as.vector in R-devel loaded 3/3/2016

I dug into this a little further and discovered the problem.  When my
package is for checking, it loads Matrix.  In the R-devel version of
Matrix, as.vector is re-defined without mode specified

as.vector

standardGeneric for "as.vector" defined from package "base"

function (x, mode)
standardGeneric("as.vector")
<environment: 0x082faf08>
Methods may be defined for arguments: x, mode
Use  showMethods("as.vector")  for currently available ones.

In R3.2.3 it is defined with mode="any" specified.

as.vector

standardGeneric for "as.vector" defined from package "base"

function (x, mode = "any")
standardGeneric("as.vector")
<environment: 0x084af110>
Methods may be defined for arguments: x, mode
Use  showMethods("as.vector")  for currently available ones.

Until this is fixed I'll copy over the devel version of Matrix.

--jeff


On Thu, Mar 3, 2016 at 7:23 AM, Jeff Laake - NOAA Federal <

I just installed R-devel to check my package before submitting.  I got an
error in my vignette in regards to as.vector.  When I looked at the code
for as.vector in R-devel it is

standardGeneric for "as.vector" defined from package "base"

function (x, mode)
standardGeneric("as.vector")
<environment: 0x0918ad70>
Methods may be defined for arguments: x, mode
Use  showMethods("as.vector")  for currently available ones.

The code from R3.2.3 is

as.vector

function (x, mode = "any")
.Internal(as.vector(x, mode))
<bytecode: 0x02dfb858>
<environment: namespace:base>

Is default for mode missing as I suspect or will mode be required from now
on?

Er, until _what_ is fixed?

I see no anomalies with the version in R-pre:

library(Matrix)
as.vector

standardGeneric for "as.vector" defined from package "base"

function (x, mode = "any") 
standardGeneric("as.vector")
<environment: 0x7fe8f4516640>
Methods may be defined for arguments: x, mode
Use  showMethods("as.vector")  for currently available ones.

str(as.vector(1:3))

int [1:3] 1 2 3

str(as.vector(1:3+0))

num [1:3] 1 2 3

str(as.vector(list(1,2,3))

+ )
List of 3
 $ : num 1
 $ : num 2
 $ : num 3

str(as.vector(list(1,2,3), mode="integer"))

int [1:3] 1 2 3

str(as.vector(list(1,2,3), mode="numeric"))

num [1:3] 1 2 3


Also, *current* r-devel has the same definition:

$ ~/r-devel/BUILD-dist/bin/R

R Under development (unstable) (2016-03-03 r70270) -- "Unsuffered Consequences"
[...yadayada...]

library(Matrix)
as.vector

function (x, mode = "any") 
.Internal(as.vector(x, mode))
<bytecode: 0x7fdf69279780>
<environment: namespace:base>

On 04 Mar 2016, at 01:09 , Jeff Laake - NOAA Federal <jeff.laake at noaa.gov> wrote:

I dug into this a little further and discovered the problem.  When my
package is for checking, it loads Matrix.  In the R-devel version of
Matrix, as.vector is re-defined without mode specified

as.vector

standardGeneric for "as.vector" defined from package "base"

function (x, mode)
standardGeneric("as.vector")
<environment: 0x082faf08>
Methods may be defined for arguments: x, mode
Use  showMethods("as.vector")  for currently available ones.

In R3.2.3 it is defined with mode="any" specified.

as.vector

standardGeneric for "as.vector" defined from package "base"

function (x, mode = "any")
standardGeneric("as.vector")
<environment: 0x084af110>
Methods may be defined for arguments: x, mode
Use  showMethods("as.vector")  for currently available ones.

Until this is fixed I'll copy over the devel version of Matrix.

--jeff


On Thu, Mar 3, 2016 at 7:23 AM, Jeff Laake - NOAA Federal <
jeff.laake at noaa.gov> wrote:

I just installed R-devel to check my package before submitting.  I got an
error in my vignette in regards to as.vector.  When I looked at the code
for as.vector in R-devel it is

standardGeneric for "as.vector" defined from package "base"

function (x, mode)
standardGeneric("as.vector")
<environment: 0x0918ad70>
Methods may be defined for arguments: x, mode
Use  showMethods("as.vector")  for currently available ones.

The code from R3.2.3 is

as.vector

function (x, mode = "any")
.Internal(as.vector(x, mode))
<bytecode: 0x02dfb858>
<environment: namespace:base>

Is default for mode missing as I suspect or will mode be required from now
on?

	[[alternative HTML version deleted]]

______________________________________________
R-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com

peter dalgaard <pdalgd at gmail.com>
    on Fri, 4 Mar 2016 09:21:48 +0100 writes:

> Er, until _what_ is fixed?
    > I see no anomalies with the version in R-pre:

Indeed.

The problem ... I also have stumbled over ..
is that I'm sure Jeff is accidentally loading a different
version of 'Matrix' than the one that is part of R-devel.

Jeff you must accidentally be loading a version Matrix made with
R 3.2.x in R 3.3.0  and that will fail with the as.vector()
mismatch error message.

(and IIRC, you also get such an error message if you load a
 3.3.0-built version of Matrix into a non-3.3.0 version of R).


Martin

I see as below, where getGeneric and getMethod imply a different signature; the signature is mode="any" for both cases in R version 3.2.3 Patched (2016-01-28 r70038)I don't know how to reproduce Jeff's error, though.

library(Matrix)
as.vector

function (x, mode = "any") 
.Internal(as.vector(x, mode))
<bytecode: 0xe79f88>
<environment: namespace:base>

getGeneric("as.vector")

standardGeneric for "as.vector" defined from package "base"

function (x, mode) 
standardGeneric("as.vector")
<bytecode: 0x29a6bd0>
<environment: 0x299f988>
Methods may be defined for arguments: x
Use  showMethods("as.vector")  for currently available ones.

selectMethod("as.vector", "ANY")

Method Definition (Class "internalDispatchMethod"):

function (x, mode) 
.Internal(as.vector(x, mode))
<environment: base>

Signatures:
        x    
target  "ANY"
defined "ANY"

sessionInfo()

R Under development (unstable) (2016-02-27 r70232)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Matrix_1.2-4

loaded via a namespace (and not attached):
[1] grid_3.3.0      lattice_0.20-33

>>>>> peter dalgaard <pdalgd at gmail.com>
>>>>>     on Fri, 4 Mar 2016 09:21:48 +0100 writes:

    > Er, until _what_ is fixed?
    > I see no anomalies with the version in R-pre:

Indeed.

The problem ... I also have stumbled over ..
is that I'm sure Jeff is accidentally loading a different
version of 'Matrix' than the one that is part of R-devel.

Jeff you must accidentally be loading a version Matrix made with
R 3.2.x in R 3.3.0  and that will fail with the as.vector()
mismatch error message.

(and IIRC, you also get such an error message if you load a
 3.3.0-built version of Matrix into a non-3.3.0 version of R).


Martin

______________________________________________
R-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.

Thanks. Indeed I was having a permission issue installing/updating packages
and had put a version of Matrix in my personal library which must have been
getting loaded ahead of the one in revel library. Sorry for the bother.

On Friday, March 4, 2016, Morgan, Martin <Martin.Morgan at roswellpark.org>
wrote:

I see as below, where getGeneric and getMethod imply a different
signature; the signature is mode="any" for both cases in R version 3.2.3
Patched (2016-01-28 r70038)I don't know how to reproduce Jeff's error,
though.

library(Matrix)
as.vector

function (x, mode = "any")
.Internal(as.vector(x, mode))
<bytecode: 0xe79f88>
<environment: namespace:base>

getGeneric("as.vector")

standardGeneric for "as.vector" defined from package "base"

function (x, mode)
standardGeneric("as.vector")
<bytecode: 0x29a6bd0>
<environment: 0x299f988>
Methods may be defined for arguments: x
Use  showMethods("as.vector")  for currently available ones.

selectMethod("as.vector", "ANY")

Method Definition (Class "internalDispatchMethod"):

function (x, mode)
.Internal(as.vector(x, mode))
<environment: base>

Signatures:
        x
target  "ANY"
defined "ANY"

sessionInfo()

R Under development (unstable) (2016-02-27 r70232)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Matrix_1.2-4

loaded via a namespace (and not attached):
[1] grid_3.3.0      lattice_0.20-33

________________________________________
From: R-devel <r-devel-bounces at r-project.org <javascript:;>> on behalf of
Martin Maechler <maechler at stat.math.ethz.ch <javascript:;>>
Sent: Friday, March 4, 2016 6:05 AM
To: peter dalgaard
Cc: r-devel at r-project.org <javascript:;>; Jeff Laake - NOAA Federal
Subject: Re: [Rd] as.vector in R-devel loaded 3/3/2016

peter dalgaard <pdalgd at gmail.com <javascript:;>>
    on Fri, 4 Mar 2016 09:21:48 +0100 writes:

    > Er, until _what_ is fixed?
    > I see no anomalies with the version in R-pre:

Indeed.

The problem ... I also have stumbled over ..
is that I'm sure Jeff is accidentally loading a different
version of 'Matrix' than the one that is part of R-devel.

Jeff you must accidentally be loading a version Matrix made with
R 3.2.x in R 3.3.0  and that will fail with the as.vector()
mismatch error message.

(and IIRC, you also get such an error message if you load a
 3.3.0-built version of Matrix into a non-3.3.0 version of R).


Martin

______________________________________________
R-devel at r-project.org <javascript:;> mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

This email message may contain legally privileged and/or confidential
information.  If you are not the intended recipient(s), or the employee or
agent responsible for the delivery of this message to the intended
recipient(s), you are hereby notified that any disclosure, copying,
distribution, or use of this email message is prohibited.  If you have
received this message in error, please notify the sender immediately by
e-mail and delete this email message from your computer. Thank you.

Morgan, Martin <Martin.Morgan at RoswellPark.org>
    on Fri, 4 Mar 2016 12:36:25 +0000 writes:

> I see as below, where getGeneric and getMethod imply a different signature; the signature is mode="any" for both cases in R version 3.2.3 Patched (2016-01-28 r70038)I don't know how to reproduce Jeff's error, though.

    >> library(Matrix)

    >> as.vector
    > function (x, mode = "any") 
    > .Internal(as.vector(x, mode))
    > <bytecode: 0xe79f88>
    > <environment: namespace:base>

so note, that even though Matrix is loaded, as.vector did not
have to change to a standardGeneric(.).

"The" reason is list among the NEWS  for R-devel :

 o   S4 dispatch works within calls to .Internal(). This means explicit
     S4 generics are no longer needed for unlist and as.vector.  

so this change was very much on purpose and has had the goal to
keep as.vector() "as fast as possible".

*BUT* indeed, the "signature mismatch" you observe has been
an bogous side effect of the change, and it may even be the
reason why versions of Matrix built in different versions of R
(3.2.x  vs  3.3.x) are problematic.

I'll commit a fix for this buglet {which also affects 'unlist' !} 
in a moment.

So after all, I'm very glad for this thread!
Martin

    >> getGeneric("as.vector")
    > standardGeneric for "as.vector" defined from package "base"

    > function (x, mode) 
    > standardGeneric("as.vector")
    > <bytecode: 0x29a6bd0>
    > <environment: 0x299f988>
    > Methods may be defined for arguments: x
    > Use  showMethods("as.vector")  for currently available ones.
    >> selectMethod("as.vector", "ANY")
    > Method Definition (Class "internalDispatchMethod"):

    > function (x, mode) 
    > .Internal(as.vector(x, mode))
    > <environment: base>

    > Signatures:
    > x    
    > target  "ANY"
    > defined "ANY"
    >> sessionInfo()
    > R Under development (unstable) (2016-02-27 r70232)
    > Platform: x86_64-pc-linux-gnu (64-bit)
    > Running under: Ubuntu 14.04.4 LTS

    > locale:
    > [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
    > [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
    > [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
    > [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
    > [9] LC_ADDRESS=C               LC_TELEPHONE=C            
    > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

    > attached base packages:
    > [1] stats     graphics  grDevices utils     datasets  methods   base     

    > other attached packages:
    > [1] Matrix_1.2-4

    > loaded via a namespace (and not attached):
    > [1] grid_3.3.0      lattice_0.20-33