Re: [Rd] R 3.2.4 rc issue
Thanks for the info, Dirk. The tarball builds don't run make check (because of a policy decision that it is better to have the sources available on all platforms for testing than to have none if it breaks on a single platform). However the build as of tonight has no problem with make check on the build machine. Did you by any chance forget that Matrix is a recommended package and expected to be available when checking? -pd > On 04 Mar 2016, at 04:52 , Dirk Eddelbuettel wrote: > > > I generally run 'make; make check' (with more settings) when building the > Debian package. Running 3.2.4 rc from last night, I see a lot of package > loading issues during 'make check'. Here is splines as one examples: > > checking package 'splines' > * using log directory '/build/r-base-3.2.3.20160303/tests/splines.Rcheck' > * using R version 3.2.4 RC (2016-03-02 r70270) > * using platform: x86_64-pc-linux-gnu (64-bit) > * using session charset: ASCII > * using option '--no-build-vignettes' > * looks like 'splines' is a base package > * skipping installation test > * checking package directory ... OK > * checking DESCRIPTION meta-information ... OK > * checking top-level files ... OK > * checking for left-over files ... OK > * checking index information ... OK > * checking package subdirectories ... OK > * checking whether the package can be loaded ... OK > * checking whether the package can be loaded with stated dependencies ... OK > * checking whether the package can be unloaded cleanly ... OK > * checking whether the namespace can be loaded with stated dependencies ... OK > * checking whether the namespace can be unloaded cleanly ... OK > * checking S3 generic/method consistency ... OK > * checking replacement functions ... OK > * checking foreign function calls ... OK > * checking R code for possible problems ... OK > * checking Rd files ... OK > * checking Rd metadata ... OK > * checking Rd cross-references ... WARNING > Unknown package 'Matrix' in Rd xrefs > * checking for missing documentation entries ... OK > * checking for code/documentation mismatches ... OK > * checking Rd \usage sections ... OK > * checking Rd contents ... OK > * checking compiled code ... OK > * checking examples ... SKIPPED > * checking tests ... > Running 'spline-tst.R' > ERROR > Running the tests in 'tests/spline-tst.R' failed. > Last 13 lines of output: >> proc.time() > user system elapsed >2.272 0.020 2.291 >> >> ###- sparse / dense interpSpline() >> --- >> >> ## from help(interpSpline) -- ../man/interpSpline.Rd >> ispl <- interpSpline( women$height, women$weight) >> isp. <- interpSpline( women$height, women$weight, sparse=TRUE) > Error in splineDesign(knots, x, ord, derivs, sparse = sparse) : >splineDesign(*, sparse=TRUE) needs package 'Matrix' correctly installed > Calls: interpSpline -> interpSpline.default -> splineDesign > Execution halted > * checking PDF version of manual ... OK > * DONE > > Status: 1 ERROR, 1 WARNING > See > '/build/r-base-3.2.3.20160303/tests/splines.Rcheck/00check.log' > for details. > > > Did something change in requirements? > > Dirk > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org > > __ > R-devel@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@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] as.vector in R-devel loaded 3/3/2016
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")
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))
> On 04 Mar 2016, at 01:09 , Jeff Laake - NOAA Federal
> 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")
>
> 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")
>
> 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.la...@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")
>>
>> 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))
>>
>>
>>>
>>
>> Is default for mode missing as I suspect or will mode be required from now
>> on?
>>
>
> [[alternative HTML version deleted]]
>
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> https://stat.ethz.ch/mailman/listinfo/r-devel
--
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Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk Priv: pda...@gmail.com
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Re: [Rd] as.vector in R-devel loaded 3/3/2016
> peter dalgaard > 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] ALLOCATE in a FORTRAN subroutine
Hi, I am a FORTRAN developer and I am 'translating' R functions in FORTRAN subroutines. I am 'new' to R. It's my first question in this mailing-list and English is not my natural language. Very often, an R function gives an 'array' as result and you don't have to bother with the dimension of the array : R creates automatically an array with the good length. It's not really the case with FORTRAN. I call FORTRAN subroutines with .fortran(). Until now, I create an array with the 'max' dimensions in R, give it to FORTRAN; FORTRAN updates the array and R retrieves it. But calculating the 'max' before calling the FORTRAN subroutine can be complicated. Is it possible to create a 'new' array in a FORTRAN subroutine and to make it be read by R ? Or is it possible to have a 'pointer' in R, to give it to the FORTRAN subroutine where an ALLOCATE can create the array and then R works with the array ? The other solution, is to work with dummies dimension in FORTRAN (REAL*8 array1(*)) but can R work with that ? TIA Jean Ce message et toutes les pièces jointes (ci-après le 'Message') sont établis à l'intention exclusive des destinataires et les informations qui y figurent sont strictement confidentielles. Toute utilisation de ce Message non conforme à sa destination, toute diffusion ou toute publication totale ou partielle, est interdite sauf autorisation expresse. Si vous n'êtes pas le destinataire de ce Message, il vous est interdit de le copier, de le faire suivre, de le divulguer ou d'en utiliser tout ou partie. Si vous avez reçu ce Message par erreur, merci de le supprimer de votre système, ainsi que toutes ses copies, et de n'en garder aucune trace sur quelque support que ce soit. Nous vous remercions également d'en avertir immédiatement l'expéditeur par retour du message. Il est impossible de garantir que les communications par messagerie électronique arrivent en temps utile, sont sécurisées ou dénuées de toute erreur ou virus. This message and any attachments (the 'Message') are intended solely for the addressees. The information contained in this Message is confidential. Any use of information contained in this Message not in accord with its purpose, any dissemination or disclosure, either whole or partial, is prohibited except formal approval. If you are not the addressee, you may not copy, forward, disclose or use any part of it. If you have received this message in error, please delete it and all copies from your system and notify the sender immediately by return message. E-mail communication cannot be guaranteed to be timely secure, error or virus-free. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] ALLOCATE in a FORTRAN subroutine
On 04/03/2016 3:34 AM, MAURICE Jean - externe wrote: Hi, I am a FORTRAN developer and I am 'translating' R functions in FORTRAN subroutines. I am 'new' to R. It's my first question in this mailing-list and English is not my natural language. Very often, an R function gives an 'array' as result and you don't have to bother with the dimension of the array : R creates automatically an array with the good length. It's not really the case with FORTRAN. I call FORTRAN subroutines with .fortran(). Until now, I create an array with the 'max' dimensions in R, give it to FORTRAN; FORTRAN updates the array and R retrieves it. But calculating the 'max' before calling the FORTRAN subroutine can be complicated. Is it possible to create a 'new' array in a FORTRAN subroutine and to make it be read by R ? I don't think this is possible in pure Fortran, but it is certainly possible in C or C++ code. You need to call the external routine using .Call() instead of .C or .Fortran. See the section 5.9 of the Writing R Extensions manual for details. Or is it possible to have a 'pointer' in R, to give it to the FORTRAN subroutine where an ALLOCATE can create the array and then R works with the array ? No. R needs to manage allocations of all the objects it uses. However, if you never need to use these arrays in R code (you just want R to keep references to them to pass to other external routines), you can (in C or C++) use the external pointer type. I don't think there's any support for that in Fortran. The other solution, is to work with dummies dimension in FORTRAN (REAL*8 array1(*)) but can R work with that ? No, for the same reason. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] as.vector in R-devel loaded 3/3/2016
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))
> getGeneric("as.vector")
standardGeneric for "as.vector" defined from package "base"
function (x, mode)
standardGeneric("as.vector")
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))
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-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_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 on behalf of Martin Maechler
Sent: Friday, March 4, 2016 6:05 AM
To: peter dalgaard
Cc: r-devel@r-project.org; Jeff Laake - NOAA Federal
Subject: Re: [Rd] as.vector in R-devel loaded 3/3/2016
> peter dalgaard
> 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
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Re: [Rd] R 3.2.4 rc issue
On 4 March 2016 at 09:11, peter dalgaard wrote: | Thanks for the info, Dirk. | | The tarball builds don't run make check (because of a policy decision that it is better to have the sources available on all platforms for testing than to have none if it breaks on a single platform). However the build as of tonight has no problem with make check on the build machine. Did you by any chance forget that Matrix is a recommended package and expected to be available when checking? Our build systems are heavily standardized and create pristine chroot environments with exactly what we prescibe. 'Recommended packages' was never part of it, yet we have been running 'make; make check' since (if memory serves) before the 1.0.0 days. "It never mattered". Yesterday, it failed. I'll try to try again on the weekend. Dirk | -pd | | > On 04 Mar 2016, at 04:52 , Dirk Eddelbuettel wrote: | > | > | > I generally run 'make; make check' (with more settings) when building the | > Debian package. Running 3.2.4 rc from last night, I see a lot of package | > loading issues during 'make check'. Here is splines as one examples: | > | > checking package 'splines' | > * using log directory '/build/r-base-3.2.3.20160303/tests/splines.Rcheck' | > * using R version 3.2.4 RC (2016-03-02 r70270) | > * using platform: x86_64-pc-linux-gnu (64-bit) | > * using session charset: ASCII | > * using option '--no-build-vignettes' | > * looks like 'splines' is a base package | > * skipping installation test | > * checking package directory ... OK | > * checking DESCRIPTION meta-information ... OK | > * checking top-level files ... OK | > * checking for left-over files ... OK | > * checking index information ... OK | > * checking package subdirectories ... OK | > * checking whether the package can be loaded ... OK | > * checking whether the package can be loaded with stated dependencies ... OK | > * checking whether the package can be unloaded cleanly ... OK | > * checking whether the namespace can be loaded with stated dependencies ... OK | > * checking whether the namespace can be unloaded cleanly ... OK | > * checking S3 generic/method consistency ... OK | > * checking replacement functions ... OK | > * checking foreign function calls ... OK | > * checking R code for possible problems ... OK | > * checking Rd files ... OK | > * checking Rd metadata ... OK | > * checking Rd cross-references ... WARNING | > Unknown package 'Matrix' in Rd xrefs | > * checking for missing documentation entries ... OK | > * checking for code/documentation mismatches ... OK | > * checking Rd \usage sections ... OK | > * checking Rd contents ... OK | > * checking compiled code ... OK | > * checking examples ... SKIPPED | > * checking tests ... | > Running 'spline-tst.R' | > ERROR | > Running the tests in 'tests/spline-tst.R' failed. | > Last 13 lines of output: | >> proc.time() | > user system elapsed | >2.272 0.020 2.291 | >> | >> ###- sparse / dense interpSpline() --- | >> | >> ## from help(interpSpline) -- ../man/interpSpline.Rd | >> ispl <- interpSpline( women$height, women$weight) | >> isp. <- interpSpline( women$height, women$weight, sparse=TRUE) | > Error in splineDesign(knots, x, ord, derivs, sparse = sparse) : | >splineDesign(*, sparse=TRUE) needs package 'Matrix' correctly installed | > Calls: interpSpline -> interpSpline.default -> splineDesign | > Execution halted | > * checking PDF version of manual ... OK | > * DONE | > | > Status: 1 ERROR, 1 WARNING | > See | > '/build/r-base-3.2.3.20160303/tests/splines.Rcheck/00check.log' | > for details. | > | > | > Did something change in requirements? | > | > Dirk | > | > -- | > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org | > | > __ | > R-devel@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@cbs.dk Priv: pda...@gmail.com | | | | | | | | | -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] as.vector in R-devel loaded 3/3/2016
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
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))
>
>
> > getGeneric("as.vector")
> standardGeneric for "as.vector" defined from package "base"
>
> function (x, mode)
> standardGeneric("as.vector")
>
>
> 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))
>
>
> 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-8LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8LC_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 > on behalf of
> Martin Maechler >
> Sent: Friday, March 4, 2016 6:05 AM
> To: peter dalgaard
> Cc: r-devel@r-project.org ; Jeff Laake - NOAA Federal
> Subject: Re: [Rd] as.vector in R-devel loaded 3/3/2016
>
> > peter dalgaard >
> > 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@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.
>
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Re: [Rd] as.vector in R-devel loaded 3/3/2016
> Morgan, Martin
> on Fri, 4 Mar 2016 12:36:25 + 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))
>
>
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")
>
>
> 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))
>
> 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-8LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8LC_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
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[Rd] vignette index
Dear helpers,
I have multiple vignette files for a package, and I would like to have the
"right" order of these files when displayed online. For instance, see below:
https://cran.r-project.org/web/packages/bst/index.html
The order of vignette links on CRAN is different from what I hoped for:
> vignette(package="bst")
Vignettes in package 'bst':
prosCancer Classification Using Mass
Spectrometry-based Proteomics Data (source,
pdf)
static_khan Classification of Cancer Types Using Gene
Expression Data (Long) (source, pdf)
khanClassification of Cancer Types Using Gene
Expression Data (Short) (source, pdf)
static_mcl Classification of UCI Machine Learning Datasets
(Long) (source, pdf)
mcl Classification of UCI Machine Learning Datasets
(Short) (source, pdf)
The package bst already has an index.html, and I thought that should have done
the job, but apparently not. Any suggestions?
Thanks,
Zhu
/bst/inst/doc/index.html
http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd";>
http://www.w3.org/1999/xhtml";>
R: Vignettes and other documentation
Vignettes and other documentation
Vignettes from package 'bst'
bst::pros
Cancer Classification Using Mass Spectrometry-based
Proteomics Data
PDF
source
R code
bst::static_khan
Classification of Cancer Types Using Gene Expression
Data (Long)
PDF
source
bst::khan
Classification of Cancer Types Using Gene Expression
Data (Short)
PDF
source
R code
bst::static_mcl
Classification of UCI Machine Learning Datasets
(Long)
PDF
source
bst::mcl
Classification of UCI Machine Learning Datasets
(Short)
PDF
source
R code
../../Rpkg/bst/inst/doc/index.html (END)
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Re: [Rd] vignette index
This probably belongs on r-package-de...@r-project.org as it is not
about the development of R itself, but about package development.
--
Brian
On Fri, 2016-03-04 at 14:44 +, Wang, Zhu wrote:
> Dear helpers,
>
> I have multiple vignette files for a package, and I would like to have the
> "right" order of these files when displayed online. For instance, see below:
>
> https://cran.r-project.org/web/packages/bst/index.html
>
> The order of vignette links on CRAN is different from what I hoped for:
>
> > vignette(package="bst")
> Vignettes in package 'bst':
>
> prosCancer Classification Using Mass
> Spectrometry-based Proteomics Data (source,
> pdf)
> static_khan Classification of Cancer Types Using Gene
> Expression Data (Long) (source, pdf)
> khanClassification of Cancer Types Using Gene
> Expression Data (Short) (source, pdf)
> static_mcl Classification of UCI Machine Learning Datasets
> (Long) (source, pdf)
> mcl Classification of UCI Machine Learning Datasets
> (Short) (source, pdf)
>
> The package bst already has an index.html, and I thought that should have
> done the job, but apparently not. Any suggestions?
>
> Thanks,
>
> Zhu
>
> /bst/inst/doc/index.html
> "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd";>
> http://www.w3.org/1999/xhtml";>
> R: Vignettes and other documentation
>
>
>
> Vignettes and other documentation
>
>
>
>
> alt="[Top]" />
>
> Vignettes from package 'bst'
>
>
>
>
>
>
>
> href="../../../library/bst/doc/pros.pdf">bst::pros
> Cancer Classification Using Mass Spectrometry-based
> Proteomics Data
> PDF
> source
> href="../../../library/bst/doc/pros.R">R code
> href="../../../library/bst/doc/static_khan.pdf">bst::static_khan
> Classification of Cancer Types Using Gene
> Expression Data (Long)
> href="../../../library/bst/doc/static_khan.pdf">PDF
> href="../../../library/bst/doc/static_khan.pdf.asis">source
>
> href="../../../library/bst/doc/khan.pdf">bst::khan
> Classification of Cancer Types Using Gene
> Expression Data (Short)
> PDF
> source
> href="../../../library/bst/doc/khan.R">R code
> href="../../../library/bst/doc/static_mcl.pdf">bst::static_mcl
> Classification of UCI Machine Learning Datasets
> (Long)
> href="../../../library/bst/doc/static_mcl.pdf">PDF
> href="../../../library/bst/doc/static_mcl.pdf.asis">source
>
> href="../../../library/bst/doc/mcl.pdf">bst::mcl
> Classification of UCI Machine Learning Datasets
> (Short)
> PDF
> source
> href="../../../library/bst/doc/mcl.R">R code
>
>
> ../../Rpkg/bst/inst/doc/index.html (END)
>
>
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Re: [Rd] vignette index
On 04/03/2016 9:44 AM, Wang, Zhu wrote: Dear helpers, I have multiple vignette files for a package, and I would like to have the "right" order of these files when displayed online. For instance, see below: https://cran.r-project.org/web/packages/bst/index.html The order of vignette links on CRAN is different from what I hoped for: > vignette(package="bst") Vignettes in package 'bst': prosCancer Classification Using Mass Spectrometry-based Proteomics Data (source, pdf) static_khan Classification of Cancer Types Using Gene Expression Data (Long) (source, pdf) khanClassification of Cancer Types Using Gene Expression Data (Short) (source, pdf) static_mcl Classification of UCI Machine Learning Datasets (Long) (source, pdf) mcl Classification of UCI Machine Learning Datasets (Short) (source, pdf) The package bst already has an index.html, and I thought that should have done the job, but apparently not. Any suggestions? The index.html file should be used in the online help system, but vignette() doesn't use that, it looks in the internal database of vignettes. I don't think you can control the order in which it displays things. This could conceivably be changed, but not by consulting your index.html file --- it is not required to follow a particular structure, so we can't find what order you want from it. One more likely possibility would be to sort alphabetically in the current locale according to filename or vignette title. So then you could get what you want by naming your vignettes 1pros, 2static_khan, etc. It would also be possible to add a new \Vignette directive so affect collation order, but that seems like overkill. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] vignette index
I think the online order of vignette files are not based on vignette title or
filename alphabetically. I am just curious: by what order these vignette files
were displayed online so I can make changes accordingly?
Thanks,
Zhu
-Original Message-
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
Sent: Friday, March 04, 2016 10:47 AM
To: Wang, Zhu; r-devel@r-project.org
Subject: Re: [Rd] vignette index
On 04/03/2016 9:44 AM, Wang, Zhu wrote:
> Dear helpers,
>
> I have multiple vignette files for a package, and I would like to have the
> "right" order of these files when displayed online. For instance, see below:
>
> https://cran.r-project.org/web/packages/bst/index.html
>
> The order of vignette links on CRAN is different from what I hoped for:
>
> > vignette(package="bst")
> Vignettes in package 'bst':
>
> prosCancer Classification Using Mass
> Spectrometry-based Proteomics Data (source,
> pdf)
> static_khan Classification of Cancer Types Using Gene
> Expression Data (Long) (source, pdf)
> khanClassification of Cancer Types Using Gene
> Expression Data (Short) (source, pdf)
> static_mcl Classification of UCI Machine Learning Datasets
> (Long) (source, pdf)
> mcl Classification of UCI Machine Learning Datasets
> (Short) (source, pdf)
>
> The package bst already has an index.html, and I thought that should have
> done the job, but apparently not. Any suggestions?
>
The index.html file should be used in the online help system, but
vignette() doesn't use that, it looks in the internal database of vignettes. I
don't think you can control the order in which it displays things.
This could conceivably be changed, but not by consulting your index.html file
--- it is not required to follow a particular structure, so we can't find what
order you want from it. One more likely possibility would be to sort
alphabetically in the current locale according to filename or vignette title.
So then you could get what you want by naming your vignettes 1pros,
2static_khan, etc.
It would also be possible to add a new \Vignette directive so affect
collation order, but that seems like overkill.
Duncan Murdoch
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Re: [Rd] ALLOCATE in a FORTRAN subroutine
Hi,
Until you get a more definitive answer, I will make an attempt to give some
advice.
When using an assumed sized array (i.e. REAL*8 array1(*)) you still need to
allocate the memory prior to calling the Fortran subroutine, so you would still
need to know its maximum length.
Arrays created in a Fortran subroutine via the use of the ALLOCATE statements
are not simple arrays (in the sense of C like pointers), but are more akin to a
C structure, in that they also contain information concerning the size of the
array, stride etc. These structures are compiler dependent, their contents
often not clearly documented and subject to change. They are therefore not very
good for cross-language computing (or even cross-compiler computing).
To try and alleviate this the Fortran standard introduced C interoperability
(see https://gcc.gnu.org/onlinedocs/gfortran/Interoperability-with-C.html for
example) and I expect you are going to have to take a look at this in order to
pass memory allocated in your Fortran program back up to R. Care is going to
have be taken to make sure that the memory is deallocated when it has been
finished with (which is probably going to have to be done in Fortran).
The easiest way of getting all this to interact nicely with R is probably
through the R C API which is described in documents like
https://cran.r-project.org/doc/manuals/R-exts.pdf.
Martyn
-Original Message-
From: R-devel [mailto:r-devel-boun...@r-project.org] On Behalf Of MAURICE Jean
- externe
Sent: 04 March 2016 08:34
To: r-devel@r-project.org
Subject: [Rd] ALLOCATE in a FORTRAN subroutine
Hi,
I am a FORTRAN developer and I am 'translating' R functions in FORTRAN
subroutines. I am 'new' to R. It's my first question in this mailing-list and
English is not my natural language.
Very often, an R function gives an 'array' as result and you don't have to
bother with the dimension of the array : R creates automatically an array with
the good length. It's not really the case with FORTRAN. I call FORTRAN
subroutines with .fortran().
Until now, I create an array with the 'max' dimensions in R, give it to
FORTRAN; FORTRAN updates the array and R retrieves it. But calculating the
'max' before calling the FORTRAN subroutine can be complicated. Is it possible
to create a 'new' array in a FORTRAN subroutine and to make it be read by R ?
Or is it possible to have a 'pointer' in R, to give it to the FORTRAN
subroutine where an ALLOCATE can create the array and then R works with the
array ?
The other solution, is to work with dummies dimension in FORTRAN (REAL*8
array1(*)) but can R work with that ?
TIA
Jean
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Re: [Rd] vignette index
Within R these are determined by \VignetteIndexEntry{}. I think you are
referring to the order on the CRAN landing page for your package
https://cran.r-project.org/web/packages/bst/index.html, and then the question
is for a CRAN member.
In Rnw
\documentclass{article}
% \VignetteIndexEntry{01-Foo}
\begin{document}
01-Foo
\end{document}
or Rmd as
---
title: "Demo"
author: Ima Scientist
vignette: >
% \VignetteIndexEntry{01-Foo}
% \VignetteEngine{knitr::rmarkdown}
---
From: R-devel on behalf of Wang, Zhu
Sent: Friday, March 4, 2016 11:18 AM
To: Duncan Murdoch; r-devel@r-project.org
Subject: Re: [Rd] vignette index
I think the online order of vignette files are not based on vignette title or
filename alphabetically. I am just curious: by what order these vignette files
were displayed online so I can make changes accordingly?
Thanks,
Zhu
-Original Message-
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
Sent: Friday, March 04, 2016 10:47 AM
To: Wang, Zhu; r-devel@r-project.org
Subject: Re: [Rd] vignette index
On 04/03/2016 9:44 AM, Wang, Zhu wrote:
> Dear helpers,
>
> I have multiple vignette files for a package, and I would like to have the
> "right" order of these files when displayed online. For instance, see below:
>
> https://cran.r-project.org/web/packages/bst/index.html
>
> The order of vignette links on CRAN is different from what I hoped for:
>
> > vignette(package="bst")
> Vignettes in package 'bst':
>
> prosCancer Classification Using Mass
> Spectrometry-based Proteomics Data (source,
> pdf)
> static_khan Classification of Cancer Types Using Gene
> Expression Data (Long) (source, pdf)
> khanClassification of Cancer Types Using Gene
> Expression Data (Short) (source, pdf)
> static_mcl Classification of UCI Machine Learning Datasets
> (Long) (source, pdf)
> mcl Classification of UCI Machine Learning Datasets
> (Short) (source, pdf)
>
> The package bst already has an index.html, and I thought that should have
> done the job, but apparently not. Any suggestions?
>
The index.html file should be used in the online help system, but
vignette() doesn't use that, it looks in the internal database of vignettes. I
don't think you can control the order in which it displays things.
This could conceivably be changed, but not by consulting your index.html file
--- it is not required to follow a particular structure, so we can't find what
order you want from it. One more likely possibility would be to sort
alphabetically in the current locale according to filename or vignette title.
So then you could get what you want by naming your vignettes 1pros,
2static_khan, etc.
It would also be possible to add a new \Vignette directive so affect
collation order, but that seems like overkill.
Duncan Murdoch
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Re: [Rd] vignette index
On 04/03/2016 11:18 AM, Wang, Zhu wrote:
I think the online order of vignette files are not based on vignette title or
filename alphabetically. I am just curious: by what order these vignette files
were displayed online so I can make changes accordingly?
You have the source code, and can figure it out as well as I can.
Duncan Murdoch
Thanks,
Zhu
-Original Message-
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
Sent: Friday, March 04, 2016 10:47 AM
To: Wang, Zhu; r-devel@r-project.org
Subject: Re: [Rd] vignette index
On 04/03/2016 9:44 AM, Wang, Zhu wrote:
Dear helpers,
I have multiple vignette files for a package, and I would like to have the
"right" order of these files when displayed online. For instance, see below:
https://cran.r-project.org/web/packages/bst/index.html
The order of vignette links on CRAN is different from what I hoped for:
vignette(package="bst")
Vignettes in package 'bst':
prosCancer Classification Using Mass
Spectrometry-based Proteomics Data (source,
pdf)
static_khan Classification of Cancer Types Using Gene
Expression Data (Long) (source, pdf)
khanClassification of Cancer Types Using Gene
Expression Data (Short) (source, pdf)
static_mcl Classification of UCI Machine Learning Datasets
(Long) (source, pdf)
mcl Classification of UCI Machine Learning Datasets
(Short) (source, pdf)
The package bst already has an index.html, and I thought that should have done
the job, but apparently not. Any suggestions?
The index.html file should be used in the online help system, but
vignette() doesn't use that, it looks in the internal database of vignettes. I
don't think you can control the order in which it displays things.
This could conceivably be changed, but not by consulting your index.html file
--- it is not required to follow a particular structure, so we can't find what
order you want from it. One more likely possibility would be to sort
alphabetically in the current locale according to filename or vignette title.
So then you could get what you want by naming your vignettes 1pros,
2static_khan, etc.
It would also be possible to add a new \Vignette directive so affect
collation order, but that seems like overkill.
Duncan Murdoch
**Connecticut Children's Confidentiality Notice**
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__
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[Rd] Problem installing R-devel data 4 March 2016.
I am trying to install the latest development version of R so as to be able to perform a package check according the rules specified for CRAN. I performed the following steps: (1) Downloaded R-devel.tar.gz, dated 04-Mar-2016 03:21, from CRAN (2) Upacked. (3) Created directory "BldDir" next to the directory "R-devel". (4) Changed directories to BldDir. (5) Executed ../R-devel/configure --with-tcltk --with-cairo . (6) Executed make . (7) Executed sudo make install . I got the error messages: . . . mkdir -p -- /usr/local/lib64/R/doc /usr/bin/install: cannot stat `FAQ': No such file or directory /usr/bin/install: cannot stat `RESOURCES': No such file or directory /usr/bin/install: cannot stat `NEWS': No such file or directory /usr/bin/install: cannot stat `NEWS.pdf': No such file or directory /usr/bin/install: cannot stat `NEWS.rds': No such file or directory /usr/bin/install: cannot stat `NEWS': No such file or directory /usr/bin/install: cannot stat `NEWS.pdf': No such file or directory make[1]: *** [install-sources2] Error 1 make[1]: Leaving directory `/home/rolf/Desktop/R-dev-inst/BldDir/doc' make: *** [install] Error 1 Can someone/anyone tell me what I am missing or doing wrong? Ta. cheers, Rolf Turner -- Technical Editor ANZJS Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
