
.
Cheers,
H.
Regards,
John
On 3/31/10 3:52 PM, Hervé Pagès wrote:
Hi,
class(as(1:4, numeric))
[1] integer
Surprising but an explanation could be that an integer
vector being a particular case of numeric vector, this
coercion has nothing to do because 1:4 is already numeric.
And indeed
names, so the user doesn't have to
switch between select*/show* tools depending on whether f=coerce
or not.
H.
John
On 4/1/10 12:31 AM, Hervé Pagès wrote:
Hi John,
John Chambers wrote:
The example is confusing and debatable, but not an obvious bug. And
your presentation of it is the cause
] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
--
Hervé
Hi,
Having
foo - function(x, y, z) {TRUE}
in my code and
foo(x, y=NULL, z=0)
in the \usage section of my man page will trigger the
following warning during R CMD check:
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'foo':
foo
Code:
Hi,
x - c(aa=22, bb=555)
unname(x[FALSE])
named numeric(0)
Cheers,
H.
sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=C
Hi,
as.integer(100) # 10 billions
[1] NA
Warning message:
NAs introduced by coercion
as.integer(-100) # minus 10 billions
[1] NA
Warning message:
NAs introduced by coercion
as.integer(100) # 10 billions as a string
[1] 2147483647
Warning message:
inaccurate
Seth Falcon wrote:
2009/9/24 Hervé Pagès hpa...@fhcrc.org:
x - charToRaw(ABCDEFGx)
x[c(1:3, NA, 6)] - x[8]
*** caught segfault ***
address 0x8402423f, cause 'memory not mapped'
Thanks for the report. I have a fix which I will commit after some testing.
Thanks Seth! H
LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred
Thanks Martin! The latest snapshot (R-devel_2009-09-03.tar.gz) looks OK.
FYI the tarballs with a broken name are still here
(ftp://ftp.stat.math.ethz.ch/Software/R/):
R-devel_.tar.bz2
R-devel_.tar.gz
Cheers,
H.
Martin Maechler wrote:
HP == Hervé Pagès hpa...@fhcrc.org
on Wed, 02 Sep
Duncan Murdoch wrote:
On 15/07/2009 10:15 PM, Hervé Pagès wrote:
I have to confess that I'm a little bit puzzled by how the
PROTECT/UNPROTECT mechanism is used in the C code of R.
Duncan, you say the problem you just fixed was an easy one.
I looked at the C code too and was able to recognize
Duncan Murdoch wrote:
On 7/16/2009 2:34 PM, Hervé Pagès wrote:
Duncan Murdoch wrote:
On 15/07/2009 10:15 PM, Hervé Pagès wrote:
I have to confess that I'm a little bit puzzled by how the
PROTECT/UNPROTECT mechanism is used in the C code of R.
Duncan, you say the problem you just fixed
Duncan Murdoch wrote:
On 16/07/2009 5:06 PM, Hervé Pagès wrote:
Duncan Murdoch wrote:
On 7/16/2009 2:34 PM, Hervé Pagès wrote:
Duncan Murdoch wrote:
On 15/07/2009 10:15 PM, Hervé Pagès wrote:
I have to confess that I'm a little bit puzzled by how the
PROTECT/UNPROTECT mechanism is used
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax:(206
murd...@stats.uwo.ca wrote:
On 15/07/2009 8:30 PM, murd...@stats.uwo.ca wrote:
On 15/07/2009 8:08 PM, Hervé Pagès wrote:
Hi,
x - c(a=10, b=20)
length(x) - 1
x
a
10
But with gctorture turned on, I get:
gctorture(TRUE)
x - c(a=10, b=20)
length(x) - 1
x
trigger garbage collection
(e.g. PROTECT(allocVector()) is close to the return statement).
Because making exceptions like this can make your code
really hard to maintain in the long term.
Cheers,
H.
Hervé Pagès wrote:
murd...@stats.uwo.ca wrote:
On 15/07/2009 8:30 PM, murd...@stats.uwo.ca wrote
/mailman/listinfo/r-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667-1319
/053607.html
Also note that if I make foo() a function of one argument only, I don't
get the protection stack overflow anymore.
Cheers,
H.
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box
-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
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred
attached base packages:
[1] stats graphics grDevices utils datasets methods base
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa
datasets methods base
Cheers,
H.
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667
,
H.
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box
symbolic links into
src/library/Recommended/ as they used to.
I don't know what OS this procedure is running on but maybe 'tar'
started to do some strange strings with symlinks after an OS
update/upgrade...
Thanks,
H.
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
to be reported to the site which makes them.
Perhaps you mean
ftp://ftp.stat.math.ethz.ch/Software/R/R-devel_2008-12-03.tar.bz2
? In which case see the README in that directory for how to report a
problem.
Will do. Thanks!
H.
--
Hervé Pagès
Program in Computational Biology
Division of Public Health
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