Re: [R-SIG-Mac] List of unnecessary messages when I plot something in R from Terminal

[Jeff Newmiller]

Operating systems are designed to be as backward-compatible as possible... R 
Core doesn't generally know what distinguishing features will identify a new OS 
until it is released, nor what it will be called, so R has a handicap.

On February 11, 2023 1:12:42 PM PST, Christofer Bogaso 
 wrote:
>Actually when I check from the Apple icon, then I see that I am
>actually running Ventura
>
>For some reason, R's sessionInfo() is reporting that I am running Big Sur.
>
>Not sure why R is reporting wrong. Thanks,
>
>On Sun, Feb 12, 2023 at 2:38 AM Christofer Bogaso
> wrote:
>>
>> Hi,
>>
>> I am running Big Sur. Below is my sessionInfo()
>>
>> > sessionInfo()
>>
>> R version 4.2.1 (2022-06-23)
>>
>> Platform: x86_64-apple-darwin17.0 (64-bit)
>>
>> Running under: macOS Big Sur ... 10.16
>>
>>
>> Matrix products: default
>>
>> BLAS:   
>> /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
>>
>> LAPACK: 
>> /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
>>
>>
>> locale:
>>
>> [1] C/UTF-8/C/C/C/C
>>
>>
>> attached base packages:
>>
>> [1] stats graphics  grDevices utils datasets  methods   base
>>
>>
>> loaded via a namespace (and not attached):
>>
>> [1] compiler_4.2.1
>>
>> On Sun, Feb 12, 2023 at 1:55 AM Simon Urbanek
>>  wrote:
>> >
>> > Christofer,
>> >
>> > yes, unfortunately this is a known bug in macOS Ventura affecting a lot of 
>> > command-line programs that use GUI. Do not upgrade to Ventura (usually a 
>> > good advice given the long list of known bugs in Ventura) or wait for a 
>> > fix from Apple.
>> >
>> > Cheers,
>> > Simon
>> >
>> >
>> >
>> > > On Feb 11, 2023, at 11:28 PM, Christofer Bogaso 
>> > >  wrote:
>> > >
>> > > Hi,
>> > >
>> > > When I plot something in R, then it open Quartz and in the console I
>> > > see below messages
>> > >
>> > >> plot(1:4)
>> > >
>> > >> 1   HIToolbox   0x7ff8229a2726 
>> > >> _ZN15MenuBarInstance22EnsureAutoShowObserverEv + 102
>> > >
>> > > 2   HIToolbox   0x7ff8229a22b8
>> > > _ZN15MenuBarInstance14EnableAutoShowEv + 52
>> > >
>> > > 3   HIToolbox   0x7ff822946908
>> > > SetMenuBarObscured + 408
>> > >
>> > > 4   HIToolbox   0x7ff8229464ca
>> > > _ZN13HIApplication15HandleActivatedEP14OpaqueEventRefhP15OpaqueWindowPtrh
>> > > + 164
>> > >
>> > > 5   HIToolbox   0x7ff822940996
>> > > _ZN13HIApplication13EventObserverEjP14OpaqueEventRefPv + 252
>> > >
>> > > 6   HIToolbox   0x7ff822908bd2
>> > > _NotifyEventLoopObservers + 153
>> > >
>> > > 7   HIToolbox   0x7ff8229403e6
>> > > AcquireEventFromQueue + 494
>> > >
>> > > 8   HIToolbox   0x7ff82292f3ec
>> > > ReceiveNextEventCommon + 285
>> > >
>> > > 9   HIToolbox   0x7ff82292f2b3
>> > > _BlockUntilNextEventMatchingListInModeWithFilter + 70
>> > >
>> > > 10  AppKit  0x7ff81c136f33 _DPSNextEvent 
>> > > + 909
>> > >
>> > > 11  AppKit  0x7ff81c135db4
>> > > -[NSApplication(NSEvent)
>> > > _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1219
>> > >
>> > > 12  grDevices.so0x0001086f7a3b input_handler 
>> > > + 155
>> > >
>> > > 13  libR.dylib  0x000108b142cf
>> > > Rstd_ReadConsole + 2127
>> > >
>> > > 14  libR.dylib  0x000108a15b74
>> > > Rf_ReplIteration + 100
>> > >
>> > > 15  libR.dylib  0x000108a174b1 R_ReplConsole 
>> > > + 161
>> > >
>> > > 16  libR.dylib  0x000108a17402 run_Rmainloop 
>> > > + 82
>> > >
>> > > 17  libR.dylib  0x000108a1753e Rf_mainloop + 
>> > > 14
>> > >
>> > > 18  R   0x00010847af5b main + 27
>> > >
>> > > 19  dyld0x7ff818bde310 start + 2432
>> > >
>> > > 1   HIToolbox   0x7ff822aa952b
>> > > _ZN15MenuBarInstance21IsAutoShowHideAllowedEv + 259
>> > >
>> > > 2   HIToolbox   0x7ff8229a233e
>> > > _ZN15MenuBarInstance24UpdateAutoShowVisibilityE5Pointh + 34
>> > >
>> > > 3   HIToolbox   0x7ff8229117a4
>> > > _ZN15MenuBarInstance16ForEachMenuBarDoEU13block_pointerFvPS_E + 46
>> > >
>> > > 4   HIToolbox   0x7ff8229a293d
>> > > _ZN15MenuBarInstance20AutoShowHideObserverEjP14OpaqueEventRefPv + 165
>> > >
>> > > 5   HIToolbox   0x7ff822908bd2
>> > > _NotifyEventLoopObservers + 153
>> > >
>> > > 6   HIToolbox   0x7ff82293afb8
>> > > PostEventToQueueInternal + 700
>> > >
>> > > 7   HIToolbox   0x7ff82293c871
>> > > _ZL29CreateAndPostEventWithCGEventP9__CGEventjhP17__CFMachPortBoost +
>> > > 404
>> > 

Re: [R-SIG-Mac] Contributing to documentation [Was: Installing gfortran]

[Jeff Newmiller]

Generating patch files is one of the most fundamental capabilities of git. 
Changes to the Linux kernel are (almost?) universally submitted via patch files 
generated from git.

Re git and empty directories... git is structurally incapable of recording them 
in the repo. A common workaround is to touch a .gitkeep file in the directory, 
but I suspect this will never become an automated feature of git because it 
cannot be hidden from the user without making the chosen filename off-limits to 
the user.

On April 30, 2022 7:45:40 AM PDT, Duncan Murdoch  
wrote:
>On 30/04/2022 9:53 a.m., Patrick Schratz wrote:
>> If that is the case, why not contribute to the documentation? That
>> is the whole point of an open source project after all.
>> 
>> Because often it is not easily accessible, e.g. living in an ancient SVN 
>> repo or lacking (an easy) and clear contribution guide.
>
>There's a mirror of that repo at https://github.com/wch/r-source .  It is of 
>course unofficial and not maintained by R Core so I could understand you might 
>worry about using it, but as far as I know it is well maintained.  The only 
>difference that I ever heard about in the past was that the official svn repo 
>had an empty directory somewhere or other, and git at the time didn't support 
>empty directories.  I don't know if either of those is still true.
>
>
>> WRT to the Mac dev instructions, I can see that the source lives in 
>> https://github.com/R-macos/R-mac-dev  
>> which is definitely a good start.
>> Yet I think it needs way more cross-linking between the repos, more 
>> “official” pointers and “how-tos” to really also encourage people to 
>> contribute.
>> The README could give more detailed contribution instructions, such as whom 
>> to tag for a PR, what should go there and what not, possibly stating that 
>> it’s the official documentation and define it from other “random” orgs on 
>> developer portals - all of these could e.g. go into a |CONTRIBUTING.md| 
>> which is a widely known source for such information.
>> Just some personal thoughts though which could potentially considered to 
>> improve things.
>> 
>> To be clear, I acknowledge your effort in opening things up to platforms 
>> like GH - which not all parts of R/CRAN are doing at the moment AFAIK.
>> And yes, when complaining about things not being optimal, one should also 
>> put in effort to make things better.
>> So I’ll see if I can put some time in to improve things and see how the 
>> experience is.
>
>If you're happier working in git than in svn, what you could do is fork the 
>mirror repo to your own git repo, and make your proposed changes there.  If 
>they are good changes it won't be hard for someone (maybe even you) to convert 
>into the appropriate format to merge into svn.
>
>The way R development changes is when a change makes things easier for the 
>devs.  I suspect whether it's easier for you is only important to them if 
>you've got a history of making helpful contributions: they like help, they 
>don't like arguments about how to do things.  (I'm saying this as a former 
>member of R Core.)
>
>Duncan Murdoch
>
>> 
>> The problem is that generally they cannot. You are looking something
>> up, because you don't know about it so you can't judge whether it is
>> a good answer (SO is good example proving why crowd-souring the
>> definition of truth doesn't generally work). At best you may know
>> the person and thus judge by that, but even then you may not know if
>> the information is still accurate.
>> 
>> I see your point here and generally agree that it’s hard making such 
>> judgements in this position.
>> Yet I disagree on referring to Stackoverflow as a “crowd-souring the 
>> definition of truth doesn't generally work”. Without SO, we would be nowhere 
>> where we are today and I’d argue it has done a lot more positive things than 
>> negative ones to every single person who ever accessed it. >
>> Cheers
>> Patrick
>> 
>> On 25 Apr 2022, at 1:04, Simon Urbanek wrote:
>> 
>> On Apr 23, 2022, at 7:44 PM, Patrick Schratz
>>  wrote:
>> 
>> FWIW blog posts which explain such things usually have a (good)
>> reason - they aim to help people getting started when the
>> official documentation is either unclear, hard to find or
>> incomplete.
>> 
>> If that is the case, why not contribute to the documentation? That
>> is the whole point of an open source project after all.
>> 
>> The problem with random blogs is that many of them are written by
>> people trying to find an answer without much knowledge on the
>> subject and often post very bad advice that does not necesarily
>> address the actual issue. There are rare exceptions of knowledgeable
>> people posting explanatory blogs, but if you search for an answer
>> you have no way of knowing whether it is of the good kind. In
>> addition, blogs 

Re: [R-SIG-Mac] strange segfault error in R from command-line on Mac laptop

[Jeff Newmiller]

I cannot address your observed symptoms, but shouldn't you have already 
upgraded your R to the latest version before asking this?

On September 29, 2021 11:17:02 AM PDT, Jeffrey Rosenthal 
 wrote:
>Hello.  I often use R from the command-line (i.e. just typing "R") 
>within the "Terminal" application on my MacBook Pro laptop.  And 
>sometimes I get a sudden strange error "*** caught segfault *** address 
>0x10, cause 'memory not mapped'" (after which R allows me to 
>abort/exit/etc, but not to continue).  It occurs when using the arrow or 
>delete keys (perhaps related to readline?).  After much testing, I have 
>found a very simple reproducible minimal example. Namely, if I start R 
>from the command line, and then type "plot(0)", and then type any 
>character (e.g. "a") and then the delete key, then it always triggers 
>this error.  Does this error occur for anyone else?  Any ideas how to 
>fix it?
>
>I know that this problem is quite specific to my Mac laptop set-up; it 
>does not occur on my iMac nor on my friend's Mac.  On the other hand, I 
>did try upgrading R and that did not fix it.  My sessionInfo() output 
>follows.  I am *not* saving R history, nor setting R_SAVEHIST, and I do 
>*not* have any .Rhistory or .Rapp.history file in my directory.  Thank 
>you very much for any suggestions!
>
>
>
>> sessionInfo()
>
>R version 4.0.2 (2020-06-22)
>Platform: x86_64-apple-darwin17.0 (64-bit)
>Running under: macOS Catalina 10.15.7
>
>Matrix products: default
>BLAS:
>/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
>LAPACK:
>/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
>
>locale:
>[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
>
>attached base packages:
>[1] stats graphics  grDevices utils datasets  methods   base
>
>loaded via a namespace (and not attached):
>[1] compiler_4.0.2
>
>
>   Jeffrey S. Rosenthal
>   Professor of Statistics, University of Toronto
>   Web site: http://probability.ca/jeff/
>
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Re: [R-SIG-Mac] Corrupt R installation

[Jeff Newmiller]

Also, symlinking an X.Y R version package library to any other major-minor 
version is never supported (even if it sometimes works). Re-install your 
packages when the minor version Y increments.

On June 8, 2021 5:07:28 PM PDT, Simon Urbanek  
wrote:
>
>You seem to have entirely non-standard setup that you're on your own
>and I assume you're not using CRAN R since you involve homebrew (which
>explains the chaos) so presumably you re-compiled R yourself and all
>packages, but I'd like to point out that if all you are after is OpenMP
>support then you don't need any of that fragile mess as explained at
>https://mac.r-project.org/openmp/
>
>Cheers,
>Simon
>
>
>> On 9/06/2021, at 8:46 AM, moleps islon  wrote:
>> 
>> Copied from SO (
>>
>https://stackoverflow.com/questions/67892321/major-r-installation-corruption)
>> and sent here instead at the suggestion of  Dirk Eddelbuettel
>> 
>> 
>> I have no idea why, but my R installation (Mac OS X - Big Sur)
>> automatically updates causing havoc with my libraries each time. My
>Mac is
>> under administration from the university and their software center,
>but
>> they claim it is not their fault - but I still suspect them for
>causing all
>> the trouble.
>> 
>> Anyhow - after that last update to 4.1.0 the packages were again all
>lost.
>> I tried a dirty hack just symlinking to the old version and updating
>(I
>> know-- very stupid, but I didnt have time for a major update of all
>the
>> packages), but after this my R-installation has been totally chaos
>for the
>> past week. I´ve reinstalled everything multiple times (brew, llvm,
>gcc,
>> CLI, X-code -- you name it) and I´ve finally managed to get
>data.table
>> working again with openMP support using the instructions at SO
>>
>
>> (
>>
>https://stackoverflow.com/questions/65251887/clang-7-error-linker-command-failed-with-exit-code-1-for-macos-big-sur/65334247#65334247
>> ).
>> 
>> However I still get the following error message when installing
>data.table
>> from source:
>> 
>> dylib (/usr/local/opt/llvm/lib/libunwind.dylib) was built for newer
>macOS
>> version (11.0) than being linked (10.16)
>> Does it matter? Any idea how I can fix it?
>> 
>>  [[alternative HTML version deleted]]
>> 
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>> 
>
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Re: [R-SIG-Mac] rlang and the new R version 4.1.0

[Jeff Newmiller]

There are many of these. Some of these "solutions" copy the actual installed 
packages and then run "update.packages"... which is a very bad idea. Other 
solutions identify the names of the packages and install fresh (good idea) but 
they will hiccup when you install from non-standard sources. So some people 
will conclude that the former are "better" and then complain that "things don't 
work" when they should have preferred the latter and invested the effort needed 
for those non-standard sources.

You would be doing a service if you identified the blog you used so the mailing 
list archive can clarify to future readers which category of "solution" you had 
followed when you encountered this problem.

Do read snippets from the Internets before running them.

On May 25, 2021 1:28:20 PM PDT, Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
 wrote:
>When R4.0 came out,  someone on R-Bloggers post a very nice to automate
>updating your packages from R3.6.  I just used it to do my update from
>R4.0 to R4.1 - it works perfectly.  I would include the script here, 
>but since I don't have the exact reference I don't like posting someone
>else's script without appropriate credit.  Do a search and you should
>be able to find the entry.
>
>-Roy
>
>> On May 25, 2021, at 1:10 PM, Simon Urbanek
> wrote:
>> 
>> 
>> Hans,
>> 
>> you seem to be using old library from 4.0 (see the 4.0 in the path).
>Make sure you remove old packages and use a clean library for 4.1 since
>you cannot mix packages from R 4.0.x and R 4.1.0. I would best
>recommend removing (or re-naming) ~/Library/R before installation to
>make sure you don't have incompatible old packages. Also don't forget
>to re-start R.
>> 
>> (Marc, I can't parse your post, it makes no sense to me, there no
>R-devel involved in any of this, so please post separately about
>whatever is on your heart as that doesn't seem to be related).
>> 
>> Cheers,
>> Simon
>> 
>> 
>> 
>>> On May 26, 2021, at 2:06 AM, Marc Schwartz 
>wrote:
>>> 
>>> Hi,
>>> 
>>> You might try a different CRAN mirror to see if perhaps the rlang
>binary that you are getting is corrupted.
>>> 
>>> Looking at CRAN for the package, the results for rlang on what is
>supposed to be R release on macOS:
>>> 
>>> https://cran.r-project.org/web/checks/check_results_rlang.html
>>> 
>>> shows a header indicating that R devel is being used, not R release:
>>> 
>>>
>https://www.r-project.org/nosvn/R.check/r-release-macos-x86_64/rlang-00check.html
>>> 
>>> So, I am not clear if there is a macOS binary build issue that may
>be resulting in a conflict of sorts.
>>> 
>>> A spot check of other CRAN packages (including my own) shows the
>same use of R devel for macOS, and not R release, so perhaps there is a
>wider issue going on with CRAN builds, unless I am missing something
>here.
>>> 
>>> Simon (cc'd now) may be able to address that issue.
>>> 
>>> Regards,
>>> 
>>> Marc Schwartz
>>> 
>>> 
>>> Hans W wrote on 5/25/21 9:16 AM:
 I installed the new R version 4.1.0 on my (normal) Macbook, and
 everything seemed to work fine until one of the packages depended
>on
 the 'rlang' package and I got the following error:
> library(rlang)
Error: package or namespace load failed for ‘rlang’ in
dyn.load(file, DLLpath = DLLpath, ...): unable to load
shared object
>'/Users/hwb/Library/R/4.0/library/rlang/libs/rlang.so':
dlopen(/Users/hwb/Library/R/4.0/library/rlang/libs/rlang.so, 6):
Library not loaded:
   
>/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib
Referenced from:
>/Users/hwb/Library/R/4.0/library/rlang/libs/rlang.so
Reason: image not found
 So I removed 'rlang' and reinstalled it. There was no error
>message,
 but when I tried to load it, the error message was:
Error: package or namespace load failed for ‘rlang’ in
get(Info[i, 1], envir = env): lazy-load database
'/Users/hwb/Library/R/4.0/library/rlang/R/rlang.rdb' is corrupt
In addition: Warning message:
In get(Info[i, 1], envir = env) : internal error -3 in
>R_decompress1
 One of my current applications relies on 'rvest' which depends on
 'rlang'. For the moment I am using it from a Linux computer, but
>it's
 quite unfortunate that I cannot run it from macOS as well.
 I also uninstalled the new R version and reinstalled it, but
>nothing
 changed. Could you give me a hint on what to do (or what I did
>wrong)?
 ___
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>>> 
>> 
>> ___
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>
>**
>"The contents of this message do not reflect any position of the U.S.
>Government or NOAA."
>**
>Roy Mendelssohn
>Supervisory Operations 

Re: [R-SIG-Mac] How to find the path for a file to be read with read.table() in a Mac

[Jeff Newmiller]

Even better is to learn one of the many ways to start R in a working directory 
of your choice, so you don't have to mix code and data from different projects 
together in one directory just because that happens to be where your default R 
icon sets it up.

Some ways:
a) Use Terminal and the cd command before invoking R.
b) Create a .RData file with nothing in it in the desired directory. 
Double-click that to automatically set the working directory there in R.
c) Use RStudio, which lets you create an Rproj file that serves the same 
purpose as the .RData file but doesn't risk injecting broken code or old data 
into your working environment.

On February 13, 2021 8:02:54 AM PST, "Parkhurst, David F." 
 wrote:
>Ah.  That will simplify the process a lot!
>
>From: Duncan Murdoch 
>Date: Saturday, February 13, 2021 at 10:52 AM
>To: Parkhurst, David F. , r-sig-mac@r-project.org
>
>Subject: Re: [R-SIG-Mac] How to find the path for a file to be read
>with read.table() in a Mac
>On 13/02/2021 10:42 a.m., Parkhurst, David F. wrote:
>> I�ve several times to figure this out with no luck.  I�ve moved a tab
>delimited text file (created from excel) to the desktop to simplify the
>path.  If I click on the file and ask Get Info, it lists �Where� as 
>iCloud Drive > Desktop.  If I copy that to the clipboard and paste that
>into a read.table command in the R console, it comes up as
>/Users/DFP/Desktop.  But if I try
>read.table("\\Users\\DFP\\Desktop\\moabsitechem"),
>I get No such file or directory.  How can I get that file into a data
>frame?
>>
>> Is there some place in my Mac that I can put the file so I could
>enter just the file name, and not the whole path?
>
>Sorry, forget to answer your actual question:
>
>You can use getwd() to find the working directory.  If you put the file
>there, you won't need to specify the path.
>
>Duncan Murdoch
>
>   [[alternative HTML version deleted]]

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Re: [R-SIG-Mac] Problem with CHECK --as-cran on Catalina

[Jeff Newmiller]

No, it has been this way for longer than I have been building packages. I think 
the variable that determines whether a check of the working files will break is 
what additional files that get filtered out when you build the source package. 
Anyway, checking the source package is the recommended practice.

On June 7, 2020 10:32:45 AM PDT, Carl Witthoft  wrote:
>Looks like I found a way to succeed.
>
>If I type
>
>R CMD CHECK --as-cran  mypackage.tar.gz
>
>then I get a successful check executed.  So this is a bit different
>from 
>the "good old days" under R 3.6.X  and my old 10.11 OSX, but now I know
>
>how to get it done.
>
>
>
>On 6/6/20 4:29 PM, Jeff Newmiller wrote:
>> AFAIK tgz is one possible file name extension equivalent to .tar.gz,
>which implies gzip compression, so I think Bob was just being a bit
>sloppy when he wrote tar.tgz.
>> 
>> Key point is not that a particular compression makes a difference,
>but that the check needs to be run on a source archive rather than the
>in-place source you have been editing. He was confirming that you are
>making that file and specifying it when checking.
>> 
>> On June 6, 2020 11:59:24 AM PDT, Carl Witthoft 
>wrote:
>>> I plead ignorance here: I don't see an option to create .tgz . The
>>> R CMD BUILD --help just lists "gzip" (default), "none", "bzip2",
>"xz"
>>> .Does one of those create the .tgz -type compression?
>>>
>>> Carl
>>>
>>> On 6/6/20 2:37 PM, Bob Rudis wrote:
>>>> Does it still do it if you build a tar.tgz archive and run it on
>>> that?
>>>>
>>>> I could not dup your problem, but when I tried to run it on a
>couple
>>>> of my packages that work fine with tar.gz (I use Authors@R) in dir
>>> (`R
>>>> CMD check --as-cran .` or parent dir and specify the pkg dir) I
>get:
>>>>
>>>>   Required field missing or empty:
>>>> ‘Author’
>>>>
>>>> (running last R 4.0.1 beta before the release of R 4.0.1, latest
>>>> Catalina beta AND R 4.0.0 on ubuntu)
>>>>
>>>> So, def something strange going on.
>>>>
>>>> On Sat, Jun 6, 2020 at 12:47 PM Carl Witthoft 
>>> wrote:
>>>>>
>>>>> Hi,
>>>>> I recently upgraded to a new iMac w/ Catalina.  Something really
>>> strange
>>>>> is happening when I try to run "R CMD CHECK --as-cran  " .
>>>>> If I run it on various older packages that have previously passed
>>> the
>>>>> check, all is well.
>>>>>
>>>>> I am writing a new package, and here's the response I get:
>>>>>
>>>>>
>>>>> * using log directory ‘/Users/cgw/Rgames/fitConic.Rcheck’
>>>>> * using R version 4.0.0 (2020-04-24)
>>>>> * using platform: x86_64-apple-darwin17.0 (64-bit)
>>>>> * using session charset: UTF-8
>>>>> * using option ‘--as-cran’
>>>>> * checking for file ‘fitConic/DESCRIPTION’ ... OK
>>>>> * this is package ‘fitConic’ version ‘1.0’
>>>>> * checking CRAN incoming feasibility ...Error:  file
>'./DESCRIPTION'
>>>>> does not exist
>>>>> Execution halted
>>>>>
>>>>>
>>>>> This happens whether I run R CMD CHECK  from the parent dirctory
>>>>> /Users/cgw/Rgames  or from the source directory
>>> /Users/cgw/Rgames/fitConic .
>>>>>
>>>>> I verified I can edit the DESCRIPTION file in my previous packages
>&
>>>>> still pass the check.  I even took one of those old DESCRIPTION
>>> files
>>>>> and put it into the fitConic directory, and changed only the
>>> "Package:"
>>>>> line  .
>>>>>
>>>>> I'm guessing that last error message is not telling me what
>actually
>>>>> went wrong, but I'm at a loss as to why this new package fails.
>>> I've
>>>>> created a new directory and moved all my files (DESCRIPTION,
>>> NAMESPACE,
>>>>> and the R & man folders) over. No luck.
>>>>>
>>>>> Is this a hangup somewhere in R 4.0 for OSX, or is there something
>>> else
>>>>> going on?   (do I need, for example to do something to give
>XQuartz
>>> more
>>>>> permissions, or some other called app? )
>>>>>
>>>>> thanks
>>>>> --
>>>>> Carl Witthoft
>>>>> c...@witthoft.com
>>>>> resume: https://app.box.com/file/498153801347
>>>>>
>>>>> ___
>>>>> R-SIG-Mac mailing list
>>>>> R-SIG-Mac@r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 

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Re: [R-SIG-Mac] Problem with CHECK --as-cran on Catalina

[Jeff Newmiller]

AFAIK tgz is one possible file name extension equivalent to .tar.gz, which 
implies gzip compression, so I think Bob was just being a bit sloppy when he 
wrote tar.tgz.

Key point is not that a particular compression makes a difference, but that the 
check needs to be run on a source archive rather than the in-place source you 
have been editing. He was confirming that you are making that file and 
specifying it when checking.

On June 6, 2020 11:59:24 AM PDT, Carl Witthoft  wrote:
>I plead ignorance here: I don't see an option to create .tgz . The
>R CMD BUILD --help just lists "gzip" (default), "none", "bzip2", "xz" 
>.Does one of those create the .tgz -type compression?
>
>Carl
>
>On 6/6/20 2:37 PM, Bob Rudis wrote:
>> Does it still do it if you build a tar.tgz archive and run it on
>that?
>> 
>> I could not dup your problem, but when I tried to run it on a couple
>> of my packages that work fine with tar.gz (I use Authors@R) in dir
>(`R
>> CMD check --as-cran .` or parent dir and specify the pkg dir) I get:
>> 
>>  Required field missing or empty:
>>‘Author’
>> 
>> (running last R 4.0.1 beta before the release of R 4.0.1, latest
>> Catalina beta AND R 4.0.0 on ubuntu)
>> 
>> So, def something strange going on.
>> 
>> On Sat, Jun 6, 2020 at 12:47 PM Carl Witthoft 
>wrote:
>>>
>>> Hi,
>>> I recently upgraded to a new iMac w/ Catalina.  Something really
>strange
>>> is happening when I try to run "R CMD CHECK --as-cran  " .
>>> If I run it on various older packages that have previously passed
>the
>>> check, all is well.
>>>
>>> I am writing a new package, and here's the response I get:
>>>
>>>
>>> * using log directory ‘/Users/cgw/Rgames/fitConic.Rcheck’
>>> * using R version 4.0.0 (2020-04-24)
>>> * using platform: x86_64-apple-darwin17.0 (64-bit)
>>> * using session charset: UTF-8
>>> * using option ‘--as-cran’
>>> * checking for file ‘fitConic/DESCRIPTION’ ... OK
>>> * this is package ‘fitConic’ version ‘1.0’
>>> * checking CRAN incoming feasibility ...Error:  file './DESCRIPTION'
>>> does not exist
>>> Execution halted
>>>
>>>
>>> This happens whether I run R CMD CHECK  from the parent dirctory
>>> /Users/cgw/Rgames  or from the source directory
>/Users/cgw/Rgames/fitConic .
>>>
>>> I verified I can edit the DESCRIPTION file in my previous packages &
>>> still pass the check.  I even took one of those old DESCRIPTION
>files
>>> and put it into the fitConic directory, and changed only the
>"Package: "
>>> line  .
>>>
>>> I'm guessing that last error message is not telling me what actually
>>> went wrong, but I'm at a loss as to why this new package fails. 
>I've
>>> created a new directory and moved all my files (DESCRIPTION,
>NAMESPACE,
>>> and the R & man folders) over. No luck.
>>>
>>> Is this a hangup somewhere in R 4.0 for OSX, or is there something
>else
>>> going on?   (do I need, for example to do something to give XQuartz
>more
>>> permissions, or some other called app? )
>>>
>>> thanks
>>> --
>>> Carl Witthoft
>>> c...@witthoft.com
>>> resume: https://app.box.com/file/498153801347
>>>
>>> ___
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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Re: [R-SIG-Mac] High end performance desktop/laptop for statistical simulations

[Jeff Newmiller]

Use a cloud solution?

On March 28, 2020 9:44:45 AM PDT, Prathiba Natesan  
wrote:
>Hi all:
>I am looking for a high end performance desktop/laptop for statistical
>simulations. I typically run hundreds of thousands of simulations using
>JAGS and other packages. Any suggestions?
>Cheers
>P
>
>   [[alternative HTML version deleted]]
>
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Re: [R-SIG-Mac] R CMD build "cannot open compressed file" with R 3.6.2

[Jeff Newmiller]

I am glad my response helped direct you toward a resolution, but antivirus 
interference did not actually occur to me. Thanks for reporting back.

On January 1, 2020 7:23:12 AM PST, Spencer Graves  
wrote:
>   Thanks to Jeff Newmiller for his reply.  He was correct.  My 
>Bitdefender internet security automatically upgraded itself and started
>
>blocking R in ways it had not before.  Please excuse me for taking the 
>time of this list with this issue (and for my delay in sending this 
>"issue resolution" email).
>
>
>   Spencer Graves
>
>
>On 2019-12-25 13:18, Spencer Graves wrote:
>>
>>
>> On 2019-12-25 12:02, Jeff Newmiller wrote:
>>> "Permission denied" suggests that this is not related to R. Perhaps
>you ran R with elevated permissions yesterday?
>>>
>>> On December 25, 2019 8:37:36 AM PST, Spencer
>Graves  wrote:
>>>> Hello, All:
>>>>
>>>>
>>>>    I just upgraded to R 3.6.2 and suddenly got, "cannot open
>>>> compressed file" with "R CMD build" of a package that I built
>yesterday
>>>>
>>>> with R 3.6.1, and I don't recall having gotten an error message
>with
>>>> 3.6.1.
>>>>
>>>>
>>>>    What do you suggest I do to get around this?
>>>>    Thanks,
>>>>    Spencer Graves
>>>>
>>>>
>>>> $ R CMD build Ecfun
>>>> * checking for file ‘Ecfun/DESCRIPTION’ ... OK
>>>> * preparing ‘Ecfun’:
>>>> * checking DESCRIPTION meta-information ... OK
>>>> * installing the package to build vignettes
>>>> * creating vignettes ... OK
>>>> * checking for LF line-endings in source and make files and shell
>>>> scripts
>>>> * checking for empty or unneeded directories
>>>> * building ‘Ecfun_0.2-2.tar.gz’
>>>> Warning in gzfile(tarfile, "wb", compression = compression_level) :
>>>>    cannot open compressed file
>>>> '/Users/sbgraves/Documents/current/R/Ecfun_0.2-2.tar.gz', probable
>>>> reason 'Permission denied'
>>>> Error in gzfile(tarfile, "wb", compression = compression_level) :
>>>>    cannot open the connection
>>>> Execution halted
>>>>
>>>> $ r
>>>>> sessionInfo()
>>>> R version 3.6.2 (2019-12-12)
>>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>>> Running under: macOS Catalina 10.15.2
>>>>
>>>> Matrix products: default
>>>> BLAS:
>>>>
>/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
>>>> LAPACK:
>>>>
>/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
>>>>
>>>> locale:
>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>
>>>> attached base packages:
>>>> [1] stats graphics  grDevices utils datasets  methods base
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] compiler_3.6.2
>>>> ___
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>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>

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Re: [R-SIG-Mac] R CMD build "cannot open compressed file" with R 3.6.2

[Jeff Newmiller]

"Permission denied" suggests that this is not related to R. Perhaps you ran R 
with elevated permissions yesterday?

On December 25, 2019 8:37:36 AM PST, Spencer Graves 
 wrote:
>Hello, All:
>
>
>   I just upgraded to R 3.6.2 and suddenly got, "cannot open 
>compressed file" with "R CMD build" of a package that I built yesterday
>
>with R 3.6.1, and I don't recall having gotten an error message with
>3.6.1.
>
>
>   What do you suggest I do to get around this?
>   Thanks,
>   Spencer Graves
>
>
>$ R CMD build Ecfun
>* checking for file ‘Ecfun/DESCRIPTION’ ... OK
>* preparing ‘Ecfun’:
>* checking DESCRIPTION meta-information ... OK
>* installing the package to build vignettes
>* creating vignettes ... OK
>* checking for LF line-endings in source and make files and shell
>scripts
>* checking for empty or unneeded directories
>* building ‘Ecfun_0.2-2.tar.gz’
>Warning in gzfile(tarfile, "wb", compression = compression_level) :
>   cannot open compressed file 
>'/Users/sbgraves/Documents/current/R/Ecfun_0.2-2.tar.gz', probable 
>reason 'Permission denied'
>Error in gzfile(tarfile, "wb", compression = compression_level) :
>   cannot open the connection
>Execution halted
>
>$ r
> >sessionInfo()
>R version 3.6.2 (2019-12-12)
>Platform: x86_64-apple-darwin15.6.0 (64-bit)
>Running under: macOS Catalina 10.15.2
>
>Matrix products: default
>BLAS: 
>/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
>LAPACK: 
>/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
>
>locale:
>[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
>attached base packages:
>[1] stats graphics  grDevices utils datasets  methods base
>
>loaded via a namespace (and not attached):
>[1] compiler_3.6.2
> >
>
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Re: [R-SIG-Mac] Saving a *.R file hangs R GUI under certain sequences of operations

[Jeff Newmiller]

Are you really entering an asterisk as part of the file name? That sounds like 
an extremely bad idea.

On October 23, 2019 3:13:48 PM PDT, Bryan Hanson  wrote:
>Duncan…
>
>I’m creating a new file. The menu item is “New Document”.   I called it
>*.R to distinguish it from “New Rd Document”, and since when you
>attempt to save it the suggested name is “untitled.R”.
>
>I don’t see anything in the console.  When I click an existing folder
>in the dialog, there is a brief delay and then the pinwheel, then it’s
>stuck.
>
>Bryan
>
>> On Oct 23, 2019, at 5:39 PM, Duncan Murdoch
> wrote:
>> 
>> On 23/10/2019 4:32 p.m., Bryan Hanson wrote:
>>> I have found a sequence of actions that causes the R GUI on Mac to
>hang:
>>> 1. Launch R GUI.
>>> 2. Open an empty *.R file via the button or menu or shortcut.
>> 
>> Could you clarify this:  Are you opening an existing file that is
>empty, or creating a new document?  I don't see any way to specify *.R
>in the former, and I don't see a problem with the latter.  A bit more
>below...
>> 
>>> 3. Add something to the file.
>>> 4. Save the file via menu or shortcut (technically a Save as…).  In
>the save dialog box:
>>>   a. If you save in whatever directory is pointing to, everything
>works fine.
>>>   b. If you attempt to change the directory, for instance by
>clicking on the icon for a folder w/i the current directory, one gets
>the pinwheel of death and R must be forced to quit.
>>> Can anyone else reproduce this?
>>> Bryan
>>> sessionInfo:
>>> R version 3.6.1 (2019-07-05)
>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>> Running under: macOS Mojave 10.14.6
>> 
>> I'm using the same R, but macOS High Sierra 10.13.6.
>> 
>> At some point in the exercise I saw this warning in the console:
>> 
>> objc[27995]: Class FIFinderSyncExtensionHost is implemented in both
>/System/Library/PrivateFrameworks/FinderKit.framework/Versions/A/FinderKit
>(0x7fffadb52cd0) and
>/System/Library/PrivateFrameworks/FileProvider.framework/OverrideBundles/FinderSyncCollaborationFileProviderOverride.bundle/Contents/MacOS/FinderSyncCollaborationFileProviderOverride
>(0x112670cd8). One of the two will be used. Which one is undefined.
>> 
>> It might be that in the newer MacOS this is fatal.
>> 
>> Duncan Murdoch
>> 
>>> Matrix products: default
>>> BLAS:  
>/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
>>> LAPACK:
>/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>> attached base packages:
>>> [1] stats graphics  grDevices utils datasets  methods
>>> [7] base
>>> loaded via a namespace (and not attached):
>>> [1] compiler_3.6.1
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>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>
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Re: [R-SIG-Mac] libcurl

[Jeff Newmiller]

If your goal is to interoperate with Python (esp. when using numpy and friends) 
then Anaconda is actually a good option... just learn how activate a conda 
environment before doing anything within that ecosystem and remember that each 
conda environment you create will be independent of all others. [1] Sadly, it 
is just a PITA if you are not looking for those interoperability benefits and 
fail to get on the conda tool bandwagon, so don't take this as advocating for 
Anaconda in general.

FWIW I run both the standard distribution of R and an Anaconda distribution on 
the same machine, and only use the Anaconda version when I have to... but I 
have avoided installing R (or any custom Python libraries) into the default 
Anaconda environment, which may be a key point that makes this work.

[1] https://samrelton.wordpress.com/2015/07/02/rconda/amp/

On February 25, 2019 5:28:58 PM PST, robin hankin  
wrote:
>Simon, thanks for this.  Can we add your comment to the mac os x FAQ
>please?What is the recommended way to install libcurl?
>
>My feeling is that I have somehow messed up my system so badly that
>reimaging is the only way forward.
>
>hankin.ro...@gmail.com
>
>
>
>hankin.ro...@gmail.com
>
>
>
>
>On Tue, Feb 26, 2019 at 12:32 PM Simon Urbanek
> wrote:
>>
>> You're apparently using anaconda - it means you have to activate it
>first because it doesn't include paths in its binaries so ti won't work
>without explicit path override. Also note that anaconda is by design
>incompatible with the system libraries, so you'll have to make sure
>everything you use comes from anacoda or else it won't work. I'd very
>strongly suggest not using anaconda when compiling - it pretty much
>only works if you use their binaries but nothing else will.
>>
>> Cheers,
>> Simon
>>
>>
>> > On Feb 24, 2019, at 7:28 PM, robin hankin 
>wrote:
>> >
>> > thanks for this Peter, my config.log file looks like this:
>> >
>> > configure:42615: result: yes
>> > configure:42629: checking if libcurl is version 7 and >= 7.22.0
>> > configure:42658: gcc -o conftest  -g -O2
>> > -I/Users/rhankin/anaconda3/include -I/usr/local/include
>> > -I/usr/local/include  -L/usr/local/lib conftest.c
>> > -L/Users/rhankin/anaconda3/lib -lcurl -lssh2 -lssh2 -lssl -lcrypto
>> > -lssl -lcrypto -lgssapi_krb5 -lresolv -lz -L/usr\
>> > /local/lib -lpcre2-8 -lpcre -llzma -lbz2 -lz -licucore -ldl -lm 
>-liconv >&5
>> > configure:42658: $? = 0
>> > configure:42658: ./conftest
>> > dyld: Library not loaded: @rpath/libcurl.4.dylib
>> >  Referenced from: /Users/rhankin/Downloads/R-devel/./conftest
>> >  Reason: image not found
>> > ./configure: line 2254: 73408 Abort trap: 6  
>./conftest$ac_exeext
>> > configure:42658: $? = 134
>> > configure: program exited with status 134
>> > configure: failed program was:
>> > | /* confdefs.h */
>> > | #define PACKAGE_NAME "R"
>> > | #define PACKAGE_TARNAME "R"
>> >
>> >
>> >
>> > Best wishes
>> >
>> >
>> > Robin
>> >
>> >
>> > hankin.ro...@gmail.com
>> >
>> >
>> >
>> > hankin.ro...@gmail.com
>> >
>> >
>> >
>> >
>> > On Mon, Feb 25, 2019 at 11:41 AM peter dalgaard 
>wrote:
>> >>
>> >> It doesn't usually happen on 10.13.6... Best guess is that somehow
>you are picking up an older library (e.g. in /usr/local/lib) even if
>you are using curl-config from a newer version.
>> >>
>> >> The detective work needed could take off from config.log, region
>around this:
>> >>
>> >> configure:39937: checking if libcurl is version 7 and >= 7.22.0
>> >> configure:39966: gcc -arch x86_64 -o conftest -g -O2  
>-I/usr/local/include  -L/usr/local/lib conftest.c -lcurl -lpcre -llzma
>-lbz2 -lz -licucore -lm  -liconv >&5
>> >> configure:39966: $? = 0
>> >> configure:39966: ./conftest
>> >> configure:39966: $? = 0
>> >> configure:39976: result: yes
>> >>
>> >> That's for a succesful build, a failed one will usually give more
>info including the failing program code.
>> >>
>> >> -pd
>> >>
>> >>> On 24 Feb 2019, at 22:45 , robin hankin 
>wrote:
>> >>>
>> >>> Hi,  macos 10.13.6, trying to compile 3.6.0, revision 76152.
>> >>>
>> >>> ./configure
>> >>> [snip]
>> >>>
>> >>> checking for curl-config...
>/Users/rhankin/anaconda3/bin/curl-config
>> >>> checking libcurl version ... 7.63.0
>> >>> checking curl/curl.h usability... yes
>> >>> checking curl/curl.h presence... yes
>> >>> checking for curl/curl.h... yes
>> >>> checking if libcurl is version 7 and >= 7.22.0... no
>> >>> configure: error: libcurl >= 7.22.0 library and headers are
>required
>> >>> with support for https
>> >>>
>> >>> if we have libcurl 7.63, as it says in the output, why the error?
> How
>> >>> to proceed?
>> >>>
>> >>> hankin.ro...@gmail.com
>> >>>
>> >>> ___
>> >>> R-SIG-Mac mailing list
>> >>> R-SIG-Mac@r-project.org
>> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> >>
>> >> --
>> >> Peter Dalgaard, Professor,
>> >> Center for Statistics, Copenhagen Business School
>> >> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> >> 

Re: [R-SIG-Mac] [R] R and Java 10 ➜ rJava not able to build

[Jeff Newmiller]

I am not a Mac user, but I do use Linux and I would recommend not running R 
with sudo unless you are an admin ninja. That defensive practice would render 
the answer to your question moot.

It is possible that your problem may have started with inappropriate use of 
sudo in configuring java, but configuring Java is not on-topic here.
-- 
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On March 27, 2018 12:25:33 PM PDT, Luis Puerto  wrote:
>Hi! 
>
>I’m on macOS 10.13.3 and just installed the new Java 10 using Homebrew
>Cask. I also have installed R with Homebrew. Everything seems to work
>fine, however I just get different outputs if I run sudo R CMD
>javareconf or R CMD javareconf. With sudo I get pointed to Java 9 and
>without sudo I get pointed to Java 10. I really don’t know why. 
>
>Without sudo:
>
>$ R CMD javareconf 
>  
>Java interpreter :
>/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/java
>Java version : 10
>Java home path   :
>/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home
>Java compiler:
>/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/javac
>Java headers gen.: /usr/bin/javah
>Java archive tool:
>/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/jar
>Non-system Java on macOS
>
>trying to compile and link a JNI program
>detected JNI cpp flags: -I$(JAVA_HOME)/include
>-I$(JAVA_HOME)/include/darwin
>detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
>/usr/local/opt/llvm/bin/clang 
>-I/usr/local/Cellar/r/3.4.4/lib/R/include -DNDEBUG
>-I/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/include
>-I/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/include/darwin
>-I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC 
>-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c conftest.c -o
>conftest.o
>/usr/local/opt/llvm/bin/clang++ -dynamiclib
>-Wl,-headerpad_max_install_names -undefined dynamic_lookup
>-single_module -multiply_defined suppress -L/usr/local/opt/gettext/lib
>-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib
>-L/usr/local/Cellar/r/3.4.4/lib/R/lib -L/usr/local/opt/gettext/lib
>-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -o
>conftest.so conftest.o
>-L/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/lib/server
>-ljvm -L/usr/local/Cellar/r/3.4.4/lib/R/lib -lR -lintl -Wl,-framework
>-Wl,CoreFoundation
>
>
>JAVA_HOME:
>/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home
>Java library path: $(JAVA_HOME)/lib/server
>JNI cpp flags: -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/darwin
>JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
>Updating Java configuration in /usr/local/Cellar/r/3.4.4/lib/R
>override rw-r--r--  root/admin for
>/usr/local/Cellar/r/3.4.4/lib/R/etc/Makeconf? (y/n [n]) y
>override rw-r--r--  root/admin for
>/usr/local/Cellar/r/3.4.4/lib/R/etc/ldpaths? (y/n [n]) y
>Done.
>With sudo:
>
>$ sudo R CMD javareconf
>  
>Java interpreter :
>/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/bin/java
>Java version : 9.0.4
>Java home path   :
>/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home
>Java compiler:
>/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/bin/javac
>Java headers gen.:
>/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/bin/javah
>Java archive tool:
>/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/bin/jar
>Non-system Java on macOS
>
>trying to compile and link a JNI program
>detected JNI cpp flags: -I$(JAVA_HOME)/include
>-I$(JAVA_HOME)/include/darwin
>detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
>/usr/local/opt/llvm/bin/clang 
>-I/usr/local/Cellar/r/3.4.4/lib/R/include -DNDEBUG
>-I/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/include
>-I/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/include/darwin
>-I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC 
>-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c conftest.c -o
>conftest.o
>/usr/local/opt/llvm/bin/clang++ -dynamiclib
>-Wl,-headerpad_max_install_names -undefined dynamic_lookup
>-single_module -multiply_defined suppress -L/usr/local/opt/gettext/lib
>-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib
>-L/usr/local/Cellar/r/3.4.4/lib/R/lib -L/usr/local/opt/gettext/lib
>-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -o
>conftest.so conftest.o
>-L/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home/lib/server
>-ljvm -L/usr/local/Cellar/r/3.4.4/lib/R/lib -lR -lintl -Wl,-framework
>-Wl,CoreFoundation
>
>
>JAVA_HOME:
>/Library/Java/JavaVirtualMachines/jdk-9.0.4.jdk/Contents/Home
>Java library path: $(JAVA_HOME)/lib/server
>JNI cpp flags: -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/darwin
>JNI linker flags :