Re: [Rd] GPL and R Community Policies (Rcpp)

[Dominick Samperi]

On Thu, Dec 2, 2010 at 2:45 AM, Sean O'Riordain  wrote:

> Good morning Dominick,
>
> I don't use the Rcpp package and have only the vaguest notions of its
> history.
>
> One of your requests is that your name might be removed from the project as
> you no longer wish to be associated with it.  However, I suspect that it is
> simply not legal to remove your copyright notice once the project has been
> distributed.  The only way this could happen is if the project is completely
> rewritten from scratch by people who have not worked on the project using a
> 'clean-room' methodology - this seems quite unlikely.
>

The GPL requirement is that my name appear in copyright notices at the top
of source files in
precisely the way that it appeared in my original work. It does not require
that my name appear
anywhere else, not on author lines, not in README files, not in THANKS
files, nowhere else.


> Just a thought,
>
> Kind regards,
> Sean O'Riordain
> Dublin
>
> On 2 December 2010 04:29, Adrian Dragulescu  wrote:
>
>>
>> Dominick,
>>
>> I don't use the Rcpp package but I have been aware of the changes made to
>> the package over the years.
>>
>> I don't see what you are after.  I don't consider the mention about your
>> contribution in the authors section disparaging in ANY way.  It seems
>> reasonable that as the code base grows, your initial contribution to have a
>> smaller and smaller share.  That's all it says.  If you would start
>> contributing again to the package development, I'm sure that line can be
>> changed.  Romain has gone from 0% to a sizeable share in a quick period with
>> some great contributions.  Other authors seem to find a way to contribute to
>> the project too.
>>
>> If it's peer recognition you're after, everybody on this list is already
>> aware that you're the original developer of the package.  I personally still
>> have a good memory so I don't need another reminder email on this topic.
>>
>> I'm sure there are other projects that you can work on, alone or with
>> collaborators, that would benefit the R community.
>>
>> Cheers, Adrian
>>
>>
>>
>>
>>
>> On Wed, 1 Dec 2010, Dominick Samperi wrote:
>>
>>  This post asks members of the R community, users and developers,
>>> to comment on issues related to the GNU Public License
>>> and R community policies more generally.
>>>
>>> The GPL says very little about protecting the the rights of original
>>> contributors by not disseminating  misleading information about them.
>>> Indeed, for pragmatic reasons it effectively assumes that original
>>> authors
>>> have no rights regarding their GPL-ed software, and it implicitly leaves
>>> it up to the community of developers and users to conduct themselves in a
>>> fair and
>>> reasonable manner.
>>>
>>> After discussing these matters with Richard Stallman I think
>>> we more-or-less agreed that a GPL "copyright" notice is nothing
>>> more than a way to deputise people to serve as protectors of the
>>> principles of the Free Software Foundation (FSF). It has nothing to
>>> do with protecting the "rights" or the "ideas" of original
>>> contributors. There is no peer review, no requirement to
>>> explain your contributions, and anybody can essentially
>>> do as they please with the software provided they retain
>>> the copyright/FSF deputy notice---of course, you can
>>> always work-around this last restriction by modifying the
>>> implementation and placing it in a new file, because
>>> nobody is checking (GPL doesn't require it).
>>>
>>> The GPL is all about "freedom", not responsibility. It is entirely
>>> focused on "deregulation", not on the protection of intellectual
>>> property or professional reputations. It serves the useful purpose
>>> of making great software more widely available, but it does not
>>> dictate how people should behave and should not be used
>>> as a moral compass.  (See recent book titled
>>> "You are not a gadget: a manifesto", a rejoinder to the
>>> GNU manifesto.)
>>>
>>> As a counterbalance I think the community of developers and
>>> users need to play a more active role in the evolution of
>>> shared values and expectations. In this spirit I respectfully request
>>> that the R community consider the following.
>>>
>>> The author line of the latest release of the R package
>>> Rcpp (0.8.9) was revised as follows:
>>>
>>> From: "based on code written during 2005 and 2006 by Dominick Samperi"
>>>
>>> To: "a small portion of the code is based on code written during 2005 and
>>> 2006 by Dominick Samperi"
>>>
>>> As it is highly unusual (and largely impossible) to quantify the relative
>>> size of the the contribution made by each author of GPL'ed software, this
>>> has
>>> effectively changed an acknowledgment into a disparaging remark. It
>>> is also misleading, because I am the original creator of the Rcpp library
>>> and package (it was forked by Dirk Eddelbuettel and is now effectively
>>> part of R core development). Incidentally, the README file for
>>> Rcpp 0.6.7

Re: [Rd] [Rcpp-devel] GPL and R Community Policies (Rcpp)

[Dominick Samperi]

On Thu, Dec 2, 2010 at 2:51 AM, Gavin Simpson wrote:

> On Wed, 2010-12-01 at 20:24 -0500, Dominick Samperi wrote:
> 
> > > Just to be clear I have never used the package and am not truly
> > > commenting on this particular case but only the general ideas in this
> > > thread.  Also I was not suggesting that the comments in the code were
> > > purposefully misleading, only that they might be misleading since they
> > > could be interpreted in terms of contribution even though they are
> > > stated in terms of lines of code.  The author of the phrase may very
> > > well have felt that the current team had done a lot of work to add
> > > design ideas and develop and promote the software but perhaps the
> > > unfortunate way in how it was expressed in that phrase that came out
> > > as a seeming comment on the original creator's contribution rather
> > > than the intended comment on their own, presumably also significant,
> > > contribution.
> > >
> >
> > There is no reason given why this
> > should happen now, at this moment, and no explanation why
> > the same standard should not be applied to other package authors,
> > including other authors of Rcpp.
>
> Dominick,
>
> You feel you are the aggrieved party so of course you will find
> conspiracy in the timing. An equally plausible explanation is that the
> current set of developers on Rcpp intended to alter the "contributions",
> to better reflect the current state of the package, some time ago but it
> slipped through the cracks.
>

While we are in the housecleaning mood, perhaps the "contributions"
can be reflected even better by removing all references to my name
as I have suggested.


>
> You are predisposed to see the bad where non may exist. But also, you
> should be discussing this in private with the package developers.
>
> There is nothing in this thread of relevance to R-devel (other than to
> publicly refute your claims so as to balance the record should someone
> come across this in the archives) as this has nothing to do with
> developing R. There is no-one here who can speak for the "R Community",
> because such a thing is not a concrete entity - you will just get the
> opinions of individuals. It is to the credit of this list (R-Devel) that
> this has not descended into a vitriolic stream of claim and counter
> claim.
>
> As for your claims about R Core, Doug has succinctly and clearly
> addressed your claims in that regard, regardless what you may personally
> believe. Rcpp is *not* an official product of the R Foundation, and
> neither is it part of the R distribution.
>
> Can we please take this elsewhere?
>
> Gavin.
>
> > This is not about this particular case, it is about "general ideas"
> > along the lines of your original post.
> >
> > Thanks,
> > Dominick
> >
> >
> > >
> > > --
> > > Statistics & Software Consulting
> > > GKX Group, GKX Associates Inc.
> > > tel: 1-877-GKX-GROUP
> > > email: ggrothendieck at gmail.com
> > >
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
> --
> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
>  Dr. Gavin Simpson [t] +44 (0)20 7679 0522
>  ECRC, UCL Geography,  [f] +44 (0)20 7679 0565
>  Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
>  Gower Street, London  [w] 
> http://www.ucl.ac.uk/~ucfagls/
>  UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
>
>

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Re: [Rd] GPL and R Community Policies (Rcpp)

[Liviu Andronic]

Dear all

On Wed, Dec 1, 2010 at 7:21 PM, Dominick Samperi  wrote:
> The author line of the latest release of the R package
> Rcpp (0.8.9) was revised as follows:
>
> From: "based on code written during 2005 and 2006 by Dominick Samperi"
>
> To: "a small portion of the code is based on code written during 2005 and
> 2006 by Dominick Samperi"
>
>From the info given in the thread, personally I'm sympathetic to
Dominick's complaint: the latter message is no proper way to
acknowledge the original author of the package. As I see it, the
project either:
- explicitly mentions the original author and the active (current)
contributors (and perhaps previous ones), or
- lines up all previous contributors in a line and singles out the
active contributors

But saying that the original author's contributions represented some
coding of random importance (implied in the message above), only a
subset of which made it to the current release, sounds disparaging to
my ears, too.

My humble opinion
Liviu

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Re: [Rd] GPL and R Community Policies (Rcpp)

[Martyn Plummer]

Dear Dominick,

The R community does not have a conflict resolution mechanism.  We are
quite used to disputes that end with one party, usually a recognized
authority, saying "No, you are objectively, verifiably wrong".   We
cannot, as a group, deal with anything else.

Everybody knows that you have an acrimonious relationship with the
current developers of Rcpp (and if they don't then a cursory look at the
rcpp-devel archives will confirm this).  The issue of the acknowledgment
that you are complaining about is merely a symptom of the further
deterioration of this relationship.   Appeals to authority or public
opinion are not going to help you obtain satisfaction.

Having your free software taken up and developed by other people is not
the worst thing that can happen.  For a free software developer, the
worst thing that can happen is that they get run over by a proverbial
bus and their software dies with them.

Martyn

On Wed, 2010-12-01 at 13:21 -0500, Dominick Samperi wrote:
> This post asks members of the R community, users and developers,
> to comment on issues related to the GNU Public License
> and R community policies more generally.
> 
> The GPL says very little about protecting the the rights of original
> contributors by not disseminating  misleading information about them.
> Indeed, for pragmatic reasons it effectively assumes that original authors
> have no rights regarding their GPL-ed software, and it implicitly leaves
> it up to the community of developers and users to conduct themselves in a
> fair and
> reasonable manner.
> 
> After discussing these matters with Richard Stallman I think
> we more-or-less agreed that a GPL "copyright" notice is nothing
> more than a way to deputise people to serve as protectors of the
> principles of the Free Software Foundation (FSF). It has nothing to
> do with protecting the "rights" or the "ideas" of original
> contributors. There is no peer review, no requirement to
> explain your contributions, and anybody can essentially
> do as they please with the software provided they retain
> the copyright/FSF deputy notice---of course, you can
> always work-around this last restriction by modifying the
> implementation and placing it in a new file, because
> nobody is checking (GPL doesn't require it).
> 
> The GPL is all about "freedom", not responsibility. It is entirely
> focused on "deregulation", not on the protection of intellectual
> property or professional reputations. It serves the useful purpose
> of making great software more widely available, but it does not
> dictate how people should behave and should not be used
> as a moral compass.  (See recent book titled
> "You are not a gadget: a manifesto", a rejoinder to the
> GNU manifesto.)
> 
> As a counterbalance I think the community of developers and
> users need to play a more active role in the evolution of
> shared values and expectations. In this spirit I respectfully request
> that the R community consider the following.
> 
> The author line of the latest release of the R package
> Rcpp (0.8.9) was revised as follows:
> 
> From: "based on code written during 2005 and 2006 by Dominick Samperi"
> 
> To: "a small portion of the code is based on code written during 2005 and
> 2006 by Dominick Samperi"
> 
> As it is highly unusual (and largely impossible) to quantify the relative
> size of the the contribution made by each author of GPL'ed software, this
> has
> effectively changed an acknowledgment into a disparaging remark. It
> is also misleading, because I am the original creator of the Rcpp library
> and package (it was forked by Dirk Eddelbuettel and is now effectively
> part of R core development). Incidentally, the README file for
> Rcpp 0.6.7 shows that my contributions and influence were not
> confined to the period 2005-2006.
> 
> A look at the change history of Rcpp would quickly reveal that to be
> fair other authors of Rcpp (and perhaps other R package authors)
> should have their contributions qualified with "a small portion of the
> code",
> or "administered by", but this is precisely the kind of monitoring that
> inspired Richard Stallman to say we must "chuck the masks" in the
> GNU Manifesto.
> 
> It is obviously a great benefit for the R community to have Rcpp actively
> supported by the R core team. I am very grateful for this. What I do
> have a problem with is the fact that my contributions are disparaged
> by people who have benefited from my past work.
> 
> It seems to me that there are two possible resolutions. First, if my
> name is used in the Rcpp package it should be used to provide fair,
> accurate, and courteous acknowledgement for my past contributions.
> Second, if this is not possible, then my name should not be used at all.
> If the second option is selected then the only place my name should
> appear is in the copyright ("deputy") notices.
> 
> Incidentally, the fact that the word "copyright" is profoundly misleading in
> the context of GPL is not a new idea, and

Re: [Rd] GPL and R Community Policies (Rcpp)

[Spencer Graves]

On 12/2/2010 6:20 AM, Martyn Plummer wrote:

Dear Dominick,

The R community does not have a conflict resolution mechanism.  We are
quite used to disputes that end with one party, usually a recognized
authority, saying "No, you are objectively, verifiably wrong".   We
cannot, as a group, deal with anything else.

Everybody knows that you have an acrimonious relationship with the
current developers of Rcpp (and if they don't then a cursory look at the
rcpp-devel archives will confirm this).  The issue of the acknowledgment
that you are complaining about is merely a symptom of the further
deterioration of this relationship.   Appeals to authority or public
opinion are not going to help you obtain satisfaction.

Having your free software taken up and developed by other people is not
the worst thing that can happen.  For a free software developer, the
worst thing that can happen is that they get run over by a proverbial
bus and their software dies with them.


Somewhere close to the worst is that no one every uses your software.

Martyn

On Wed, 2010-12-01 at 13:21 -0500, Dominick Samperi wrote:

This post asks members of the R community, users and developers,
to comment on issues related to the GNU Public License
and R community policies more generally.

The GPL says very little about protecting the the rights of original
contributors by not disseminating  misleading information about them.
Indeed, for pragmatic reasons it effectively assumes that original authors
have no rights regarding their GPL-ed software, and it implicitly leaves
it up to the community of developers and users to conduct themselves in a
fair and
reasonable manner.

After discussing these matters with Richard Stallman I think
we more-or-less agreed that a GPL "copyright" notice is nothing
more than a way to deputise people to serve as protectors of the
principles of the Free Software Foundation (FSF). It has nothing to
do with protecting the "rights" or the "ideas" of original
contributors. There is no peer review, no requirement to
explain your contributions, and anybody can essentially
do as they please with the software provided they retain
the copyright/FSF deputy notice---of course, you can
always work-around this last restriction by modifying the
implementation and placing it in a new file, because
nobody is checking (GPL doesn't require it).

The GPL is all about "freedom", not responsibility. It is entirely
focused on "deregulation", not on the protection of intellectual
property or professional reputations. It serves the useful purpose
of making great software more widely available, but it does not
dictate how people should behave and should not be used
as a moral compass.  (See recent book titled
"You are not a gadget: a manifesto", a rejoinder to the
GNU manifesto.)

As a counterbalance I think the community of developers and
users need to play a more active role in the evolution of
shared values and expectations. In this spirit I respectfully request
that the R community consider the following.

The author line of the latest release of the R package
Rcpp (0.8.9) was revised as follows:

From: "based on code written during 2005 and 2006 by Dominick Samperi"

To: "a small portion of the code is based on code written during 2005 and
2006 by Dominick Samperi"

As it is highly unusual (and largely impossible) to quantify the relative
size of the the contribution made by each author of GPL'ed software, this
has
effectively changed an acknowledgment into a disparaging remark. It
is also misleading, because I am the original creator of the Rcpp library
and package (it was forked by Dirk Eddelbuettel and is now effectively
part of R core development). Incidentally, the README file for
Rcpp 0.6.7 shows that my contributions and influence were not
confined to the period 2005-2006.

A look at the change history of Rcpp would quickly reveal that to be
fair other authors of Rcpp (and perhaps other R package authors)
should have their contributions qualified with "a small portion of the
code",
or "administered by", but this is precisely the kind of monitoring that
inspired Richard Stallman to say we must "chuck the masks" in the
GNU Manifesto.

It is obviously a great benefit for the R community to have Rcpp actively
supported by the R core team. I am very grateful for this. What I do
have a problem with is the fact that my contributions are disparaged
by people who have benefited from my past work.

It seems to me that there are two possible resolutions. First, if my
name is used in the Rcpp package it should be used to provide fair,
accurate, and courteous acknowledgement for my past contributions.
Second, if this is not possible, then my name should not be used at all.
If the second option is selected then the only place my name should
appear is in the copyright ("deputy") notices.

Incidentally, the fact that the word "copyright" is profoundly misleading in
the context of GPL is not a new idea, and the word "copyleft" is
sometimes used 

Re: [Rd] GPL and R Community Policies (Rcpp)

[Dominick Samperi]

On Thu, Dec 2, 2010 at 9:20 AM, Martyn Plummer  wrote:

> Dear Dominick,
>
> The R community does not have a conflict resolution mechanism.  We are
> quite used to disputes that end with one party, usually a recognized
> authority, saying "No, you are objectively, verifiably wrong".   We
> cannot, as a group, deal with anything else.
>
> Everybody knows that you have an acrimonious relationship with the
> current developers of Rcpp (and if they don't then a cursory look at the
> rcpp-devel archives will confirm this).  The issue of the acknowledgment
> that you are complaining about is merely a symptom of the further
> deterioration of this relationship.   Appeals to authority or public
> opinion are not going to help you obtain satisfaction.
>
> Having your free software taken up and developed by other people is not
> the worst thing that can happen.  For a free software developer, the
> worst thing that can happen is that they get run over by a proverbial
> bus and their software dies with them.
>

Martyn
>

I think I made it clear that I am not complaining about the fact that
software originally created by me continues to be developed by others.
I think this is a good thing. I am not complaining about GPL either.

If more people in the R community agree that the edit amounts to
a disparaging remark about an original contributor (and are not
afraid to say so publicly), then this is a good thing for the
R community, because it would discourage this kind of thing
from happening in the future, and would encourage more people
to contribute quality software.

If, on the other hand, people disagree or do not what to make
a public comment, then I have offered a simple resolution.
See option two of my original post.

Dominick


>
> On Wed, 2010-12-01 at 13:21 -0500, Dominick Samperi wrote:
> > This post asks members of the R community, users and developers,
> > to comment on issues related to the GNU Public License
> > and R community policies more generally.
> >
> > The GPL says very little about protecting the the rights of original
> > contributors by not disseminating  misleading information about them.
> > Indeed, for pragmatic reasons it effectively assumes that original
> authors
> > have no rights regarding their GPL-ed software, and it implicitly leaves
> > it up to the community of developers and users to conduct themselves in a
> > fair and
> > reasonable manner.
> >
> > After discussing these matters with Richard Stallman I think
> > we more-or-less agreed that a GPL "copyright" notice is nothing
> > more than a way to deputise people to serve as protectors of the
> > principles of the Free Software Foundation (FSF). It has nothing to
> > do with protecting the "rights" or the "ideas" of original
> > contributors. There is no peer review, no requirement to
> > explain your contributions, and anybody can essentially
> > do as they please with the software provided they retain
> > the copyright/FSF deputy notice---of course, you can
> > always work-around this last restriction by modifying the
> > implementation and placing it in a new file, because
> > nobody is checking (GPL doesn't require it).
> >
> > The GPL is all about "freedom", not responsibility. It is entirely
> > focused on "deregulation", not on the protection of intellectual
> > property or professional reputations. It serves the useful purpose
> > of making great software more widely available, but it does not
> > dictate how people should behave and should not be used
> > as a moral compass.  (See recent book titled
> > "You are not a gadget: a manifesto", a rejoinder to the
> > GNU manifesto.)
> >
> > As a counterbalance I think the community of developers and
> > users need to play a more active role in the evolution of
> > shared values and expectations. In this spirit I respectfully request
> > that the R community consider the following.
> >
> > The author line of the latest release of the R package
> > Rcpp (0.8.9) was revised as follows:
> >
> > From: "based on code written during 2005 and 2006 by Dominick Samperi"
> >
> > To: "a small portion of the code is based on code written during 2005 and
> > 2006 by Dominick Samperi"
> >
> > As it is highly unusual (and largely impossible) to quantify the relative
> > size of the the contribution made by each author of GPL'ed software, this
> > has
> > effectively changed an acknowledgment into a disparaging remark. It
> > is also misleading, because I am the original creator of the Rcpp library
> > and package (it was forked by Dirk Eddelbuettel and is now effectively
> > part of R core development). Incidentally, the README file for
> > Rcpp 0.6.7 shows that my contributions and influence were not
> > confined to the period 2005-2006.
> >
> > A look at the change history of Rcpp would quickly reveal that to be
> > fair other authors of Rcpp (and perhaps other R package authors)
> > should have their contributions qualified with "a small portion of the
> > code",
> > or "administered by"

Re: [Rd] GPL and R Community Policies (Rcpp)

[Dominick Samperi]

On Thu, Dec 2, 2010 at 10:21 AM, Spencer Graves <
spencer.gra...@structuremonitoring.com> wrote:

> On 12/2/2010 6:20 AM, Martyn Plummer wrote:
>
>> Dear Dominick,
>>
>> The R community does not have a conflict resolution mechanism.  We are
>> quite used to disputes that end with one party, usually a recognized
>> authority, saying "No, you are objectively, verifiably wrong".   We
>> cannot, as a group, deal with anything else.
>>
>> Everybody knows that you have an acrimonious relationship with the
>> current developers of Rcpp (and if they don't then a cursory look at the
>> rcpp-devel archives will confirm this).  The issue of the acknowledgment
>> that you are complaining about is merely a symptom of the further
>> deterioration of this relationship.   Appeals to authority or public
>> opinion are not going to help you obtain satisfaction.
>>
>> Having your free software taken up and developed by other people is not
>> the worst thing that can happen.  For a free software developer, the
>> worst thing that can happen is that they get run over by a proverbial
>> bus and their software dies with them.
>>
>
> Somewhere close to the worst is that no one every uses your software.
>

Worst yet is having to compete with your own work.



>  Martyn
>>
>> On Wed, 2010-12-01 at 13:21 -0500, Dominick Samperi wrote:
>>
>>> This post asks members of the R community, users and developers,
>>> to comment on issues related to the GNU Public License
>>> and R community policies more generally.
>>>
>>> The GPL says very little about protecting the the rights of original
>>> contributors by not disseminating  misleading information about them.
>>> Indeed, for pragmatic reasons it effectively assumes that original
>>> authors
>>> have no rights regarding their GPL-ed software, and it implicitly leaves
>>> it up to the community of developers and users to conduct themselves in a
>>> fair and
>>> reasonable manner.
>>>
>>> After discussing these matters with Richard Stallman I think
>>> we more-or-less agreed that a GPL "copyright" notice is nothing
>>> more than a way to deputise people to serve as protectors of the
>>> principles of the Free Software Foundation (FSF). It has nothing to
>>> do with protecting the "rights" or the "ideas" of original
>>> contributors. There is no peer review, no requirement to
>>> explain your contributions, and anybody can essentially
>>> do as they please with the software provided they retain
>>> the copyright/FSF deputy notice---of course, you can
>>> always work-around this last restriction by modifying the
>>> implementation and placing it in a new file, because
>>> nobody is checking (GPL doesn't require it).
>>>
>>> The GPL is all about "freedom", not responsibility. It is entirely
>>> focused on "deregulation", not on the protection of intellectual
>>> property or professional reputations. It serves the useful purpose
>>> of making great software more widely available, but it does not
>>> dictate how people should behave and should not be used
>>> as a moral compass.  (See recent book titled
>>> "You are not a gadget: a manifesto", a rejoinder to the
>>> GNU manifesto.)
>>>
>>> As a counterbalance I think the community of developers and
>>> users need to play a more active role in the evolution of
>>> shared values and expectations. In this spirit I respectfully request
>>> that the R community consider the following.
>>>
>>> The author line of the latest release of the R package
>>> Rcpp (0.8.9) was revised as follows:
>>>
>>> From: "based on code written during 2005 and 2006 by Dominick Samperi"
>>>
>>> To: "a small portion of the code is based on code written during 2005 and
>>> 2006 by Dominick Samperi"
>>>
>>> As it is highly unusual (and largely impossible) to quantify the relative
>>> size of the the contribution made by each author of GPL'ed software, this
>>> has
>>> effectively changed an acknowledgment into a disparaging remark. It
>>> is also misleading, because I am the original creator of the Rcpp library
>>> and package (it was forked by Dirk Eddelbuettel and is now effectively
>>> part of R core development). Incidentally, the README file for
>>> Rcpp 0.6.7 shows that my contributions and influence were not
>>> confined to the period 2005-2006.
>>>
>>> A look at the change history of Rcpp would quickly reveal that to be
>>> fair other authors of Rcpp (and perhaps other R package authors)
>>> should have their contributions qualified with "a small portion of the
>>> code",
>>> or "administered by", but this is precisely the kind of monitoring that
>>> inspired Richard Stallman to say we must "chuck the masks" in the
>>> GNU Manifesto.
>>>
>>> It is obviously a great benefit for the R community to have Rcpp actively
>>> supported by the R core team. I am very grateful for this. What I do
>>> have a problem with is the fact that my contributions are disparaged
>>> by people who have benefited from my past work.
>>>
>>> It seems to me that there are two possible resoluti

Re: [Rd] GPL and R Community Policies (Rcpp)

[Ravi Varadhan]

Yes, I agree, Spencer.  The worst thing that can happen is for your
ideas/creations to go completely unnoticed.

Here is what David Hume had to say about how his first philosophical work
(Treatise of Human Nature) was received:

"Never literary attempt was more unfortunate than my Treatise of Human
Nature. It fell dead-born from the press, without reaching such distinction
as even to excite a murmur among the zealots"

So, Dominick - please cheer up and try to find some solace in that your work
has had an influence on the R community!

Best,
Ravi.

---
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology School of Medicine Johns
Hopkins University

Ph. (410) 502-2619
email: rvarad...@jhmi.edu

-Original Message-
From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org]
On Behalf Of Spencer Graves
Sent: Thursday, December 02, 2010 10:22 AM
To: Martyn Plummer
Cc: r-devel@r-project.org; rcpp-devel
Subject: Re: [Rd] GPL and R Community Policies (Rcpp)

On 12/2/2010 6:20 AM, Martyn Plummer wrote:
> Dear Dominick,
>
> The R community does not have a conflict resolution mechanism.  We are
> quite used to disputes that end with one party, usually a recognized
> authority, saying "No, you are objectively, verifiably wrong".   We
> cannot, as a group, deal with anything else.
>
> Everybody knows that you have an acrimonious relationship with the
> current developers of Rcpp (and if they don't then a cursory look at the
> rcpp-devel archives will confirm this).  The issue of the acknowledgment
> that you are complaining about is merely a symptom of the further
> deterioration of this relationship.   Appeals to authority or public
> opinion are not going to help you obtain satisfaction.
>
> Having your free software taken up and developed by other people is not
> the worst thing that can happen.  For a free software developer, the
> worst thing that can happen is that they get run over by a proverbial
> bus and their software dies with them.

Somewhere close to the worst is that no one every uses your software.
> Martyn
>
> On Wed, 2010-12-01 at 13:21 -0500, Dominick Samperi wrote:
>> This post asks members of the R community, users and developers,
>> to comment on issues related to the GNU Public License
>> and R community policies more generally.
>>
>> The GPL says very little about protecting the the rights of original
>> contributors by not disseminating  misleading information about them.
>> Indeed, for pragmatic reasons it effectively assumes that original
authors
>> have no rights regarding their GPL-ed software, and it implicitly leaves
>> it up to the community of developers and users to conduct themselves in a
>> fair and
>> reasonable manner.
>>
>> After discussing these matters with Richard Stallman I think
>> we more-or-less agreed that a GPL "copyright" notice is nothing
>> more than a way to deputise people to serve as protectors of the
>> principles of the Free Software Foundation (FSF). It has nothing to
>> do with protecting the "rights" or the "ideas" of original
>> contributors. There is no peer review, no requirement to
>> explain your contributions, and anybody can essentially
>> do as they please with the software provided they retain
>> the copyright/FSF deputy notice---of course, you can
>> always work-around this last restriction by modifying the
>> implementation and placing it in a new file, because
>> nobody is checking (GPL doesn't require it).
>>
>> The GPL is all about "freedom", not responsibility. It is entirely
>> focused on "deregulation", not on the protection of intellectual
>> property or professional reputations. It serves the useful purpose
>> of making great software more widely available, but it does not
>> dictate how people should behave and should not be used
>> as a moral compass.  (See recent book titled
>> "You are not a gadget: a manifesto", a rejoinder to the
>> GNU manifesto.)
>>
>> As a counterbalance I think the community of developers and
>> users need to play a more active role in the evolution of
>> shared values and expectations. In this spirit I respectfully request
>> that the R community consider the following.
>>
>> The author line of the latest release of the R package
>> Rcpp (0.8.9) was revised as follows:
>>
>> From: "based on code written during 2005 and 2006 by Dominick Samperi"
>>
>> To: "a small portion of the code is based on code written during 2005 and
>> 2006 by Dominick Samperi"
>>
>> As it is highly unusual (and largely impossible) to quantify the relative
>> size of the the contribution made by each author of GPL'ed software, this
>> has
>> effectively changed an acknowledgment into a disparaging remark. It
>> is also misleading, because I am the original creator of the Rcpp library
>> and package (it was forked by Dirk Eddelbuettel and is now effectively
>> part of R core development). Incidentally, the README file for
>> Rcpp 0.6

Re: [Rd] GPL and R Community Policies (Rcpp)

[Joris Meys]

On Thu, Dec 2, 2010 at 4:31 PM, Dominick Samperi  wrote:
>
> Worst yet is having to compete with your own work.
>
About which competition are we talking then? I'm sorry, but the vast
majority of the 7 lines of code of the rcpp are not your work. And
honestly, I don't know of any package that would be able to compete
with the rcpp as it is now. Great package by the way, Dirk, Romain and
the other contributors made something really nice from it.

Cheers
Joris
-- 
Joris Meys
Statistical consultant

Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control

tel : +32 9 264 59 87
joris.m...@ugent.be
---
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Re: [Rd] GPL and R Community Policies (Rcpp)

[Dominick Samperi]

On Thu, Dec 2, 2010 at 10:47 AM, Joris Meys  wrote:

> On Thu, Dec 2, 2010 at 4:31 PM, Dominick Samperi 
> wrote:
> >
> > Worst yet is having to compete with your own work.
> >
> About which competition are we talking then? I'm sorry, but the vast
> majority of the 7 lines of code of the rcpp are not your work. And
> honestly, I don't know of any package that would be able to compete
> with the rcpp as it is now. Great package by the way, Dirk, Romain and
> the other contributors made something really nice from it.
>

You can not dissolve my original creator status by adding more names
to the author line or more lines of code or more unit tests.


>
> Cheers
> Joris
> --
> Joris Meys
> Statistical consultant
>
> Ghent University
> Faculty of Bioscience Engineering
> Department of Applied mathematics, biometrics and process control
>
> tel : +32 9 264 59 87
> joris.m...@ugent.be
> ---
> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>

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Re: [Rd] GPL and R Community Policies (Rcpp)

[Shane Conway]

Your original question is predicated on the notion that people are
"disseminating misleading information about" you, with this phrase: "a
small portion of the code is based on code written during 2005 and
2006 by Dominick Samperi".  While it may be difficult to qualify
contributions to a joint project, there is absolutely nothing
misleading in this.  It is a statement of fact.  I simply read it to
imply that all the other names listed are still actively involved, and
that the code has evolved significantly since 2006.

As others have already said: please take this up with the package
authors off this list.  There is no basis for trying to introduce a
general discussion with a broader audience about licensing, copyright,
etc. around this issue.

As a side note: I think that the Rcpp package authors should give
serious consideration to appending "The development of this package
was driven by the godawful code that Hadley wrote" to the end of the
acknowledgements.


On Thu, Dec 2, 2010 at 10:47 AM, Joris Meys  wrote:
> On Thu, Dec 2, 2010 at 4:31 PM, Dominick Samperi  wrote:
>>
>> Worst yet is having to compete with your own work.
>>
> About which competition are we talking then? I'm sorry, but the vast
> majority of the 7 lines of code of the rcpp are not your work. And
> honestly, I don't know of any package that would be able to compete
> with the rcpp as it is now. Great package by the way, Dirk, Romain and
> the other contributors made something really nice from it.
>
> Cheers
> Joris
> --
> Joris Meys
> Statistical consultant
>
> Ghent University
> Faculty of Bioscience Engineering
> Department of Applied mathematics, biometrics and process control
>
> tel : +32 9 264 59 87
> joris.m...@ugent.be
> ---
> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>
> __
> R-devel@r-project.org mailing list
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>

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Re: [Rd] [Rcpp-devel] GPL and R Community Policies (Rcpp)

[Martin Maechler]

> Dominick Samperi 
> on Thu, 2 Dec 2010 03:27:58 -0500 writes:

> On Thu, Dec 2, 2010 at 2:51 AM, Gavin Simpson 
wrote:
>> On Wed, 2010-12-01 at 20:24 -0500, Dominick Samperi wrote:
>> 
>> > > Just to be clear I have never used the package and am not truly
>> > > commenting on this particular case but only the general ideas in this
>> > > thread.  Also I was not suggesting that the comments in the code were
>> > > purposefully misleading, only that they might be misleading since 
they
>> > > could be interpreted in terms of contribution even though they are
>> > > stated in terms of lines of code.  The author of the phrase may very
>> > > well have felt that the current team had done a lot of work to add
>> > > design ideas and develop and promote the software but perhaps the
>> > > unfortunate way in how it was expressed in that phrase that came out
>> > > as a seeming comment on the original creator's contribution rather
>> > > than the intended comment on their own, presumably also significant,
>> > > contribution.
>> > >
>> >
>> > There is no reason given why this
>> > should happen now, at this moment, and no explanation why
>> > the same standard should not be applied to other package authors,
>> > including other authors of Rcpp.
>> 
>> Dominick,
>> 
>> You feel you are the aggrieved party so of course you will find
>> conspiracy in the timing. An equally plausible explanation is that the
>> current set of developers on Rcpp intended to alter the "contributions",
>> to better reflect the current state of the package, some time ago but it
>> slipped through the cracks.
>> 

> While we are in the housecleaning mood, perhaps the "contributions"
> can be reflected even better by removing all references to my name
> as I have suggested.


>> 
>> You are predisposed to see the bad where non may exist. But also, you
>> should be discussing this in private with the package developers.
>> 
>> There is nothing in this thread of relevance to R-devel (other than to
>> publicly refute your claims so as to balance the record should someone
>> come across this in the archives) as this has nothing to do with
>> developing R. There is no-one here who can speak for the "R Community",
>> because such a thing is not a concrete entity - you will just get the
>> opinions of individuals. It is to the credit of this list (R-Devel) that
>> this has not descended into a vitriolic stream of claim and counter
>> claim.
>> 
>> As for your claims about R Core, Doug has succinctly and clearly
>> addressed your claims in that regard, regardless what you may personally
>> believe. Rcpp is *not* an official product of the R Foundation, and
>> neither is it part of the R distribution.
>> 
>> Can we please take this elsewhere?
>> 
>> Gavin.

Yes, please.
I think Dominick has received several suggestions and has got a few
views from a tiny but not insignificant fraction of "the R
community". 
--> Thanks to all contributors
...
and that should be *it*.

Martin Maechler, ETH Zurich
(Administrator of the R-devel mailing list)

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Re: [Rd] GPL and R Community Policies (Rcpp)

[peter dalgaard]

On Dec 2, 2010, at 15:20 , Martyn Plummer wrote:

> Everybody knows that you have an acrimonious relationship with the
> current developers of Rcpp (and if they don't then a cursory look at the
> rcpp-devel archives will confirm this).  The issue of the acknowledgment
> that you are complaining about is merely a symptom of the further
> deterioration of this relationship.   Appeals to authority or public
> opinion are not going to help you obtain satisfaction.

Or, to be precise, YOU (Dominick) have offended people so deeply that they feel 
compelled to state that your original contributions are by now dwarfed by their 
own efforts. Rationally, it would have been much more sensible for them just to 
leave the attribution in place and let it grow old all by itself. 

Given that we are not just a Free Software community but also a scientific one, 
it is quite reasonable to require proper attribution when people take up 
someone else's earlier work, but that is as far as it goes. It is not in itself 
an issue that someone picks up "your" ball and runs with it. That is what I see 
as the rational stance on the matter.

Unfortunately, the trenches by now have been dug so deeply that any attempt of 
impartial mediation will be seen by both parties as siding with the other.

-- 
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [Rd] GPL and R Community Policies (Rcpp)

[Claudia Beleites]

On 12/02/2010 10:32 AM, Liviu Andronic wrote:

Dear all

On Wed, Dec 1, 2010 at 7:21 PM, Dominick Samperi  wrote:

The author line of the latest release of the R package
Rcpp (0.8.9) was revised as follows:

From: "based on code written during 2005 and 2006 by Dominick Samperi"

To: "a small portion of the code is based on code written during 2005 and
2006 by Dominick Samperi"

From the info given in the thread, personally I'm sympathetic to

Dominick's complaint: the latter message is no proper way to
acknowledge the original author of the package. As I see it, the
project either:
- explicitly mentions the original author and the active (current)
contributors (and perhaps previous ones), or
- lines up all previous contributors in a line and singles out the
active contributors

- or in this case say that it was forked (when) from (Author)'s (package) 
(version)


But saying that the original author's contributions represented some
coding of random importance (implied in the message above), only a
subset of which made it to the current release, sounds disparaging to
my ears, too.

My humble opinion
Liviu

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--
Claudia Beleites
Dipartimento dei Materiali e delle Risorse Naturali
Università degli Studi di Trieste
Via Alfonso Valerio 6/a
I-34127 Trieste

phone: +39 0 40 5 58-37 68
email: cbelei...@units.it

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Re: [Rd] GPL and R Community Policies (Rcpp)

[Gabor Grothendieck]

On Thu, Dec 2, 2010 at 11:24 AM, Claudia Beleites  wrote:
> On 12/02/2010 10:32 AM, Liviu Andronic wrote:
>>
>> Dear all
>>
>> On Wed, Dec 1, 2010 at 7:21 PM, Dominick Samperi
>>  wrote:
>>>
>>> The author line of the latest release of the R package
>>> Rcpp (0.8.9) was revised as follows:
>>>
>>> From: "based on code written during 2005 and 2006 by Dominick Samperi"
>>>
>>> To: "a small portion of the code is based on code written during 2005 and
>>> 2006 by Dominick Samperi"
>>>
>>> From the info given in the thread, personally I'm sympathetic to
>>
>> Dominick's complaint: the latter message is no proper way to
>> acknowledge the original author of the package. As I see it, the
>> project either:
>> - explicitly mentions the original author and the active (current)
>> contributors (and perhaps previous ones), or
>> - lines up all previous contributors in a line and singles out the
>> active contributors
>
> - or in this case say that it was forked (when) from (Author)'s (package)
> (version)

I think the danger in all this is that future developers might see
this discussion and then conclude that they would be better off
redeveloping existing packages encouraging a wasteful Not Invented
Here attitude rather than stand on the shoulders of others. That would
divert resources into nonproductive duplicative activities and slow
the growth of R.

Perhaps the takeaway is (1) to be particularly careful about forking a
project and (2) also for package developers to try as hard as they can
to write their packages in a such a way that they can be added onto
externally rather than requiring modification of the package itself.
For example, DBI allows external database drivers and Rcmdr allows
external plugins.  zoo can accommodate new classes of index without
modifying zoo itself.  And of course R itself has specific facilities
for encouraging user contributed packages which do not require any
change at all to R itself.

In fact, I wonder if its still not too late for the package in
question.  Perhaps it would be possible to divide it into two packages
-- one would be the new code and the other would be the original base
package with just sufficient modifications to allow the new package to
consist of add-ons to it.  (I haven't actually used the package in
question so I am not sure if this is realistic but thought I would
throw it out as a potential resolution.)

-- 
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com

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Re: [Rd] GPL and R Community Policies (Rcpp)

[Dominick Samperi]

On Thu, Dec 2, 2010 at 12:29 PM, Gabor Grothendieck  wrote:

> On Thu, Dec 2, 2010 at 11:24 AM, Claudia Beleites 
> wrote:
> > On 12/02/2010 10:32 AM, Liviu Andronic wrote:
> >>
> >> Dear all
> >>
> >> On Wed, Dec 1, 2010 at 7:21 PM, Dominick Samperi
> >>  wrote:
> >>>
> >>> The author line of the latest release of the R package
> >>> Rcpp (0.8.9) was revised as follows:
> >>>
> >>> From: "based on code written during 2005 and 2006 by Dominick Samperi"
> >>>
> >>> To: "a small portion of the code is based on code written during 2005
> and
> >>> 2006 by Dominick Samperi"
> >>>
> >>> From the info given in the thread, personally I'm sympathetic to
> >>
> >> Dominick's complaint: the latter message is no proper way to
> >> acknowledge the original author of the package. As I see it, the
> >> project either:
> >> - explicitly mentions the original author and the active (current)
> >> contributors (and perhaps previous ones), or
> >> - lines up all previous contributors in a line and singles out the
> >> active contributors
> >
> > - or in this case say that it was forked (when) from (Author)'s (package)
> > (version)
>
> I think the danger in all this is that future developers might see
> this discussion and then conclude that they would be better off
> redeveloping existing packages encouraging a wasteful Not Invented
> Here attitude rather than stand on the shoulders of others. That would
> divert resources into nonproductive duplicative activities and slow
> the growth of R.
>
> Perhaps the takeaway is (1) to be particularly careful about forking a
> project and (2) also for package developers to try as hard as they can
> to write their packages in a such a way that they can be added onto
> externally rather than requiring modification of the package itself.
> For example, DBI allows external database drivers and Rcmdr allows
> external plugins.  zoo can accommodate new classes of index without
> modifying zoo itself.  And of course R itself has specific facilities
> for encouraging user contributed packages which do not require any
> change at all to R itself.
>
> In fact, I wonder if its still not too late for the package in
> question.  Perhaps it would be possible to divide it into two packages
> -- one would be the new code and the other would be the original base
> package with just sufficient modifications to allow the new package to
> consist of add-ons to it.  (I haven't actually used the package in
> question so I am not sure if this is realistic but thought I would
> throw it out as a potential resolution.)
>

Actually, I attempted the reverse and created cxxPack (previosly
known as RcppTemplate, and Rcpp before that), a package that
depends on Rcpp (current version), and is designed to provide
a kind of C++ application level interface on top of the lower-level
interface provided by Rcpp, with particular focus on financial
applications.

For example, there is a C++ class ZooSeries that represents a
zoo time series, and a C++ class DataFrame that represents
an R data frame. These classes have C++ SEXP constructors,
and the resulting object has no linkage to a corresponding object
on the R side. In contrast, Rcpp tends to provide C++ classes
that are wrappers for R objects. Objects of type ZooSeries
and DataFrame can be mapped to the corresponding R
objects and passed back to R, for example.

Designing C++ classes that embed the logic of
corresponding R objects is more difficult than just wrapping
the corresponding R object, and I'm not sure this will
pay dividends, but it is there nevertheless. There
appears to be zero interest from the R community.

It turns out that Rcpp (in its various incarnations) was always
just a tool that I have used to build scientific applications,
and it is unfortunate that issues related to this tool have
overshadowed the real work. I surely do not want to
waste my time merging cxxPack/Rcpp into yet another
R/C++ solution, and I hope that the outcome of this
discussion does not lead to this.

Thanks,
Dominick



>
> --
> Statistics & Software Consulting
> GKX Group, GKX Associates Inc.
> tel: 1-877-GKX-GROUP
> email: ggrothendieck at gmail.com
>
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Re: [Rd] Install package 'Matrix' problem

[Zhang,Jun]

Prof. Ripley,
 I've just done the installation of the R package 'Matrix' to my 64-bit R 
2.12.0, and it is loaded fine. Seems adding -m64 to the CXX line solved the 
problem.

I had,
CC="cc -xc99 -m64 -xarch=sparcvis2"
CXX="CC -library=stlport4"

And now I have (the working version),
CC="cc -xc99 -m64 -xarch=sparcvis2"
CXX="CC -m64 -library=stlport4"

Thank you!

Jun Zhang
System Analyst III
Division of Quantitative Science
FCT4.6109
713-792-2606



-Original Message-
From: Prof Brian Ripley [mailto:rip...@stats.ox.ac.uk] 
Sent: Thursday, December 02, 2010 12:30 AM
To: Zhang,Jun
Cc: 'r-devel@r-project.org'
Subject: Re: [Rd] Install package 'Matrix' problem

We need more information, at the minimum the line which compiled 
CHMfactor.o.  Can you make the install log (you may need to run this 
again) and your etc/Makeconf available on-line?

At first sight your C++ compiler is missing -m64: the R-admin manual 
says

'For a 64-bit target add -m64 to the compiler macros and use something 
like LDFLAGS=-L/opt/csw/lib/sparcv9 or LDFLAGS=-L/usr/local/lib/amd64 
as appropriate.'

I see I used

CC="cc -xc99 -m64"
CFLAGS="-O -xlibmieee"
F77="f95 -m64"
FFLAGS=-O4
CXX="CC -m64 -library=stlport4"
CXXFLAGS=-O
FC=$F77
FCFLAGS=$FFLAGS
LDFLAGS=-L/usr/local/lib/sparcv9
FCLIBS="-lfai -lfsu -lfai2"

in config.site.  And BTW, it is always worth checking the manuals of 
current R-patched: your compiler postdates the pre-release period for 
R 2.12.0.

On Wed, 1 Dec 2010, Zhang,Jun wrote:

> 64-bit R-2.12.0 was installed on Sun SPARC Solaris 10. Compiler used is 
> solstudio12.2. Attached is the configure script.
> I then tried to install a recommended package called Matrix. The compilation 
> failed with the following messages,
> ...

> CC -library=stlport4 -G -L/opt/csw/lib/sparcv9 
> -L/opt/solstudio12.2/prod/lib/v9 -o Matrix.so CHMfactor.o Csparse.o 
> TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o 
> dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o 
> dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o 
> dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o 
> sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a 
> -L/apps/sparcv9/R-2.12.0/lib/R/lib -lRlapack 
> -L/apps/sparcv9/R-2.12.0/lib/R/lib -lRblas -lifai -lsunimath -lfai 
> -lfai2 -lfsumai -lfprodai -lfminlai -lfmaxlai -lfminvai -lfmaxvai 
> -lfui -lfsu -lsunmath -lmtsk -lm

> ld: fatal: file CHMfactor.o: wrong ELF class: ELFCLASS64
> ld: fatal: File processing errors. No output written to Matrix.so
> make: *** [Matrix.so] Error 2
> ERROR: compilation failed for package 'Matrix'
> * removing '/apps/sparcv9/R-2.12.0/lib/R/library/Matrix'
>
> Some article suggests theorectically that ld or compiler driver

You need to give references for what you are quoting here (there is 
much misinformation on the Internet).  I suspect it is simply that you 
didn't specify the C++ compiler correctly.

> first sees a component .o file which is 32-bit (don't know which one 
> here), and decides that other components should be 32-bit, too, 
> hence the error message, since CHMfactor.o must be a 64-bit object. 
> I just don't know what is the practical way to avoid this situation. 
> I guess I'm posting in the right list, can somebody help?

Maybe, but really your local IT support is there to help your use of 
your OS: this is a Solaris issue, not an R one.

-- 
Brian D. Ripley,  rip...@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595

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Re: [Rd] segfault interest?

[Matt Shotwell]

On Wed, 2010-11-24 at 12:12 -0500, ivo welch wrote: 
> I just figured out what is happening.  The root drive (presumably OSX
> virtual memory) becomes depleted.  The error message about "memory not
> mapped" was a hint, too.  So, not really R's fault.  However, I wonder

It still may be R's fault. This segfault occurs because R (or third
party code called by R) attempts to access memory beyond what is
allocated/mapped. It's very likely a programming error. A bug report is
warranted, subject to Duncan's earlier comments. 

Does the segfault only occur when a memory limit is reached?

The top five functions in your traceback (below) are all defined in the
base package...

-Matt

 *** caught segfault *** 
address 0xdc3f9b48, cause 'memory not mapped'
Traceback:
 1: rep.int(seq_len(nx), rep.int(rep.fac, nx))
 2: rep.int(rep.int(seq_len(nx), rep.int(rep.fac, nx)), orep)
 3: expand.grid(seq_len(nx), seq_len(ny))
 4: merge.data.frame(d, ss)
 5: merge(d, ss)
 6: valid.range(opt)
 7: eval.with.vis(expr, envir, enclos)
 8: eval.with.vis(ei, envir)
 9: source("fut-into-opts.R")

> whether R can be made to abort more gracefully, or at least trap the
> error message and translate it into something more meaningful ("you
> have run out of [virtual] memory when executing 'R statement' ").  of
> course, this may not be possible at all.
> 
> /iaw
> 
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

-- 
Matthew S. Shotwell
Graduate Student 
Division of Biostatistics and Epidemiology
Medical University of South Carolina

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[Rd] Terminology clarification (Re: GPL and R Community Policies (Rcpp)

[Dirk Eddelbuettel]

There are repeated claims concerning a "Rcpp fork".  Let's address both terms
in turn.

i)  Rcpp was used in November 2008 as the name for a re-launch of a package
which had seen releases on CRAN in 2005/2006 during which it was also
renamed to RcppTemplate. Hence no package of name Rcpp had existed for
years; the package's own author had moved on to anther name (RcppTemplate
as it were).  As such, no other package conflicted with the name.

To my knowledge, there is no 'namespace reservation into eternity' for
project names their very authors have liberated. If I missed a precedent,
I would appreciate a pointer.

We still use the name Rcpp today (in what is an almost entirely rewritten
package with vastly expanded functionality) as it is useful in
communicating the basic purpose: integrating R and C++.

ii) The usage of "fork" is simply wrong.  As running 'dict fork' on my Unix
machine shows (among many other entries covering anything from the eating
utensil to the system call):

fork In the open-source community, a fork is what occurs when two (or
   more) versions of a software package's source code are being 
developed
   in parallel which once shared a common code base, and these multiple
   versions of the source code have irreconcilable differences between
   them. This should not be confused with a development branch, which 
may
   later be folded back into the original source code base. Nor should 
it
   be confused with what happens when a new distribution of Linux or 
some
   other distribution is created, because that largely assembles pieces
   than can and will be used in other distributions without conflict.

   Forking is uncommon; in fact, it is so uncommon that individual
   instances loom large in hacker folklore. Notable in this class were 
the
   http://www.xemacs.org/About/XEmacsVsGNUemacs.html (Emacs/XEmacs 
fork),
   the GCC/EGCS fork (later healed by a merger) and the forks among the
   FreeBSD, NetBSD, and OpenBSD operating systems.

Note the "when two (or more) versions of a software package's source code
are being developed in parallel".  

Ergo, a "fork" would have required another living project with on-going
development.  But the code previously known at Rcpp/RcppTemplate was
anything but "living", this can easily be verified by looking at the
(preferably time-sorted) directory at CRAN (see link [1] below).

So let's please stop calling this a "fork" of Rcpp.  The Rcpp / RcppTemplate
project was not live in late 2008; we changed that and started a relaunch
under the (unused !!) name Rcpp which now, a good two years later, looks
pretty healthy with four contributor and growing use within the R community.
Rcpp has been almost completely rewritten and enhanced, but I fail to see the
bitterness of its original author.  There could be some pride in seeing ideas
re-used.  But to each their own.

Lastly, for the associated 'remove my name' request: I have emails from 2008
requesting this (which I accomodated), I also have emails from 2009 that
requested the reversal (also accomodated).  This is getting old.

Finally, as Ravi wrote:

On 2 December 2010 at 10:36, Ravi Varadhan wrote:
| So, Dominick - please cheer up and try to find some solace in that your work
| has had an influence on the R community!

Seconded.  

I have even older emails (from 2005/2006) where the author complains that no
other R packages use what was then Rcpp.  The code changed a lot, but there
is still some pride to be had in an idea living on, even if (as Peter wrote)
someone else picks up "your" ball and runs with it.

Regards, Dirk


[1] http://cran.r-project.org/src/contrib/Archive/cxxPack/Ancestry/?C=M;O=A

-- 
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Re: [Rd] segfault interest?

[Simon Urbanek]

Matt,

please use
R -d gdb
and then "bt" for a more useful trace.

Thanks,
Simon


On Dec 2, 2010, at 4:06 PM, Matt Shotwell wrote:

> On Wed, 2010-11-24 at 12:12 -0500, ivo welch wrote: 
>> I just figured out what is happening.  The root drive (presumably OSX
>> virtual memory) becomes depleted.  The error message about "memory not
>> mapped" was a hint, too.  So, not really R's fault.  However, I wonder
> 
> It still may be R's fault. This segfault occurs because R (or third
> party code called by R) attempts to access memory beyond what is
> allocated/mapped. It's very likely a programming error. A bug report is
> warranted, subject to Duncan's earlier comments. 
> 
> Does the segfault only occur when a memory limit is reached?
> 
> The top five functions in your traceback (below) are all defined in the
> base package...
> 
> -Matt
> 
> *** caught segfault *** 
> address 0xdc3f9b48, cause 'memory not mapped'
> Traceback:
> 1: rep.int(seq_len(nx), rep.int(rep.fac, nx))
> 2: rep.int(rep.int(seq_len(nx), rep.int(rep.fac, nx)), orep)
> 3: expand.grid(seq_len(nx), seq_len(ny))
> 4: merge.data.frame(d, ss)
> 5: merge(d, ss)
> 6: valid.range(opt)
> 7: eval.with.vis(expr, envir, enclos)
> 8: eval.with.vis(ei, envir)
> 9: source("fut-into-opts.R")
> 
>> whether R can be made to abort more gracefully, or at least trap the
>> error message and translate it into something more meaningful ("you
>> have run out of [virtual] memory when executing 'R statement' ").  of
>> course, this may not be possible at all.
>> 
>> /iaw
>> 
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> -- 
> Matthew S. Shotwell
> Graduate Student 
> Division of Biostatistics and Epidemiology
> Medical University of South Carolina
> 
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
>

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Re: [Rd] Terminology clarification (Re: GPL and R Community Policies (Rcpp)

[Dominick Samperi]

On Thu, Dec 2, 2010 at 4:35 PM, Dirk Eddelbuettel  wrote:

>
> There are repeated claims concerning a "Rcpp fork".  Let's address both
> terms
> in turn.
>
> i)  Rcpp was used in November 2008 as the name for a re-launch of a package
>which had seen releases on CRAN in 2005/2006 during which it was also
>renamed to RcppTemplate. Hence no package of name Rcpp had existed for
>years; the package's own author had moved on to anther name
> (RcppTemplate
>as it were).  As such, no other package conflicted with the name.
>
>To my knowledge, there is no 'namespace reservation into eternity' for
>project names their very authors have liberated. If I missed a
> precedent,
>I would appreciate a pointer.
>
>We still use the name Rcpp today (in what is an almost entirely
> rewritten
>package with vastly expanded functionality) as it is useful in
>communicating the basic purpose: integrating R and C++.
>
> ii) The usage of "fork" is simply wrong.  As running 'dict fork' on my Unix
>machine shows (among many other entries covering anything from the
> eating
>utensil to the system call):
>
>fork In the open-source community, a fork is what occurs when two
> (or
>   more) versions of a software package's source code are being
> developed
>   in parallel which once shared a common code base, and these
> multiple
>   versions of the source code have irreconcilable differences
> between
>   them. This should not be confused with a development branch,
> which may
>   later be folded back into the original source code base. Nor
> should it
>   be confused with what happens when a new distribution of Linux or
> some
>   other distribution is created, because that largely assembles
> pieces
>   than can and will be used in other distributions without
> conflict.
>
>   Forking is uncommon; in fact, it is so uncommon that individual
>   instances loom large in hacker folklore. Notable in this class
> were the
>   http://www.xemacs.org/About/XEmacsVsGNUemacs.html (Emacs/XEmacs
> fork),
>   the GCC/EGCS fork (later healed by a merger) and the forks among
> the
>   FreeBSD, NetBSD, and OpenBSD operating systems.
>
>Note the "when two (or more) versions of a software package's source
> code
>are being developed in parallel".
>
>Ergo, a "fork" would have required another living project with on-going
>development.  But the code previously known at Rcpp/RcppTemplate was
>anything but "living", this can easily be verified by looking at the
>(preferably time-sorted) directory at CRAN (see link [1] below).
>
> So let's please stop calling this a "fork" of Rcpp.  The Rcpp /
> RcppTemplate
> project was not live in late 2008; we changed that and started a relaunch
> under the (unused !!) name Rcpp which now, a good two years later, looks
> pretty healthy with four contributor and growing use within the R
> community.
> Rcpp has been almost completely rewritten and enhanced, but I fail to see
> the
> bitterness of its original author.  There could be some pride in seeing
> ideas
> re-used.  But to each their own.
>
> Lastly, for the associated 'remove my name' request: I have emails from
> 2008
> requesting this (which I accomodated), I also have emails from 2009 that
> requested the reversal (also accomodated).  This is getting old.
>

OK, since you are so accomodating, then please remove all reference to
my name from Rcpp as I do not want to be subject to arbitrary revisions of
my status. I may not have the right to say how my prior work will be used,
but I think I have the right to ask that my name not be used in the way
it is used in the recent update.

On the "fork" question, in November of 2009 you were maintaining
an old version of my software for your own purposes because I did
not have time to contribute updates to CRAN. The changes that
you made were minimal (as a diff would show). GPL permits you
to do this. Whether you call this a fork or not is a language issue.

In November of 2009 I released an update with many improvements
including object mapping support that was missing from my old
software and from the version that you were maintaining. I asked
you to remove the version you were maintaining so there would
be only one Rcpp library, and you refused, invited Romain to
join the project, and added many of the features that I had just
released. Thus the real "fork" occured in November 2009.

Dominick

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Re: [Rd] Terminology clarification (Re: GPL and R Community Policies (Rcpp)

[Dominick Samperi]

While we are on the subject of terminology, it is important to remember
that Rcpp is a C++ library, and this is often confused with Rcpp the
package. I changed the package name to limit confusion on this
point, but the package name was changed back to Rcpp for the "fork" (or
"branch", not sure what else to call it). The one constant in all of
this is Rcpp the C++ library.

On Thu, Dec 2, 2010 at 5:23 PM, Dominick Samperi wrote:

>
>
> On Thu, Dec 2, 2010 at 4:35 PM, Dirk Eddelbuettel  wrote:
>
>>
>> There are repeated claims concerning a "Rcpp fork".  Let's address both
>> terms
>> in turn.
>>
>> i)  Rcpp was used in November 2008 as the name for a re-launch of a
>> package
>>which had seen releases on CRAN in 2005/2006 during which it was also
>>renamed to RcppTemplate. Hence no package of name Rcpp had existed for
>>years; the package's own author had moved on to anther name
>> (RcppTemplate
>>as it were).  As such, no other package conflicted with the name.
>>
>>To my knowledge, there is no 'namespace reservation into eternity' for
>>project names their very authors have liberated. If I missed a
>> precedent,
>>I would appreciate a pointer.
>>
>>We still use the name Rcpp today (in what is an almost entirely
>> rewritten
>>package with vastly expanded functionality) as it is useful in
>>communicating the basic purpose: integrating R and C++.
>>
>> ii) The usage of "fork" is simply wrong.  As running 'dict fork' on my
>> Unix
>>machine shows (among many other entries covering anything from the
>> eating
>>utensil to the system call):
>>
>>fork In the open-source community, a fork is what occurs when two
>> (or
>>   more) versions of a software package's source code are being
>> developed
>>   in parallel which once shared a common code base, and these
>> multiple
>>   versions of the source code have irreconcilable differences
>> between
>>   them. This should not be confused with a development branch,
>> which may
>>   later be folded back into the original source code base. Nor
>> should it
>>   be confused with what happens when a new distribution of Linux
>> or some
>>   other distribution is created, because that largely assembles
>> pieces
>>   than can and will be used in other distributions without
>> conflict.
>>
>>   Forking is uncommon; in fact, it is so uncommon that individual
>>   instances loom large in hacker folklore. Notable in this class
>> were the
>>   http://www.xemacs.org/About/XEmacsVsGNUemacs.html (Emacs/XEmacs
>> fork),
>>   the GCC/EGCS fork (later healed by a merger) and the forks among
>> the
>>   FreeBSD, NetBSD, and OpenBSD operating systems.
>>
>>Note the "when two (or more) versions of a software package's source
>> code
>>are being developed in parallel".
>>
>>Ergo, a "fork" would have required another living project with on-going
>>development.  But the code previously known at Rcpp/RcppTemplate was
>>anything but "living", this can easily be verified by looking at the
>>(preferably time-sorted) directory at CRAN (see link [1] below).
>>
>> So let's please stop calling this a "fork" of Rcpp.  The Rcpp /
>> RcppTemplate
>> project was not live in late 2008; we changed that and started a relaunch
>> under the (unused !!) name Rcpp which now, a good two years later, looks
>> pretty healthy with four contributor and growing use within the R
>> community.
>> Rcpp has been almost completely rewritten and enhanced, but I fail to see
>> the
>> bitterness of its original author.  There could be some pride in seeing
>> ideas
>> re-used.  But to each their own.
>>
>> Lastly, for the associated 'remove my name' request: I have emails from
>> 2008
>> requesting this (which I accomodated), I also have emails from 2009 that
>> requested the reversal (also accomodated).  This is getting old.
>>
>
> OK, since you are so accomodating, then please remove all reference to
> my name from Rcpp as I do not want to be subject to arbitrary revisions of
> my status. I may not have the right to say how my prior work will be used,
> but I think I have the right to ask that my name not be used in the way
> it is used in the recent update.
>
> On the "fork" question, in November of 2009 you were maintaining
> an old version of my software for your own purposes because I did
> not have time to contribute updates to CRAN. The changes that
> you made were minimal (as a diff would show). GPL permits you
> to do this. Whether you call this a fork or not is a language issue.
>
> In November of 2009 I released an update with many improvements
> including object mapping support that was missing from my old
> software and from the version that you were maintaining. I asked
> you to remove the version you were maintaining so there would
> be only one Rcpp library, and you refused, invited Romain to
> join the project, and added 

Re: [Rd] Terminology clarification (Re: GPL and R Community Policies (Rcpp)

[Dirk Eddelbuettel]

On 2 December 2010 at 17:23, Dominick Samperi wrote:
| OK, since you are so accomodating, then please remove all reference to
| my name from Rcpp as I do not want to be subject to arbitrary revisions of
| my status. I may not have the right to say how my prior work will be used,
| but I think I have the right to ask that my name not be used in the way
| it is used in the recent update.

As I pointed out, you change your mind on this every 12 months, limiting my
patience and willingness for these dances.  It has also been suggested by
other than attribution is clearer if you listed as the maintainer of the
2005/2006 code that we started from in 2008.
 
| On the "fork" question, in November of 2009 you were maintaining
| an old version of my software for your own purposes because I did

Well a glance at the changelog (either from the source, the SVN repo or via
the bottom of http://dirk.eddelbuettel.com/code/rcpp.changelog.html) clearly
shows that by November 2009 we were nine releases into it. There are a full
210 lines of changes including

2009-11-18  Dirk Eddelbuettel  

* DESCRIPTION: Add Dominick back into Authors per his new request
  reversing his requests to be removed from last December

As I stated, this was maintaining, enhancing, solidifying, ... a codebase I
and others used, using an API and code that we were free to use under GPL.  

You had released nothing from late 2006 to late 2009 -- and as I recall what
you released then (and withdrew weeks later) was not even compatible with
your own old API.  

But our Rcpp was -- that is called "maintaining" code.

| not have time to contribute updates to CRAN. The changes that
| you made were minimal (as a diff would show). GPL permits you

We beg to differ.

| to do this. Whether you call this a fork or not is a language issue.
| 
| In November of 2009 I released an update with many improvements
| including object mapping support that was missing from my old
| software and from the version that you were maintaining. I asked
| you to remove the version you were maintaining so there would
| be only one Rcpp library, and you refused, invited Romain to
| join the project, and added many of the features that I had just
| released. Thus the real "fork" occured in November 2009.

Nonsense -- No code, design, ideas,  of your shortlived RcppTemplate are
in Rcpp.  

Romain and I repeatedly said so, and we will not let you paint an alternate
history.  

Dirk

-- 
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Re: [Rd] Terminology clarification (Re: GPL and R Community Policies (Rcpp)

[Dominick Samperi]

On Thu, Dec 2, 2010 at 5:58 PM, Dirk Eddelbuettel  wrote:

>
> On 2 December 2010 at 17:23, Dominick Samperi wrote:
> | OK, since you are so accomodating, then please remove all reference to
> | my name from Rcpp as I do not want to be subject to arbitrary revisions
> of
> | my status. I may not have the right to say how my prior work will be
> used,
> | but I think I have the right to ask that my name not be used in the way
> | it is used in the recent update.
>
> As I pointed out, you change your mind on this every 12 months, limiting my
> patience and willingness for these dances.  It has also been suggested by
> other than attribution is clearer if you listed as the maintainer of the
> 2005/2006 code that we started from in 2008.
>

The change that this thread is a reaction to happened a few days ago, not
12 months ago. If I wavered in the past it was because I was being
forced to compete with my own work, not a pleasant place to be.

Are you telling me that you refuse to stop using my name
in Rcpp (except in copyright notices)?

Are you telling me that you will continue to use my name and
update the associated status as you see fit, whether or not I
approve or consent to those changes?

Please answer yes or no.

Thanks,
Dominick

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Re: [Rd] Terminology clarification (Re: GPL and R Community Policies (Rcpp)

[Dominick Samperi]

On Thu, Dec 2, 2010 at 5:58 PM, Dirk Eddelbuettel  wrote:

>
> On 2 December 2010 at 17:23, Dominick Samperi wrote:
> | OK, since you are so accomodating, then please remove all reference to
> | my name from Rcpp as I do not want to be subject to arbitrary revisions
> of
> | my status. I may not have the right to say how my prior work will be
> used,
> | but I think I have the right to ask that my name not be used in the way
> | it is used in the recent update.
>
> As I pointed out, you change your mind on this every 12 months, limiting my
> patience and willingness for these dances.  It has also been suggested by
> other than attribution is clearer if you listed as the maintainer of the
> 2005/2006 code that we started from in 2008.
>

We? Romain did not arrive on the scene until after November of 2009.

To live outside the law you must be honest --- Bob Dylan.

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Re: [Rd] Terminology clarification (Re: GPL and R Community Policies (Rcpp)

[Joris Meys]

On Fri, Dec 3, 2010 at 12:38 AM, Dominick Samperi  wrote:

> We? Romain did not arrive on the scene until after November of 2009.
>
> To live outside the law you must be honest --- Bob Dylan.
>
>        [[alternative HTML version deleted]]
>
Peter Dalgaard and Martin Maechler were pretty clear if you ask me.
Mud slinging can be done at 4chan.com

Goodnight.



-- 
Joris Meys
Statistical consultant

Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control

tel : +32 9 264 59 87
joris.m...@ugent.be
---
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php

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Re: [Rd] Terminology clarification (Re: GPL and R Community Policies (Rcpp)

[Dominick Samperi]

On Thu, Dec 2, 2010 at 6:43 PM, Joris Meys  wrote:

> On Fri, Dec 3, 2010 at 12:38 AM, Dominick Samperi 
> wrote:
>
> > We? Romain did not arrive on the scene until after November of 2009.
> >
> > To live outside the law you must be honest --- Bob Dylan.
> >
> >[[alternative HTML version deleted]]
> >
> Peter Dalgaard and Martin Maechler were pretty clear if you ask me.
> Mud slinging can be done at 4chan.com
>

I borrowed this Dylan quote from a recent r-devel thread ("must .Call C
function return SEXP?").
I think it sums up the Free software / Open science dilemma pretty well.
It was meant to entertain, not to offend.


> Goodnight.
>
>
>
> --
> Joris Meys
> Statistical consultant
>
> Ghent University
> Faculty of Bioscience Engineering
> Department of Applied mathematics, biometrics and process control
>
> tel : +32 9 264 59 87
> joris.m...@ugent.be
> ---
> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>

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