Re: [Rd] Installation using iconv from glibc

[Prof Brian Ripley]

On 15/05/2015 01:19, Smith, Virgil wrote:

The R Installation and Administration manual section A.1 states that glibc 
should provide a suitable iconv function, but I can't get R's configure script 
to accept/validate iconv on a Linux platform I need to support using glibc 2.20.

Is glibc is actually compatible (and/or is gnu libiconv essentially the only 
path)?


R is built daily on Fedora 21 Linux which uses glibc 2.20 and has been 
for at least a decade with that and earlier versions of glibc.  No 
problems with installing using glibc have been reported in all that time 
(and many dialects of Linux have been used successfully).



If glibc should work, what should I check to troubleshoot my environment?

The configure error I get is
 checking iconv.h usability... yes
 checking iconv.h presence... yes
 checking for iconv.h... yes
 checking for iconv... yes
 checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... no
 configure: error: a suitable iconv is essential


You look in config.log for the details we cannot even guess at.



My full list of installed glibc / libc packages is
 glibc-binary-localedata-en-gb - 2.20-r0
 glibc-binary-localedata-en-us - 2.20-r0
 glibc-gconv - 2.20-r0
 glibc-gconv-utf-16 - 2.20-r0
 glibc-locale-en-gb - 2.20-r0
 libc6 - 2.20-r0
 libc6-dev - 2.20-r0
 libc6-extra-nss - 2.20-r0
 libc6-thread-db - 2.20-r0

This is for a custom Linux build, not a major distro, so unfortunately I cannot 
use pre-packaged configurations.




--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK

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[Rd] Defining Constant variable in a package

[Christophe Genolini]

Hi all,

In my package, I define some constant. In the previous version of R, I just define then in 
"/data/constants.R" but it seems that it is no longer possible. Instead, I am asked to "define them 
in the namespace". I am not sure to understand what it means. Shall I define them in the NAMESPACE 
file?


Christophe

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[Rd] Error when comparing two variables within a dataframe and print relevant observations

[bw1984]

I'm trying to use a nested ifelse condition to compare two lines. 

Input: 


Code: 


Expected Output: 



Actual Output: 



Any idea what might be causing this problem?



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Re: [Rd] CRAN check for package on Sparc Solaris

[Viechtbauer Wolfgang (STAT)]

Yes, I did read that part but it doesn't say anything about who to contact in 
case one doesn't have access to a Sparc Solaris machine, but one still wants to 
run the tests on that architecture. As I said, I think I got the issue 
resolved, but before I resubmit, I would prefer to check this -- I am 
ultimately just trying to avoid potentially wasting people's time here.

As for Linux x86_64 without long doubles. Is this something that is part of the 
checks here?

http://cran.r-project.org/web/checks/check_results_metafor.html

Doesn't seem that way. But is this still part of the CRAN checks?

I can of course simply assume/hope that the issue, which is now hopefully 
resolved on Sparc Solaris, is the same that caused problems for Linux x86_64 
without long doubles and that is then also hopefully resolved. Or I could hope 
that another kind soul with a compiled version of R on Linux x86_64 with 
--disable-long-double is willing to give the new tarball a whirl.

> -Original Message-
> From: R-devel [mailto:r-devel-boun...@r-project.org] On Behalf Of Prof
> Brian Ripley
> Sent: Thursday, May 14, 2015 08:06
> To: r-devel@r-project.org
> Subject: Re: [Rd] CRAN check for package on Sparc Solaris
> 
> This issue is discussed in
> http://cran.r-project.org/doc/manuals/r-release/R-exts.html#Writing-
> portable-packages,
> to which he was referred by the CRAN report.  It fails in the same way
> with --disable-long-double on an x86_64 Linux box (as he was told).
> 
> On 13/05/2015 20:48, Viechtbauer Wolfgang (STAT) wrote:
> > Dear All,
> >
> > The metafor package currently fails CRAN checks on Sparc Solaris:
> >
> > http://cran.r-project.org/web/checks/check_results_metafor.html
> >
> > The problem is probably due to an unintended (= stupid) use of
> identical() in a couple tests. I have changed that to more appropriate
> tests using all.equal(). However, before I resubmit the package to CRAN,
> I would really like to make sure that the updated package passes all
> checks also on Sparc Solaris.
> >
> > The issue/question of how to test packages on Sparc Solaris has come up
> before:
> >
> > https://stat.ethz.ch/pipermail/r-devel/2010-September/058538.html
> > https://stat.ethz.ch/pipermail/r-devel/2011-November/062430.html
> >
> > Unless anything has changed in the meantime, it seems like the help of
> kind volunteers is still the only option to conduct such tests. So, is
> there anybody out there with access to a Sparc machine running Solaris
> willing to run 'R CMD check --as-cran' on the updated tarball? Would be
> very much appreciated!
> >
> > Best,
> > Wolfgang
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> 
> 
> --
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
> 1 South Parks Road, Oxford OX1 3TG, UK
> 
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Re: [Rd] Error when comparing two variables within a dataframe and print relevant observations

[Keith Jewell]

On 15/05/2015 05:35, bw1984 wrote:

I'm trying to use a nested ifelse condition to compare two lines.

Input:


Code:


Expected Output:



Actual Output:



Any idea what might be causing this problem?



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View this message in context: 
http://r.789695.n4.nabble.com/Error-when-comparing-two-variables-within-a-dataframe-and-print-relevant-observations-tp4707240.html
Sent from the R devel mailing list archive at Nabble.com.

I had to look at Nabble to see the detail. Even that omitted an error 
message:


> Transfers2 <- subset(Transfers, ChangeType != "No Change"))
Error: unexpected ')' in "Transfers2 <- subset(Transfers, ChangeType != 
"No Change"))"


When I omitted the extra closing bracket it worked.

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Re: [Rd] example fails during R CMD CHECK but works interactively?

[Charles Determan]

Does anyone else have any thoughts about troubleshooting the R CMD check
environment?

Charles

On Wed, May 13, 2015 at 1:57 PM, Charles Determan 
wrote:

> Thank you Dan but it isn't my tests that are failing (all of them pass
> without problem) but one of the examples from the inst/examples directory.
> I did try, however, to start R with the environmental variables as you
> suggest but it had no effect on my tests.
>
> Charles
>
> On Wed, May 13, 2015 at 1:51 PM, Dan Tenenbaum 
> wrote:
>
>>
>>
>> - Original Message -
>> > From: "Charles Determan" 
>> > To: r-devel@r-project.org
>> > Sent: Wednesday, May 13, 2015 11:31:36 AM
>> > Subject: [Rd] example fails during R CMD CHECK but works interactively?
>> >
>> > Greetings,
>> >
>> > I am collaborating with developing the bigmemory package and have run
>> > in to
>> > a strange problem when we run R CMD CHECK.  For some reason that
>> > isn't
>> > clear to us one of the examples crashes stating:
>> >
>> > Error:  memory could not be allocated for instance of type big.matrix
>> >
>> > You can see the output on the Travis CI page at
>> > https://travis-ci.org/kaneplusplus/bigmemory where the error starts
>> > at line
>> > 1035.  This is completely reproducible when running
>> > devtools::check(args='--as-cran') locally.  The part that is
>> > confusing is
>> > that the calls work perfectly when called interactively.
>> >
>> > Hadley comments on the 'check' page of his R packages website (
>> > http://r-pkgs.had.co.nz/check.html) regarding test failing following
>> > R CMD
>> > check:
>> >
>> > Occasionally you may have a problem where the tests pass when run
>> > interactively with devtools::test(), but fail when in R CMD check.
>> > This
>> > usually indicates that you’ve made a faulty assumption about the
>> > testing
>> > environment, and it’s often hard to figure it out.
>> >
>> > Any thoughts on how to troubleshoot this problem?  I have no idea
>> > what
>> > assumption we could have made.
>>
>> Note that R CMD check runs R with environment variables set as follows
>> (at least on my system; you can check $R_HOME/bin/check to see what it does
>> on yours):
>>
>>  R_DEFAULT_PACKAGES= LC_COLLATE=C
>>
>> So try staring R like this:
>>
>>  R_DEFAULT_PACKAGES= LC_COLLATE=C  R
>>
>> And see if that reproduces the test failure. The locale setting could
>> affect tests of sort order, and the default package setting could
>> potentially affect other things.
>>
>> Dan
>>
>>
>>
>> >
>> > Regards,
>> > Charles
>> >
>> >   [[alternative HTML version deleted]]
>> >
>> > __
>> > R-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-devel
>> >
>>
>
>

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Re: [Rd] example fails during R CMD CHECK but works interactively?

[Hadley Wickham]

Make the example print out Sys.getenv() and then manually inspect?

Otherwise, you'll need to debug the code by adding print statements.
Something clearly is not as you expect, so you need carefully
empirically verify your assumptions about the inputs to and
environment of the function.

Hadley

On Fri, May 15, 2015 at 7:05 AM, Charles Determan  wrote:
> Does anyone else have any thoughts about troubleshooting the R CMD check
> environment?
>
> Charles
>
> On Wed, May 13, 2015 at 1:57 PM, Charles Determan 
> wrote:
>
>> Thank you Dan but it isn't my tests that are failing (all of them pass
>> without problem) but one of the examples from the inst/examples directory.
>> I did try, however, to start R with the environmental variables as you
>> suggest but it had no effect on my tests.
>>
>> Charles
>>
>> On Wed, May 13, 2015 at 1:51 PM, Dan Tenenbaum 
>> wrote:
>>
>>>
>>>
>>> - Original Message -
>>> > From: "Charles Determan" 
>>> > To: r-devel@r-project.org
>>> > Sent: Wednesday, May 13, 2015 11:31:36 AM
>>> > Subject: [Rd] example fails during R CMD CHECK but works interactively?
>>> >
>>> > Greetings,
>>> >
>>> > I am collaborating with developing the bigmemory package and have run
>>> > in to
>>> > a strange problem when we run R CMD CHECK.  For some reason that
>>> > isn't
>>> > clear to us one of the examples crashes stating:
>>> >
>>> > Error:  memory could not be allocated for instance of type big.matrix
>>> >
>>> > You can see the output on the Travis CI page at
>>> > https://travis-ci.org/kaneplusplus/bigmemory where the error starts
>>> > at line
>>> > 1035.  This is completely reproducible when running
>>> > devtools::check(args='--as-cran') locally.  The part that is
>>> > confusing is
>>> > that the calls work perfectly when called interactively.
>>> >
>>> > Hadley comments on the 'check' page of his R packages website (
>>> > http://r-pkgs.had.co.nz/check.html) regarding test failing following
>>> > R CMD
>>> > check:
>>> >
>>> > Occasionally you may have a problem where the tests pass when run
>>> > interactively with devtools::test(), but fail when in R CMD check.
>>> > This
>>> > usually indicates that you’ve made a faulty assumption about the
>>> > testing
>>> > environment, and it’s often hard to figure it out.
>>> >
>>> > Any thoughts on how to troubleshoot this problem?  I have no idea
>>> > what
>>> > assumption we could have made.
>>>
>>> Note that R CMD check runs R with environment variables set as follows
>>> (at least on my system; you can check $R_HOME/bin/check to see what it does
>>> on yours):
>>>
>>>  R_DEFAULT_PACKAGES= LC_COLLATE=C
>>>
>>> So try staring R like this:
>>>
>>>  R_DEFAULT_PACKAGES= LC_COLLATE=C  R
>>>
>>> And see if that reproduces the test failure. The locale setting could
>>> affect tests of sort order, and the default package setting could
>>> potentially affect other things.
>>>
>>> Dan
>>>
>>>
>>>
>>> >
>>> > Regards,
>>> > Charles
>>> >
>>> >   [[alternative HTML version deleted]]
>>> >
>>> > __
>>> > R-devel@r-project.org mailing list
>>> > https://stat.ethz.ch/mailman/listinfo/r-devel
>>> >
>>>
>>
>>
>
> [[alternative HTML version deleted]]
>
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Re: [Rd] example fails during R CMD CHECK but works interactively?

[Dirk Eddelbuettel]

On 15 May 2015 at 07:13, Hadley Wickham wrote:
| Make the example print out Sys.getenv() and then manually inspect?

On the systems I usesystem("env") is more efficient as it gets you
all at once. 
 
| Otherwise, you'll need to debug the code by adding print statements.
| Something clearly is not as you expect, so you need carefully
| empirically verify your assumptions about the inputs to and
| environment of the function.

Exactly. No magic here, just plainstaken debugging.

As an old ~/.signature of mine said: "In theory, theory and practice are the
same. In practie, they are not."  Assumptions are good.  We all get a good
laugh out of them after the fact.

Dirk

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Re: [Rd] example fails during R CMD CHECK but works interactively?

[Martin Morgan]

On 05/15/2015 05:05 AM, Charles Determan wrote:

Does anyone else have any thoughts about troubleshooting the R CMD check
environment?


In the pkg.Rcheck directory there is a file pkg-Ex.R.

LANGUAGE=en _R_CHECK_INTERNALS2_=1 $(R_HOME)/bin/R --vanilla pkge-Ex.R

followed by the usual strategy of bisecting the file into smaller chunks that 
still reproduce the example.


(this is based on my parsing of the complicated source, most relevant at

  https://github.com/wch/r-source/blob/trunk/src/library/tools/R/check.R#L2467

and

  https://github.com/wch/r-source/blob/trunk/src/library/tools/R/check.R#L36

)

Martin



Charles

On Wed, May 13, 2015 at 1:57 PM, Charles Determan 
wrote:


Thank you Dan but it isn't my tests that are failing (all of them pass
without problem) but one of the examples from the inst/examples directory.
I did try, however, to start R with the environmental variables as you
suggest but it had no effect on my tests.

Charles

On Wed, May 13, 2015 at 1:51 PM, Dan Tenenbaum 
wrote:




- Original Message -

From: "Charles Determan" 
To: r-devel@r-project.org
Sent: Wednesday, May 13, 2015 11:31:36 AM
Subject: [Rd] example fails during R CMD CHECK but works interactively?

Greetings,

I am collaborating with developing the bigmemory package and have run
in to
a strange problem when we run R CMD CHECK.  For some reason that
isn't
clear to us one of the examples crashes stating:

Error:  memory could not be allocated for instance of type big.matrix

You can see the output on the Travis CI page at
https://travis-ci.org/kaneplusplus/bigmemory where the error starts
at line
1035.  This is completely reproducible when running
devtools::check(args='--as-cran') locally.  The part that is
confusing is
that the calls work perfectly when called interactively.

Hadley comments on the 'check' page of his R packages website (
http://r-pkgs.had.co.nz/check.html) regarding test failing following
R CMD
check:

Occasionally you may have a problem where the tests pass when run
interactively with devtools::test(), but fail when in R CMD check.
This
usually indicates that you’ve made a faulty assumption about the
testing
environment, and it’s often hard to figure it out.

Any thoughts on how to troubleshoot this problem?  I have no idea
what
assumption we could have made.


Note that R CMD check runs R with environment variables set as follows
(at least on my system; you can check $R_HOME/bin/check to see what it does
on yours):

  R_DEFAULT_PACKAGES= LC_COLLATE=C

So try staring R like this:

  R_DEFAULT_PACKAGES= LC_COLLATE=C  R

And see if that reproduces the test failure. The locale setting could
affect tests of sort order, and the default package setting could
potentially affect other things.

Dan





Regards,
Charles

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Re: [Rd] example fails during R CMD CHECK but works interactively?

[Dirk Eddelbuettel]

On 15 May 2015 at 07:47, Dirk Eddelbuettel wrote:
| 
| On 15 May 2015 at 07:13, Hadley Wickham wrote:
| | Make the example print out Sys.getenv() and then manually inspect?
| 
| On the systems I usesystem("env") is more efficient as it gets you
| all at once. 

Ahh, yes, and I have since been told (thanks, Hadley) that Sys.getenv() does
just that -- and I remain a big fan of how R generally abstracts the OS away.

Dirk

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Re: [Rd] Defining Constant variable in a package

[Michael Lawrence]

I'm guessing you just need to define them in /R/constants.R and then
export() them from the NAMESPACE.

On Fri, May 15, 2015 at 2:32 AM, Christophe Genolini 
wrote:

> Hi all,
>
> In my package, I define some constant. In the previous version of R, I
> just define then in "/data/constants.R" but it seems that it is no longer
> possible. Instead, I am asked to "define them in the namespace". I am not
> sure to understand what it means. Shall I define them in the NAMESPACE file?
>
> Christophe
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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Re: [Rd] example fails during R CMD CHECK but works interactively?

[Martyn Plummer]

The error can be reproduced by running the bigmemory-Ex.R script which
you can find in the bigmemory.Rcheck directory, either in batch mode or
via source() in an interactive session.

It seems that you have underlying memory allocation problems. I can get
the script to running by adding gc() calls when necessary (i.e. when a
failure is reported, add gc() just before this point in the script and
rerun).

Martyn

On Fri, 2015-05-15 at 07:05 -0500, Charles Determan wrote:
> Does anyone else have any thoughts about troubleshooting the R CMD check
> environment?
> 
> Charles
> 
> On Wed, May 13, 2015 at 1:57 PM, Charles Determan 
> wrote:
> 
> > Thank you Dan but it isn't my tests that are failing (all of them pass
> > without problem) but one of the examples from the inst/examples directory.
> > I did try, however, to start R with the environmental variables as you
> > suggest but it had no effect on my tests.
> >
> > Charles
> >
> > On Wed, May 13, 2015 at 1:51 PM, Dan Tenenbaum 
> > wrote:
> >
> >>
> >>
> >> - Original Message -
> >> > From: "Charles Determan" 
> >> > To: r-devel@r-project.org
> >> > Sent: Wednesday, May 13, 2015 11:31:36 AM
> >> > Subject: [Rd] example fails during R CMD CHECK but works interactively?
> >> >
> >> > Greetings,
> >> >
> >> > I am collaborating with developing the bigmemory package and have run
> >> > in to
> >> > a strange problem when we run R CMD CHECK.  For some reason that
> >> > isn't
> >> > clear to us one of the examples crashes stating:
> >> >
> >> > Error:  memory could not be allocated for instance of type big.matrix
> >> >
> >> > You can see the output on the Travis CI page at
> >> > https://travis-ci.org/kaneplusplus/bigmemory where the error starts
> >> > at line
> >> > 1035.  This is completely reproducible when running
> >> > devtools::check(args='--as-cran') locally.  The part that is
> >> > confusing is
> >> > that the calls work perfectly when called interactively.
> >> >
> >> > Hadley comments on the 'check' page of his R packages website (
> >> > http://r-pkgs.had.co.nz/check.html) regarding test failing following
> >> > R CMD
> >> > check:
> >> >
> >> > Occasionally you may have a problem where the tests pass when run
> >> > interactively with devtools::test(), but fail when in R CMD check.
> >> > This
> >> > usually indicates that you’ve made a faulty assumption about the
> >> > testing
> >> > environment, and it’s often hard to figure it out.
> >> >
> >> > Any thoughts on how to troubleshoot this problem?  I have no idea
> >> > what
> >> > assumption we could have made.
> >>
> >> Note that R CMD check runs R with environment variables set as follows
> >> (at least on my system; you can check $R_HOME/bin/check to see what it does
> >> on yours):
> >>
> >>  R_DEFAULT_PACKAGES= LC_COLLATE=C
> >>
> >> So try staring R like this:
> >>
> >>  R_DEFAULT_PACKAGES= LC_COLLATE=C  R
> >>
> >> And see if that reproduces the test failure. The locale setting could
> >> affect tests of sort order, and the default package setting could
> >> potentially affect other things.
> >>
> >> Dan
> >>
> >>
> >>
> >> >
> >> > Regards,
> >> > Charles
> >> >
> >> >   [[alternative HTML version deleted]]
> >> >
> >> > __
> >> > R-devel@r-project.org mailing list
> >> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >> >
> >>
> >
> >
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Rd] Defining Constant variable in a package

[Christophe Genolini]

Hi Michael,

It works perfectly, thanks a lot!

Christophe

> I'm guessing you just need to define them in /R/constants.R and then export() 
> them from the NAMESPACE.
>
> On Fri, May 15, 2015 at 2:32 AM, Christophe Genolini  > wrote:
>
> Hi all,
>
> In my package, I define some constant. In the previous version of R, I 
> just define then in
> "/data/constants.R" but it seems that it is no longer possible. Instead, 
> I am asked to "define
> them in the namespace". I am not sure to understand what it means. Shall 
> I define them in the
> NAMESPACE file?
>
> Christophe
>
> __
> R-devel@r-project.org  mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>


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Re: [Rd] Alternative for wildcard gnu extension in Makevars

[Simon Urbanek]

On May 13, 2015, at 2:28 PM, Henrik Bengtsson  wrote:

> While at it:  'Makevars' is an R invention (i.e. documentation of it
> is only available through the R docs), correct?  /Henrik
> 

Well, it's just a Makefile fragment that gets included along with the rest of 
the Makefiles, so for all practical purposes it's just a Makefile which 
implicitly includes R's makefile on top so you don't have to do that by hand.

Cheers,
Simon



> On Wed, May 13, 2015 at 10:10 AM, Kevin Ushey  wrote:
>> One other solution that's only a little crazy: you could have a R
>> function within your package that generates the appropriate (portable)
>> Makevars, and within the package `configure` script call that
>> function. For example"
>> 
>>R --vanilla --slave -e "source('R/makevars.R'); makevars()"
>> 
>> And that 'makevars()' function could generate portable
>> 'Makevars(.win)' files for your package.
>> 
>> Kevin
>> 
>> On Wed, May 13, 2015 at 9:08 AM, Gábor Csárdi  wrote:
>>> On Wed, May 13, 2015 at 12:05 PM, Jan van der Laan 
>>> wrote:
>>> [...]
>>> 
 Too bad. Since it is only a handful of files, I will probably move them
 directly into the src directory and prefix them. It would have been nice to
 have been able to keep them separate.
 
>>> 
>>> If it is a couple of files, then you can also just list them in SOURCES (or
>>> even just OBJECTS, with a .o suffix), and leave them where they are.
>>> 
>>> Gabor
>>> 
>>> [...]
>>> 
>>>[[alternative HTML version deleted]]
>>> 
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[Rd] Installation error with R-devel

[Therneau, Terry M., Ph.D.]

I have a local library with functions that interrogates an institution-specific web API, 
so is not of interest to anyone outside of Mayo.  For some reason the R CMD INSTALL 
command fails.  See below:


Build the library, then install it.

tmt-local2127% R CMD build dart
* checking for file ‘dart/DESCRIPTION’ ... OK
* preparing ‘dart’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘dart_1.0-6.tar.gz’

tmt-local2128% R CMD INSTALL dart_1.0-6.tar.gz
* installing to library ‘/home/therneau/Rlib’
* installing *source* package ‘dart’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
Warning in file(con, "w") :
  cannot open file '/home/therneau/Rlib/dart/doc/index.html': No such file or 
directory
Error in file(con, "w") : cannot open the connection
ERROR: installing vignettes failed
* removing ‘/home/therneau/Rlib/dart’

-- The installation works ok if I build it with the no-build-vignettes option.
-- If I do that, I can cd to the vignettes directory and Sweave runs fine, i.e., 
library(dart) works

-- A call to "tar -tf dart_1.0-6.tar.gz" reveals that the inst directory has 
only a NEWS file.
-- R CMD check fails with the same message

Hints anyone?
Here is the sessionInfo() data

> sessionInfo()
R Under development (unstable) (2015-05-14 r68368)
Platform: i686-pc-linux-gnu (32-bit)
Running under: Ubuntu 14.04.1 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8LC_COLLATE=C
 [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
>

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Re: [Rd] Installation error with R-devel

[Kevin Ushey]

It's hard to diagnose this without your package sources / a
reproducible example.

Shot in the dark: one thing worth checking is that you don't have an
entry in your `.Rbuildignore` that's removing files you don't expect
it to (maybe that's causing R to strip out the 'doc/index.html' file)

Kevin

On Fri, May 15, 2015 at 12:54 PM, Therneau, Terry M., Ph.D.
 wrote:
> I have a local library with functions that interrogates an
> institution-specific web API, so is not of interest to anyone outside of
> Mayo.  For some reason the R CMD INSTALL command fails.  See below:
>
> Build the library, then install it.
>
> tmt-local2127% R CMD build dart
> * checking for file ‘dart/DESCRIPTION’ ... OK
> * preparing ‘dart’:
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... OK
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * looking to see if a ‘data/datalist’ file should be added
> * building ‘dart_1.0-6.tar.gz’
>
> tmt-local2128% R CMD INSTALL dart_1.0-6.tar.gz
> * installing to library ‘/home/therneau/Rlib’
> * installing *source* package ‘dart’ ...
> ** R
> ** data
> *** moving datasets to lazyload DB
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> Warning in file(con, "w") :
>   cannot open file '/home/therneau/Rlib/dart/doc/index.html': No such file
> or directory
> Error in file(con, "w") : cannot open the connection
> ERROR: installing vignettes failed
> * removing ‘/home/therneau/Rlib/dart’
>
> -- The installation works ok if I build it with the no-build-vignettes
> option.
> -- If I do that, I can cd to the vignettes directory and Sweave runs fine,
> i.e., library(dart) works
> -- A call to "tar -tf dart_1.0-6.tar.gz" reveals that the inst directory has
> only a NEWS file.
> -- R CMD check fails with the same message
>
> Hints anyone?
> Here is the sessionInfo() data
>
>> sessionInfo()
> R Under development (unstable) (2015-05-14 r68368)
> Platform: i686-pc-linux-gnu (32-bit)
> Running under: Ubuntu 14.04.1 LTS
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8LC_COLLATE=C
>  [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
>>
>
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> https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: [Rd] Installation error with R-devel --solved

[Therneau, Terry M., Ph.D.]

Bingo!  So very obvious once it was pointed out.

Thanks,
   Terry

On 05/15/2015 03:05 PM, Kevin Ushey wrote:

It's hard to diagnose this without your package sources / a
reproducible example.

Shot in the dark: one thing worth checking is that you don't have an
entry in your `.Rbuildignore` that's removing files you don't expect
it to (maybe that's causing R to strip out the 'doc/index.html' file)

Kevin


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[Rd] That 'make check-all' problem with the survival package

[Hin-Tak Leung]

'make check-all' for current R has been showing this error in the middle
for a few months now - any thought on fixing this? I think cmprsk
should be either included in the recommended bundle, or
the survival vignette to not depend on it. Having 'make check-all' showing
glaring ERROR's for a few months seems to defeat the purpose of
doing any checking at all via 'make check-all'.

FWIW, I did look at when/how the issue was introduced, but it appeared
that svn://svn.r-forge.r-project.org/svnroot/survival is no longer being
updated, and git://github.com/cran/survival.git only shows release jumps.
Anyway, if first appears with survival 2.38-1 in February, and as the previous
2.37-7 was 13 months older, this info is of no use to anybody.
I didn't write earlier as I thought the issue would go away at some point;
but obviously this isn't the case after 3 months.

---
 ERROR
Errors in running code in vignettes:
when running code in ‘compete.Rnw’
  ...
> temp$fstat <- as.numeric(event)

> temp$msex <- with(temp, 1 * (sex == "M"))

> fgfit1 <- with(temp, crr(etime, fstat, cov1 = cbind(age, 
+ msex, mspike), failcode = 2, cencode = 1, variance = TRUE))

  When sourcing ‘compete.R’:
Error: could not find function "crr"
Execution halted

* checking re-building of vignette outputs ... NOTE
Error in re-building vignettes:
  ...
Warning in coxph(Surv(futime, death) ~ group:age2 + sex + strata(group),  :
  X matrix deemed to be singular; variable 23 24 25
Loading required package: cmprsk
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, 
logical.return = TRUE,  :
  there is no package called ‘cmprsk’

Error: processing vignette 'compete.Rnw' failed with diagnostics:
 chunk 15 (label = finegray) 
Error in eval(expr, envir, enclos) : could not find function "crr"
Execution halted

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