[Rd] compiler usage after successful UNIX build
Hi, I believe my question is pretty simple, but I'd like to give you brief background first: I work at a company with UNIX installed on a sparc-sun-solaris platform; the OS version is SunOS 5.9. Several of us who work here have been advocating for the installation of R on this server. The IT security group at my company prefers not to install the gcc compilers on our UNIX production servers; they're okay doing this in a test environment. My question: After a successful build, is there anytime that R might call the compiler? My (limited) understanding was that once the binaries are created, the compiler is not used unless you're doing another build, e.g., compiling source code for a package. Does R ever compile routines during execution? Does it depend on how the installation was done? Thanks for your help with this. Paul Louisell 650-833-6254 [EMAIL PROTECTED] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] bug in R environments? Was: [BioC] 'recursive default argument' error...
Dear developers, has anyone experienced the problem described below? Is it a bug in handling interrupts in R? Best, Oleg Original Message Subject: Re: [BioC] 'recursive default argument' error in GOENTREZID2GO From: Diego Diez <[EMAIL PROTECTED]> ...steps that use to reach me to that point. It happens with any environment, or at least annotation packages stored as environments. I can't think of any reason why this happens but let me show you the code: > library(rae230a) > xx <- as.list(rae230aENTREZID) ^C > xx <- as.list(rae230aENTREZID) Error in as.list(rae230aENTREZID) : recursive default argument reference now, while the as.list() is working, cancel the process with control- C, and after that, the mentioned error happens whenever you try to repeat the process of transforming the environment to a list. The cancel must be done soon after hitting return, I found one case when delaying a little made me unable to reproduce the error. Other environments found in the package are not affected (i.e. rae230aSYMBOL, rae230aGENENAME, etc). Going deeper to the problem, I found that canceling the environment "loading" with any function reproduces the problem: > is(rae230aSYMBOL) ^C > is(rae230aSYMBOL) Error in .class1(object) : recursive default argument reference > rae230aSYMBOL Error: recursive default argument reference By "loading" a mean that the first time I execute as.list (rae230aSYMBOL) or is(rae230aSYMBOL) there is a delay which I assume is the environment being loaded into memory. Any further execution of the same commands will occur almost immediately. So, why should I cancel an environment loading soon after trying to load it? It happens that I was loading an environment inside a function, ran the function and wanted to cancel the execution, thus, the error appeared and the environemnt was unusable. Anyway, this seems to me more an R related issue. HTH, Diego. > sessionInfo() R version 2.5.0 (2007-04-23) powerpc-apple-darwin8.9.1 locale: C attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base" other attached packages: rae230a "1.16.0" > On Jun 11, 2007, at 11:27 PM, Seth Falcon wrote: > "James W. MacDonald" <[EMAIL PROTECTED]> writes: > >> Hi Oleg, >> >> Oleg Sklyar wrote: >>> Hi, >>> >>> anybody has an idea as for the following error, the example is >>> actually >>> from the GO package examples. Thanks, Oleg >>> library(GO) egId <- "10043" egIdGoData <- GOENTREZID2GO[[egId]] >>> Error: recursive default argument reference >> >> I sometimes see that error as well. I have no idea what causes it, >> as it >> doesn't seem repeatable. Anyway, quitting R and starting over has >> always >> fixed the problem for me. > > Oleg, is this reproducible for you? I wasn't able to get the error. > Have you tried updating to R patched? > > + seth > > -- > Seth Falcon | Computational Biology | Fred Hutchinson Cancer > Research Center > http://bioconductor.org > > ___ > Bioconductor mailing list > [EMAIL PROTECTED] > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor -- Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] compiler usage after successful UNIX build
On Mon, 11 Jun 2007, Louisell, Paul wrote: > Hi, > > I believe my question is pretty simple, but I'd like to give you brief > background first: > > I work at a company with UNIX installed on a sparc-sun-solaris platform; > the OS version is SunOS 5.9. Several of us who work here have been > advocating for the installation of R on this server. The IT security > group at my company prefers not to install the gcc compilers on our UNIX > production servers; they're okay doing this in a test environment. Is their objection to gcc or compilers at all? Sun's own Studio 11 compilers are now free (and at least as good as gcc in that environment). > My question: After a successful build, is there anytime that R might > call the compiler? My (limited) understanding was that once the binaries > are created, the compiler is not used unless you're doing another build, > e.g., compiling source code for a package. Does R ever compile routines > during execution? Does it depend on how the installation was done? It only compiles code when asked to do so. That means running R CMD COMPILE or R CMD SHLIB. The latter is run by R CMD INSTALL and that is run by install.packages() and elsewhere. But you would need to have specified some C/C++/Fortran source code, so would be expecting this. -- 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-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] package check note: no visible global function definition (in functions using Tcl/Tk)
On Tue, 2007-06-12 at 00:42 +0200, Henrik Bengtsson wrote:
> On 6/11/07, Seth Falcon <[EMAIL PROTECTED]> wrote:
> > Prof Brian Ripley <[EMAIL PROTECTED]> writes:
> >
> > > It seems that is happens if package tcltk is missing from the Depends:
> > > list in the DESCRIPTION file. I just tested with Amelia and homals and
> > > that solved the various warnings in both cases.
> >
> > Adding tcltk to Depends may not always be the desried solution. If
> > tcltk is already in Suggests, for example, and the intention is to
> > optionally provide GUI features, then the code may be correct as-is.
> > That is, codetools will issue the NOTEs if you have a function that
> > looks like:
> >
> >f <- function() {
> > if (require("tckltk")) {
> > someTckltkFunctionHere()
> > } else
> > otherwiseFunction()
> > }
> >}
> >
> > There are a number of packages in the BioC repository that provide
> > such optional features (not just for tcltk) and it would be nice to
> > have a way of declaring the use such that the NOTE is silenced.
>
> Same scenario here: I am using Suggest and I found that the NOTEs go
> away if you call the function with double-colon (::), e.g.
> tcltk::someTckltkFunctionHere().
>
> I also got several NOTEs about non-declared objects if I used
> request(), but they go away with request("").
>
The real problem here is what are the consequences for CRAN auditing
with the new defaults. Do you have to pass these tests also? Do you
implement stricter package dependence checking? Do you still allow the
check circumvention device that Henrik, perhaps unwisely, revealed here
(that is package::function)?
Just being curious, I run checkUsagePackage() for my CRAN package
(vegan), and got 109 messages. 58 of these were "local variables
assigned but may not be used" and need be checked. My first impression
was that they were just harmless leftover, and removing those is not
among my top priorities, but may wait till September. Some were false
positives. Most of the rest (49 + 1 special case) were calls to
functions in other packages with require || stop in the function body.
I'd like to keep them like this, or at least with the circumvention
device. Please don't make this test a requirement in CRAN submissions!
One real error was detected also, but fixing that error broke the
function, since the rest of the function already was expecting erroneous
output to work correctly.
I urge for more relaxed dependence checking allowing calls to other
packages in functions. I've been a Linux user since Red Hat 5.1 and I
know what is a dependence hell (package depending on package
depending ... depending on broken package). There already are some signs
of that in R, in particular in unsupported platforms like MacOS 10.3.9
where I have trouble in installing some packages that depend on
packages... (if somebody wonders why I still use MacOS 10.3.9, I can
give 129 reasons, each worth one Euro).
cheers, Jari Oksanen
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Re: [Rd] bug in R environments? Was: [BioC] 'recursive default argument' error...
On Tue, 12 Jun 2007, Oleg Sklyar wrote:
> Dear developers,
>
> has anyone experienced the problem described below? Is it a bug in
> handling interrupts in R?
I am not sure where you think the 'bug' is in: cf your subject line.
My guess is that the package is using environments in a vulnerable way.
I cannot reproduce your example on my system: I was able to interrupt but
repeating the as.list worked. What I suspect may have happened is that
you have interrupted lazy loading. From the code
if(PRSEEN(e))
errorcall(R_GlobalContext->call,
_("recursive default argument reference"));
SET_PRSEEN(e, 1);
val = eval(PRCODE(e), PRENV(e));
SET_PRSEEN(e, 0);
so you will get this message from a promise whose evaluation was
incomplete. I can see several ways around that, but most have runtime
costs or back-compatibility issues. (Changing the message may help.)
It looks like rae230a has been implemented to use lazy-loading on whole
environments (the 'source' is already a lazyload database, so it's not
transparent). Lazy-loading was intended for members of environments.
Also, does this happen in R-devel? There lazy-loading is considerably
faster and closer to an atomic operation.
All guesswork on something I cannot reproduce, of course.
>
> Best,
> Oleg
>
> Original Message
> Subject: Re: [BioC] 'recursive default argument' error in GOENTREZID2GO
> From: Diego Diez <[EMAIL PROTECTED]>
>
> ...steps that use to reach me to that point. It happens with any
> environment, or at least annotation packages stored as environments.
> I can't think of any reason why this happens but let me show you the
> code:
>
>> library(rae230a)
>> xx <- as.list(rae230aENTREZID)
> ^C
>> xx <- as.list(rae230aENTREZID)
> Error in as.list(rae230aENTREZID) : recursive default argument reference
>
> now, while the as.list() is working, cancel the process with control-
> C, and after that, the mentioned error happens whenever you try to
> repeat the process of transforming the environment to a list. The
> cancel must be done soon after hitting return, I found one case when
> delaying a little made me unable to reproduce the error. Other
> environments found in the package are not affected (i.e.
> rae230aSYMBOL, rae230aGENENAME, etc).
>
> Going deeper to the problem, I found that canceling the environment
> "loading" with any function reproduces the problem:
>
>> is(rae230aSYMBOL)
> ^C
>> is(rae230aSYMBOL)
> Error in .class1(object) : recursive default argument reference
>> rae230aSYMBOL
> Error: recursive default argument reference
>
> By "loading" a mean that the first time I execute as.list
> (rae230aSYMBOL) or is(rae230aSYMBOL) there is a delay which I assume
> is the environment being loaded into memory. Any further execution of
> the same commands will occur almost immediately.
>
> So, why should I cancel an environment loading soon after trying to
> load it? It happens that I was loading an environment inside a
> function, ran the function and wanted to cancel the execution, thus,
> the error appeared and the environemnt was unusable. Anyway, this
> seems to me more an R related issue.
>
> HTH,
>
> Diego.
>
>
>> sessionInfo()
> R version 2.5.0 (2007-04-23)
> powerpc-apple-darwin8.9.1
>
> locale:
> C
>
> attached base packages:
> [1] "stats" "graphics" "grDevices" "utils" "datasets"
> "methods"
> [7] "base"
>
> other attached packages:
> rae230a
> "1.16.0"
>>
>
>
>
> On Jun 11, 2007, at 11:27 PM, Seth Falcon wrote:
>
>> "James W. MacDonald" <[EMAIL PROTECTED]> writes:
>>
>>> Hi Oleg,
>>>
>>> Oleg Sklyar wrote:
Hi,
anybody has an idea as for the following error, the example is
actually
from the GO package examples. Thanks, Oleg
> library(GO)
> egId <- "10043"
> egIdGoData <- GOENTREZID2GO[[egId]]
Error: recursive default argument reference
>>>
>>> I sometimes see that error as well. I have no idea what causes it,
>>> as it
>>> doesn't seem repeatable. Anyway, quitting R and starting over has
>>> always
>>> fixed the problem for me.
>>
>> Oleg, is this reproducible for you? I wasn't able to get the error.
>> Have you tried updating to R patched?
>>
>> + seth
>>
>> --
>> Seth Falcon | Computational Biology | Fred Hutchinson Cancer
>> Research Center
>> http://bioconductor.org
>>
>> ___
>> Bioconductor mailing list
>> [EMAIL PROTECTED]
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/
>> gmane.science.biology.informatics.conductor
>
>
--
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
___
[Rd] Warning under R 2.6.0: Rd files with unknown encoding
Dear R-devel list members, Under the development version of R (2.6.0), I notice that my sem package produces the following warning: checking Rd files ... WARNING Rd files with unknown encoding: residuals.Rd I wonder what the warning means. As far as I can see, residuals.Rd is similar to the other .Rd files in the package. At least for the time being, I won't reproduce residuals.Rd here in the interest of brevity. Any help would be appreciated. John John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Warning under R 2.6.0: Rd files with unknown encoding
On Tue, 12 Jun 2007, John Fox wrote:
Dear R-devel list members,
Under the development version of R (2.6.0), I notice that my sem package
produces the following warning:
checking Rd files ... WARNING
Rd files with unknown encoding:
residuals.Rd
I wonder what the warning means. As far as I can see, residuals.Rd is
similar to the other .Rd files in the package.
At least for the time being, I won't reproduce residuals.Rd here in the
interest of brevity.
You have in the \details of that file:
(s_{ij} - c_{ij})/[(c_{ii}c_{jj} - c_{ij}²)/N]^{1/2}}
and that superscript 2 (which will probably come out in your mailer but
not for all readers) is not ASCII. 'Writing R Extensions' tells you that
for files that are not entirely ASCII you need to declare the encoding:
I presume you want \encoding{latin1}.
You might also want to think about the N^{*} in the latex version and the
N in the not-so-plain text version.
--
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-devel@r-project.org mailing list
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[Rd] small typo in NEWS
The current NEWS file on the R site states that there is a new relink (sic) function, which should probably be relist ... Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Warning under R 2.6.0: Rd files with unknown encoding
Dear Brian,
> -Original Message-
> From: Prof Brian Ripley [mailto:[EMAIL PROTECTED]
> Sent: Tuesday, June 12, 2007 7:45 AM
> To: John Fox
> Cc: r-devel@r-project.org
> Subject: Re: [Rd] Warning under R 2.6.0: Rd files with
> unknown encoding
>
> On Tue, 12 Jun 2007, John Fox wrote:
>
> > Dear R-devel list members,
> >
> > Under the development version of R (2.6.0), I notice that my sem
> > package produces the following warning:
> >
> > checking Rd files ... WARNING
> > Rd files with unknown encoding:
> > residuals.Rd
> >
> > I wonder what the warning means. As far as I can see,
> residuals.Rd is
> > similar to the other .Rd files in the package.
> >
> > At least for the time being, I won't reproduce residuals.Rd here in
> > the interest of brevity.
>
> You have in the \details of that file:
>
> (s_{ij} - c_{ij})/[(c_{ii}c_{jj} - c_{ij}²)/N]^{1/2}}
>
> and that superscript 2 (which will probably come out in your
> mailer but not for all readers) is not ASCII. 'Writing R
> Extensions' tells you that for files that are not entirely
> ASCII you need to declare the encoding:
> I presume you want \encoding{latin1}.
Thanks for catching that. I wonder how it happened, since I believe that I
produced the file with a plain-text editor, probably Tinn-R.
>
> You might also want to think about the N^{*} in the latex
> version and the N in the not-so-plain text version.
Yes, I saw the missing asterisk (and the not-so-plain text) when I compared
the PDF and chtml versions of the help page in my attempt to locate the
error.
Thanks again,
John
>
> --
> 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
__
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Re: [Rd] bug in R environments? Was: [BioC] 'recursive default argument' error...
Prof Brian Ripley <[EMAIL PROTECTED]> writes:
> On Tue, 12 Jun 2007, Oleg Sklyar wrote:
>
>> Dear developers,
>>
>> has anyone experienced the problem described below? Is it a bug in
>> handling interrupts in R?
>
> I am not sure where you think the 'bug' is in: cf your subject line.
> My guess is that the package is using environments in a vulnerable
> way.
The issue at hand is, I believe, the same as that discussed here:
http://thread.gmane.org/gmane.comp.lang.r.devel/8103/focus=8104
> I cannot reproduce your example on my system: I was able to interrupt but
> repeating the as.list worked.
Try with a larger environment. I can reproduce this with a recent
R-devel using the GO package:
> library(GO)
> GOTERM
^C
> GOTERM
Error: recursive default argument reference
> What I suspect may have happened is that
> you have interrupted lazy loading. From the code
>
> if(PRSEEN(e))
> errorcall(R_GlobalContext->call,
> _("recursive default argument reference"));
> SET_PRSEEN(e, 1);
> val = eval(PRCODE(e), PRENV(e));
> SET_PRSEEN(e, 0);
>
> so you will get this message from a promise whose evaluation was
> incomplete. I can see several ways around that, but most have runtime
> costs or back-compatibility issues. (Changing the message may help.)
>
> It looks like rae230a has been implemented to use lazy-loading on whole
> environments (the 'source' is already a lazyload database, so it's not
> transparent). Lazy-loading was intended for members of environments.
>
> Also, does this happen in R-devel? There lazy-loading is considerably
> faster and closer to an atomic operation.
>
> All guesswork on something I cannot reproduce, of course.
Good guesses. Yes, _all_ Bioconductor annotation data packages
currently store each identifier mapping in a separate environment. So
the package environment contains environments. The lazy loading db is
important at runtime when users may only need to access one or two of
the environments. We generate the lazy-loading dbs by hand so that
users installing from source do not have to repeat the process
themselves. Since the environments are large, it is possible to use
the packages on a system that does not have enough memory to
"properly" install them.
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org
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Re: [Rd] small typo in NEWS
> "BB" == Ben Bolker <[EMAIL PROTECTED]> > on Tue, 12 Jun 2007 13:31:21 + (UTC) writes: BB> The current NEWS file on the R site states that there is BB> a new relink (sic) function, which should probably be BB> relist ... Yes, thanks; being fixed "as we speak" ;-) Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Warning under R 2.6.0: Rd files with unknown encoding
John Fox wrote:
> Dear Brian,
>
>
>> -Original Message-
>> From: Prof Brian Ripley [mailto:[EMAIL PROTECTED]
>> Sent: Tuesday, June 12, 2007 7:45 AM
>> To: John Fox
>> Cc: r-devel@r-project.org
>> Subject: Re: [Rd] Warning under R 2.6.0: Rd files with
>> unknown encoding
>>
>> On Tue, 12 Jun 2007, John Fox wrote:
>>
>>
>>> Dear R-devel list members,
>>>
>>> Under the development version of R (2.6.0), I notice that my sem
>>> package produces the following warning:
>>>
>>> checking Rd files ... WARNING
>>> Rd files with unknown encoding:
>>> residuals.Rd
>>>
>>> I wonder what the warning means. As far as I can see,
>>>
>> residuals.Rd is
>>
>>> similar to the other .Rd files in the package.
>>>
>>> At least for the time being, I won't reproduce residuals.Rd here in
>>> the interest of brevity.
>>>
>> You have in the \details of that file:
>>
>> (s_{ij} - c_{ij})/[(c_{ii}c_{jj} - c_{ij}²)/N]^{1/2}}
>>
>> and that superscript 2 (which will probably come out in your
>> mailer but not for all readers) is not ASCII. 'Writing R
>> Extensions' tells you that for files that are not entirely
>> ASCII you need to declare the encoding:
>> I presume you want \encoding{latin1}.
>>
>
> Thanks for catching that. I wonder how it happened, since I believe that I
> produced the file with a plain-text editor, probably Tinn-R.
>
Several tools seem to be overly helpful in doing that conversion
(x-caret-2 becomes x-superscript-2) these days. X11 keyboards without
the nodeadkeys option does it if you forget a space after the caret, and
Thunderbird does it when displaying emails, which is almost as annoying
as the automatic smiley recognition (which has been said to "turn Perl
scripts into love letters").
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Re: [Rd] Warning under R 2.6.0: Rd files with unknown encoding
These can be hard to spot. My technique (which in fact I did not need
here) is to use 'less' in a C locale, as that does things like
(s_{ij} - c_{ij})/[(c_{ii}c_{jj} - c_{ij})/N]^{1/2}}
with in reverse video so it is hard to miss.
Brian
On Tue, 12 Jun 2007, John Fox wrote:
Dear Brian,
-Original Message-
From: Prof Brian Ripley [mailto:[EMAIL PROTECTED]
Sent: Tuesday, June 12, 2007 7:45 AM
To: John Fox
Cc: r-devel@r-project.org
Subject: Re: [Rd] Warning under R 2.6.0: Rd files with
unknown encoding
On Tue, 12 Jun 2007, John Fox wrote:
Dear R-devel list members,
Under the development version of R (2.6.0), I notice that my sem
package produces the following warning:
checking Rd files ... WARNING
Rd files with unknown encoding:
residuals.Rd
I wonder what the warning means. As far as I can see,
residuals.Rd is
similar to the other .Rd files in the package.
At least for the time being, I won't reproduce residuals.Rd here in
the interest of brevity.
You have in the \details of that file:
(s_{ij} - c_{ij})/[(c_{ii}c_{jj} - c_{ij}²)/N]^{1/2}}
and that superscript 2 (which will probably come out in your
mailer but not for all readers) is not ASCII. 'Writing R
Extensions' tells you that for files that are not entirely
ASCII you need to declare the encoding:
I presume you want \encoding{latin1}.
Thanks for catching that. I wonder how it happened, since I believe that I
produced the file with a plain-text editor, probably Tinn-R.
You might also want to think about the N^{*} in the latex
version and the N in the not-so-plain text version.
Yes, I saw the missing asterisk (and the not-so-plain text) when I compared
the PDF and chtml versions of the help page in my attempt to locate the
error.
Thanks again,
John
--
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
--
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__
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[Rd] PATCH: install inst/ before doing lazyload on Windows
Hi, On Windows, package files in the inst/ subdir are installed after the lazyload creation. This differs from Linux where inst/ is installed _before_ lazyload creation. Since packages may need data in inst, I think the order on Windows should be changed. Perhaps like this: diff --git a/src/gnuwin32/MakePkg b/src/gnuwin32/MakePkg index 57af321..868e8f1 100644 --- a/src/gnuwin32/MakePkg +++ b/src/gnuwin32/MakePkg @@ -74,10 +74,10 @@ all: @$(MAKE) --no-print-directory -f $(RHOME)/src/gnuwin32/MakePkg -s nmspace @$(MAKE) --no-print-directory -f $(RHOME)/src/gnuwin32/MakePkg Dynlib @$(MAKE) --no-print-directory -f $(RHOME)/src/gnuwin32/MakePkg -s R + @$(MAKE) --no-print-directory -f $(RHOME)/src/gnuwin32/MakePkg -s $(DPKG)/demo $(DPKG)/exec $(DPKG)/inst $(DATA) ifeq ($(strip $(LAZY)),true) @$(MAKE) --no-print-directory -f $(RHOME)/src/gnuwin32/MakePkg -s lazyload endif - @$(MAKE) --no-print-directory -f $(RHOME)/src/gnuwin32/MakePkg -s $(DPKG)/demo $(DPKG)/exec $(DPKG)/inst $(DATA) ifeq ($(strip $(LAZYDATA)),true) @$(MAKE) --no-print-directory -f $(RHOME)/src/gnuwin32/MakePkg -s lazydata endif -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD SHLIB error using OS X
please report to R-sig-mac stefano On 08/giu/07, at 06:29, Richard Zur wrote: > Hello, > > I'm using R 2.5.0 with OS X 10.4.9 and Xcode 2.4.1 on a PowerPC. My > code used to compile fine with R 2.4.* and Xcode 2.2 (I think). > > I'm compiling some C code (named mhroc_prop.c) that calls a fortran > routine from mvndstpack.f I get the error > > /usr/bin/libtool: file: mvndstpack.o is not an object file (not > allowed > in a library) > > after R outputs (sorry... not sure if this is useful information or > not) > > gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 > -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup > -single_module -multiply_defined suppress -L/usr/local/lib -o > mhroc_prop.so mhroc_prop.o mvndstpack.o > -L/Library/Frameworks/R.framework/Resources/lib/ppc -lRlapack > -L/Library/Frameworks/R.framework/Resources/lib/ppc -lRblas > -L/usr/local/lib/gcc/powerpc-apple-darwin8/4.2.0 -lgfortran -lgcc_s. > 10.4 > -lSystemStubs -L/usr/local/lib/gcc/powerpc-apple-darwin8/4.2.0 > -lgfortran -lgcc_s.10.4 -lSystemStubs > -F/Library/Frameworks/R.framework/.. -framework R > > Any ideas? > > Thank you, > Richard Zur > > __ > 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
