[Bioc-devel] report package issue to Bioconductor

[Yu, Guangchuang]

Dear all,

Some packages never updated after they publish a paper, and they just
ignore bug report.

I think we need somewhere, maybe on github, to post code review and
Bioconductor core team can take action if maintainer fail to fix issue.

Here is a quick look of the CorMut package:
https://gist.github.com/GuangchuangYu/91b3396c7e49ab42c565a9cda3c35e18.

There should be more issues than I can found with quick look of the source
code.

Best wishes,
Guangchuang
​
-- 
--~--~-~--~~~---~--~~
Guangchuang Yu, PhD Candidate
State Key Laboratory of Emerging Infectious Diseases
School of Public Health
The University of Hong Kong
Hong Kong SAR, China
www: https://guangchuangyu.github.io
-~--~~~~--~~--~--~---

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Re: [Bioc-devel] Problem pushing new versions of xcms via git svn dcommit

[Rainer Johannes]

Hi Steffen and Laurent,

one problem with xcms is that the 'devel' branch on sneumann/xcms is the real 
'master' branch. I would suggest to create a new branch on github, e.g. 
'biocdevel' and to link that one to the BioC svn (means also that 
update_remotes.sh can not be user right away - the svn remote should be added 
manually). That way development can still be performed on sneumann/xcms devel 
branch and once stuff should be pushed to BioC devel could be merged into 
biocdevel and committed to svn using the git svn dcommit. I think that having 
the devel branch both for development via github and as the link to BioC svn is 
problematic.

One last thing: I experienced lots of out-of-sync problems in ensembldb, 
apparently because many individual commits were committed "too fast" to svn and 
thus the github-mirror went out-of-sync. For ensembldb I am now basically 
merging the commits from my master branch as a single commit to devel using 
"git merge --squash". I thus loose part of the history, but since github master 
contains the full history I'm fine with lacking it on BioC svn.

cheers, jo

On 3 Jan 2017, at 22:10, Laurent Gatto 
> wrote:


Hi Steffen,

The usual

 Commit to git as normal, when you want to push your commits to svn
   1. `git checkout devel` to switch to the devel branch. (use release-X.X for
 release branches)
   2. `git svn rebase` to get the latest SVN changes.
   3. `git merge master --log` to merge your changes from the master branch
 or skip this step and work directly on the current branch.
   4. `git svn dcommit --add-author-from` to sync and commit
 your changes to svn.

worked out for me. Your latest commit #4b68af1d156b73 and #a03fba48f82b7
(updated NEWS file) have now been comitted to hedgehog.

I am not sure what is going on for you, but when I desperate with
git/git-svn, right before the nervous breakdown, I go for the 'have you
tried to turn it on and off again' solution, which generally works:

1) make sure you have comitted/pushed to Github and have a backup of any
  files/dir you gitignore
2) rm -rf mzR
3) git clone g...@github.com:sneumann/mzR.git
4) use update_remotes.sh

Let me know if there's anything I can help with.

Best wishes,

Laurent

On  2 January 2017 22:12, Steffen Neumann wrote:

Hi all,and a happy new year!

I am experiencing a lot of frustration getting changes from github
pushed to BioC svn, and that includes some fixes for build issues
in packages depending on xcms. I have tried several options:

1) git svn checkout, git remote add, git merge and git svn dcommit.
2) git clone github repo, update_remotes.shand git svn rebase

both of which seem to fail due to the same reason,
which seems to be somewhere around

https://github.com/sneumann/xcms/commit/f9be4f4f23c49f56074670658bc9665e093c8f83
Author: Steffen Neumann 
Date:Fri Apr 1 14:09:29 2016 +0200
Add automatic repair for "m/z sort assumption violated !" error in findPeaks 
(centWave)

I fail to fix these issues, and I am pretty frustrated
since I fell into the git-svn tarpit not for the first time,
it seems to be not fool-proof :-(

Below are the details, hoping for help.

Yours,
Steffen

1) git svn checkout, git remote add, git merge and git svn dcommit.

So, I have a fresh

sneumann@acryl /vol/R/BioC/devel/xcms3 $ git svn checkout 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms

Then I add the github remote:

sneumann@acryl /vol/R/BioC/devel/xcms3/xcms (master) $ git remote add origin 
g...@github.com:sneumann/xcms.git
sneumann@acryl /vol/R/BioC/devel/xcms3/xcms (master) $ git fetch --tags
remote: Counting objects: 1475, done.
[...]
>From github.com:sneumann/xcms
* [new branch]devel-> origin/devel
* [new branch]master-> origin/master
* [new branch]xcms3-> origin/xcms3

The devel branch is what I use to be in sync with BioC-SVN:

sneumann@acryl /vol/R/BioC/devel/xcms3/xcms (master) $ git checkout devel
Branch devel set up to track remote branch devel from origin.
Switched to a new branch 'devel'

sneumann@acryl /vol/R/BioC/devel/xcms3/xcms (devel) $ git merge origin/xcms3
Updating a4421c3..a112206
Fast-forward
DESCRIPTION|6 +-
NAMESPACE|48 ++-
R/AllGenerics.R|38 +-
[...]
vignettes/new_functionality.org|88 -
41 files changed, 4890 insertions(+), 2250 deletions(-)

sneumann@acryl /vol/R/BioC/devel/xcms3/xcms (devel) $ git svn dcommit
Committing to https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms 
...
D R/00Generics.R

ERROR from SVN:
Filesystem has no item: 
'/bioconductor/!svn/txr/125556-1/trunk/madman/Rpacks/xcms/R/00Generics.R' path 
not found
W: a1122065a96cf6e69088417d82fe987cda188cd5 and refs/remotes/git-svn differ, 
using rebase:
:100644 100644 d36b142908ab4507e95d495d3ec450008a210e8f 
a3f97d8f779d878b86a73d534415e679415e90f3 M DESCRIPTION
:100755 100755 a58677bbe186fea1447948c7286bc47d04735efc 
fe69bdd2e969a906fac87d4bddd64bd90258f0cd M 

[Rd] cat(s, file): infinite loop of "invalid char string in output conversion" warnings with UTF-8 encoding

[Henrik Bengtsson]

The below code snippet gives a single warning:

  Warning message:
  In cat(s, file = tempfile()) : invalid char string in output conversion

when n <= 10001, whereas with n >= 10002 it appears to be generating
the same warning in an infinite loop in the call to cat().

n <- 10002L

r <- raw(length = n)
r[] <- charToRaw(" ")
r[length(r)] <- as.raw(0xa9)
s <- rawToChar(r)

message("Encoding: native.enc")
options(encoding = "native.enc")
cat(s, file = tempfile())

message("Encoding: UTF-8")
options(encoding = "UTF-8")
cat(s, file = tempfile())

message("DONE")


Here cat() never returns. The R process runs at 100% CPU, it does not
appear to increase it's memory usage, and the call can be interrupted:

^C
There were 50 or more warnings (use warnings() to see the first 50)
> traceback()
8: "factor" %in% attrib[["class", exact = TRUE]]
7: structure(list(message = as.character(message), call = call),
   class = class)
6: simpleWarning(msg, call)
5: doWithOneRestart(return(expr), restart)
4: withOneRestart(expr, restarts[[1L]])
3: withRestarts({
   .Internal(.signalCondition(simpleWarning(msg, call), msg,
   call))
   .Internal(.dfltWarn(msg, call))
   }, muffleWarning = function() NULL)
2: .signalSimpleWarning("invalid char string in output conversion",
   quote(cat(s, file = tempfile(
1: cat(s, file = tempfile())


## SOME TROUBLESHOOTING

Using options(warn = 1) shows that the "invalid char string in output
conversion" warning is outputted over and over in an infinite loop.
This warning is generated by dummy_vfprintf() defined in
src/main/connections.c
(https://github.com/wch/r-source/blob/R-3-3-branch/src/main/connections.c#L370);

# define BUFSIZE 1
int dummy_vfprintf(Rconnection con, const char *format, va_list ap)
{
[...]
if(ires == (size_t)(-1) && errno != E2BIG)
/* is this safe? */
warning(_("invalid char string in output conversion"));
[...]
}

Note BUFSIZE, note the comment /* is this safe? */ (by Brian Ripley on
2005-01-05).



## SESSION DETAILS

I can reproduce this on R 2.11.0, R 3.3.2 and R devel on Linux.  It
does not occur on R 3.3.2 for Windows under Linux Wine.

> sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu

locale:
[1] C

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


> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 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

> sessionInfo()
R Under development (unstable) (2017-01-02 r71875)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] C

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

loaded via a namespace (and not attached):
[1] compiler_3.4.0

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Re: [Bioc-devel] Problem pushing new versions of xcms via git svn dcommit

[Laurent Gatto]

Hi Steffen,

The usual

  Commit to git as normal, when you want to push your commits to svn
1. `git checkout devel` to switch to the devel branch. (use release-X.X for
  release branches)
2. `git svn rebase` to get the latest SVN changes.
3. `git merge master --log` to merge your changes from the master branch
  or skip this step and work directly on the current branch.
4. `git svn dcommit --add-author-from` to sync and commit
  your changes to svn.

worked out for me. Your latest commit #4b68af1d156b73 and #a03fba48f82b7
(updated NEWS file) have now been comitted to hedgehog. 

I am not sure what is going on for you, but when I desperate with
git/git-svn, right before the nervous breakdown, I go for the 'have you
tried to turn it on and off again' solution, which generally works:

1) make sure you have comitted/pushed to Github and have a backup of any
   files/dir you gitignore
2) rm -rf mzR
3) git clone g...@github.com:sneumann/mzR.git
4) use update_remotes.sh

Let me know if there's anything I can help with.

Best wishes,

Laurent

On  2 January 2017 22:12, Steffen Neumann wrote:

> Hi all,and a happy new year!
>
> I am experiencing a lot of frustration getting changes from github 
> pushed to BioC svn, and that includes some fixes for build issues
> in packages depending on xcms. I have tried several options:
>
> 1) git svn checkout, git remote add, git merge and git svn dcommit. 
> 2) git clone github repo, update_remotes.shand git svn rebase
>
> both of which seem to fail due to the same reason,
> which seems to be somewhere around 
>
> https://github.com/sneumann/xcms/commit/f9be4f4f23c49f56074670658bc9665e093c8f83
> Author: Steffen Neumann 
> Date:Fri Apr 1 14:09:29 2016 +0200
> Add automatic repair for "m/z sort assumption violated !" error in findPeaks 
> (centWave)
>
> I fail to fix these issues, and I am pretty frustrated 
> since I fell into the git-svn tarpit not for the first time,
> it seems to be not fool-proof :-(
>
> Below are the details, hoping for help.
>
> Yours,
> Steffen
>
> 1) git svn checkout, git remote add, git merge and git svn dcommit. 
>
> So, I have a fresh 
>
> sneumann@acryl /vol/R/BioC/devel/xcms3 $ git svn checkout 
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms
>
> Then I add the github remote:
>
> sneumann@acryl /vol/R/BioC/devel/xcms3/xcms (master) $ git remote add origin 
> g...@github.com:sneumann/xcms.git
> sneumann@acryl /vol/R/BioC/devel/xcms3/xcms (master) $ git fetch --tags
> remote: Counting objects: 1475, done.
> [...]
>>From github.com:sneumann/xcms
> * [new branch]devel-> origin/devel
> * [new branch]master-> origin/master
> * [new branch]xcms3-> origin/xcms3
>
> The devel branch is what I use to be in sync with BioC-SVN:
>
> sneumann@acryl /vol/R/BioC/devel/xcms3/xcms (master) $ git checkout devel
> Branch devel set up to track remote branch devel from origin.
> Switched to a new branch 'devel'
>
> sneumann@acryl /vol/R/BioC/devel/xcms3/xcms (devel) $ git merge origin/xcms3
> Updating a4421c3..a112206
> Fast-forward
> DESCRIPTION|6 +-
> NAMESPACE|48 ++-
> R/AllGenerics.R|38 +-
> [...]
> vignettes/new_functionality.org|88 -
> 41 files changed, 4890 insertions(+), 2250 deletions(-)
>
> sneumann@acryl /vol/R/BioC/devel/xcms3/xcms (devel) $ git svn dcommit
> Committing to 
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms ...
>   D   R/00Generics.R
>
> ERROR from SVN:
> Filesystem has no item: 
> '/bioconductor/!svn/txr/125556-1/trunk/madman/Rpacks/xcms/R/00Generics.R' 
> path not found
> W: a1122065a96cf6e69088417d82fe987cda188cd5 and refs/remotes/git-svn differ, 
> using rebase:
> :100644 100644 d36b142908ab4507e95d495d3ec450008a210e8f 
> a3f97d8f779d878b86a73d534415e679415e90f3 MDESCRIPTION
> :100755 100755 a58677bbe186fea1447948c7286bc47d04735efc 
> fe69bdd2e969a906fac87d4bddd64bd90258f0cd MNAMESPACE
> :04 04 2f5317b4c96f1d267b43ef8deba1532df6cb56db 
> c760aa2196632e99c0e0e59ed9700b27cb001fa3 MR
> :04 04 45a9a220d96c3cdabe03cd8792dfc9628f058dab 
> e89e65a3eb7db9d6590c12b8fb94306811557789 Minst
> :04 04 8284909b39e4d90eb957aadc26f92a8df9907cb2 
> 125b7635684f73f65185aea52a7564c11bf187c5 Mman
> :04 04 da9a1c166e3df0c13cd3ea61e44356039b649cd2 
> dbee4fedf371d6570b91cc7f50fe930294eac1f2 Mvignettes
> First, rewinding head to replay your work on top of it...
> Applying: Add automatic repair for "m/z sort assumption violated !" error in 
> findPeaks (centWave)
> Using index info to reconstruct a base tree...
> A R/xcmsRaw.R
> .git/rebase-apply/patch:37: trailing whitespace.
> scan <- getScan(object, scan=i)
> .git/rebase-apply/patch:82: trailing whitespace.
> xr@env$mz[1:length(o)] <- scan[o, "mz"]
> .git/rebase-apply/patch:83: trailing whitespace.
> xr@env$intensity[1:length(o)] <- scan[o, "intensity"]
> .git/rebase-apply/patch:88: trailing whitespace.
>
> .git/rebase-apply/patch:90: new 

Re: [Rd] [R] Problems when trying to install and load package "rzmq"

[Whit Armstrong]

sounds great!

On Tue, Jan 3, 2017 at 11:32 AM, Jeroen Ooms  wrote:

> On Tue, Jan 3, 2017 at 3:53 PM, Whit Armstrong 
> wrote:
> >
> > I maintian the rzmq project.
> >
> > love to get it running on windows, but zmq doesn't play nicely with R's
> > mingw.
>
> It's fairly easy to link against the libraries from rwinlib:
> https://github.com/rwinlib/zeromq. I'll send you a pull request later
> this week to fix the binary packages for win+mac.
>

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Re: [Bioc-devel] Problem pushing new versions of xcms via git svn dcommit

[McDavid, Andrew]

Hi Steffen,

Option 2 worked for me recently with a repo that had previous git history.  I 
think you after you run

git branch --track biocmaster bioc/master

You need to run

git checkout biocmaster

Then you may run git svn dcommit, which should just be a null op at this point. 
 I will add that if your repo has previous git history (like yours) you 
absolutely must cherry pick onto the svn repo or great suffering will ensue.  
This is because, I believe, the histories of the svn repo and git repo are 
different.  Rebasing or merging tries to replay from the first commit of your 
git repo

-Andrew



On Jan 3, 2017, at 6:00 AM, 
bioc-devel-requ...@r-project.org wrote:

Hi all,?and a happy new year!

I am experiencing a lot of frustration getting changes from github
pushed to BioC svn, and that includes some fixes for build issues
in packages depending on xcms. I have tried several options:

1) git svn checkout, git remote add, git merge and git svn dcommit.
2) git clone github repo, update_remotes.sh?and git svn rebase

both of which seem to fail due to the same reason,
which seems to be somewhere around


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Re: [Rd] [R] Problems when trying to install and load package "rzmq"

[Jeroen Ooms]

On Tue, Jan 3, 2017 at 3:53 PM, Whit Armstrong  wrote:
>
> I maintian the rzmq project.
>
> love to get it running on windows, but zmq doesn't play nicely with R's
> mingw.

It's fairly easy to link against the libraries from rwinlib:
https://github.com/rwinlib/zeromq. I'll send you a pull request later
this week to fix the binary packages for win+mac.

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[Rd] seq.int/seq.default

[Mick Jordan]

This is a message for someone familiar with the implementation.

Superficially the R code for seq.default and the C code for seq.int 
appear to be semantically very similar. My question is whether, in fact, 
it is intended that behave identically for all inputs. I have found two 
cases so far where they differ, first that seq.int will coerce a 
character string to a real (via Rf_asReal) whereas seq.default appears 
to coerce it to NA and then throws an error:


> seq.default("2", "5")
Error in seq.default("2", "5") : 'from' cannot be NA, NaN or infinite
> seq.int("2", "5")
[1] 2 3 4 5
>

and second, that the error messages for non-numeric arguments differ:

seq.default(to=quote(b), by=2)
Error in is.finite(to) : default method not implemented for type 'symbol'

seq.int(to=quote(b), by=2)
Error in seq.int(to = quote(b), by = 2) :
  'to' cannot be NA, NaN or infinite


Please reply off list.

Thanks
Mick Jordan

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Re: [Rd] [R] Problems when trying to install and load package "rzmq"

[Whit Armstrong]

Hi, Paul.

I maintian the rzmq project.

love to get it running on windows, but zmq doesn't play nicely with R's
mingw.

These guys have taken the approach of building the entire zmq library
inside the R package:
https://github.com/snoweye/pbdZMQ

I suggest you give it a try. or if you want to attempt to compile libzmq
sources for windows w/ R's mingw, that would be welcome.

-Whit


On Tue, Jan 3, 2017 at 9:36 AM, peter dalgaard  wrote:

> Possibly so.
>
> However, the ZeroMQ libraries do exist for Windows, so it might be
> possible to get the package working there. However, CRAN probably won't
> have the libraries, so cannot produce a binary package, and it is also
> quite possible that the package author is not a Windows person.
>
> At the very least, you'll need some familiarity with the Windows toolchain
> and be prepared to apply a fair amount of elbow grease.
>
> -pd
>
> (crosspost to r-help removed)
>
> On 29 Dec 2016, at 22:04 , Paul Bernal  wrote:
>
> > Dear Jeff,
> >
> > Thank you for your fast and kind reply. When you say that you do not
> think
> > this can be done on windows, then I would have to use something like
> Ubuntu
> > or Linux?
> >
> > Best regards
> >
> > Paul
> >
> > 2016-12-29 16:00 GMT-05:00 Jeff Newmiller :
> >
> >> Read the system requirements [1]. I don't think you can do this on
> windows.
> >>
> >> [1] https://cran.r-project.org/web/packages/rzmq/index.html
> >> --
> >> Sent from my phone. Please excuse my brevity.
> >>
> >> On December 29, 2016 12:23:26 PM PST, Paul Bernal <
> paulberna...@gmail.com>
> >> wrote:
> >>> After connecting to a mirror, I typed the following command:
> >>>
> >>> install.packages("rzqm")
> >>>
> >>> but I received the following message:
> >>>
> >>> ERROR: compilation failed for package 'rzmq'
> >>>
> >>> removing 'E:/Documents/R/win-library/3.3/rzmq'
> >>>
> >>> package which is only available in source form, and may need
> >>> compilation of
> >>> C/C++/Fortran: 'rzmq'
> >>> These will not be installed
> >>>
> >>> The computer environment is Windows 8 64x bits
> >>>
> >>>
> >>> Any help and/or guidance will be greatly appreciated
> >>>
> >>>  [[alternative HTML version deleted]]
> >>>
> >>> __
> >>> r-h...@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >>> https://stat.ethz.ch/mailman/listinfo/r-help
> >>> PLEASE do read the posting guide
> >>> http://www.R-project.org/posting-guide.html
> >>> and provide commented, minimal, self-contained, reproducible code.
> >>
> >>
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > r-h...@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> --
> 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
>

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Re: [Rd] [R] Problems when trying to install and load package "rzmq"

[peter dalgaard]

Possibly so. 

However, the ZeroMQ libraries do exist for Windows, so it might be possible to 
get the package working there. However, CRAN probably won't have the libraries, 
so cannot produce a binary package, and it is also quite possible that the 
package author is not a Windows person. 

At the very least, you'll need some familiarity with the Windows toolchain and 
be prepared to apply a fair amount of elbow grease.

-pd

(crosspost to r-help removed)

On 29 Dec 2016, at 22:04 , Paul Bernal  wrote:

> Dear Jeff,
> 
> Thank you for your fast and kind reply. When you say that you do not think
> this can be done on windows, then I would have to use something like Ubuntu
> or Linux?
> 
> Best regards
> 
> Paul
> 
> 2016-12-29 16:00 GMT-05:00 Jeff Newmiller :
> 
>> Read the system requirements [1]. I don't think you can do this on windows.
>> 
>> [1] https://cran.r-project.org/web/packages/rzmq/index.html
>> --
>> Sent from my phone. Please excuse my brevity.
>> 
>> On December 29, 2016 12:23:26 PM PST, Paul Bernal 
>> wrote:
>>> After connecting to a mirror, I typed the following command:
>>> 
>>> install.packages("rzqm")
>>> 
>>> but I received the following message:
>>> 
>>> ERROR: compilation failed for package 'rzmq'
>>> 
>>> removing 'E:/Documents/R/win-library/3.3/rzmq'
>>> 
>>> package which is only available in source form, and may need
>>> compilation of
>>> C/C++/Fortran: 'rzmq'
>>> These will not be installed
>>> 
>>> The computer environment is Windows 8 64x bits
>>> 
>>> 
>>> Any help and/or guidance will be greatly appreciated
>>> 
>>>  [[alternative HTML version deleted]]
>>> 
>>> __
>>> r-h...@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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Re: [Rd] .Internal for functions in distn.R

[luke-tierney]

The .Internal support in the C code is still i use for experimental
purposes.

Best,

luke

On Tue, 3 Jan 2017, Lukas Stadler wrote:


Hi,

the functions in distn.R were converted from .Internal to .External ([1], in 
2012), and to .Call ([2], in 2014).
They are still listed as .Internal in names.c, although they are not used in 
that way.

Shouldn’t they be removed?
There’s quite some simplification to be had, e.g., do_math3 could go away and 
do_math2 would be simpler.

If that makes sense (I may be missing something?), I’d be happy to create a 
patch that does this.

Best,
Lukas

[1] https://github.com/wch/r-source/commit/e430853d37cda69505e7452ddceb06a2008821d2 

[2] https://github.com/wch/r-source/commit/34fa67ca4c1dae13ed6a2ad74af7dbb27c8f3cb2 

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University of Iowa  Phone: 319-335-3386
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[Rd] .Internal for functions in distn.R

[Lukas Stadler]

Hi,

the functions in distn.R were converted from .Internal to .External ([1], in 
2012), and to .Call ([2], in 2014).
They are still listed as .Internal in names.c, although they are not used in 
that way.

Shouldn’t they be removed?
There’s quite some simplification to be had, e.g., do_math3 could go away and 
do_math2 would be simpler.

If that makes sense (I may be missing something?), I’d be happy to create a 
patch that does this.

Best,
 Lukas

[1] 
https://github.com/wch/r-source/commit/e430853d37cda69505e7452ddceb06a2008821d2 

[2] 
https://github.com/wch/r-source/commit/34fa67ca4c1dae13ed6a2ad74af7dbb27c8f3cb2 

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Re: [Rd] utils::ls.str(): Partial argument name 'digits' to seq() (should be digits.d?)

[Martin Maechler]

You are right (though picky).  I have updated it now.

Thank you Henrik!
Martin

> Should utils::ls.str() be updated as:

> svn diff src/library/utils/R/str.R
> Index: src/library/utils/R/str.R
> ===
> --- src/library/utils/R/str.R (revision 71879)
> +++ src/library/utils/R/str.R (working copy)
> @@ -622,7 +622,7 @@
>  args$digits.d <- NULL
>  }
>  strargs <- c(list(max.level = max.level, give.attr = give.attr,
> -  digits = digits), args)
> +  digits.d = digits), args)
>  for(nam in x) {
>   cat(nam, ": ")


[...]

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