Re: [R-SIG-Mac] Quanteda on mac with M2 advice

[David Winsemius]

On 5/3/24 05:26, Elyse Thulin wrote:

Hi, all,

Can someone point me to any resources for figuring out how to run quanteda
on my m2 mac?



Seems like going to the "URL:" entry in the DESCRIPTION file would be 
the obvious first place to try.



--

David.



Thanks!
Elyse



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Re: [R-SIG-Mac] R 4.3.1 fails on Mac OS X Sonoma

[David Winsemius]

Neither of you have mentioned anything about the need for reinstallation of 
Xquartz. Was that done?

— 
David. 

Sent from my iPhone

> On Oct 1, 2023, at 10:02 AM, William Revelle  wrote:
> 
> Rodney,
> 
> Thanks for your quick reply.
> 
> It turns out this is just a problem with the base R  for Mac graphics window 
> (which is to say, the version I like).  I can still use R-studio (which I 
> don’t like as much).  
> 
> I can wait patiently for a patch to the Mac version while using R-Studio.
> 
> That way I don’t have to go through the hassle of trying to reinstall 13.x 
> and dumping 14.0.
> 
> Bill
> 
> 
>> On Oct 1, 2023, at 11:22 AM, Sparapani, Rodney  wrote:
>> 
>> Hi Bill:
>> Well, I am usually pretty cautious about this.  I don’t move to the
>> next release until R is ready.  For Ventura, it took quite awhile
>> before that happened.  Sorry
>> -- 
>> Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His
>> Vice President, Wisconsin Chapter of the American Statistical Association
>> Institute for Health and Equity, Division of Biostatistics
>> Medical College of Wisconsin, Milwaukee Campus
>> From: R-SIG-Mac  on behalf of William 
>> Revelle 
>> Date: Sunday, October 1, 2023 at 11:19 AM
>> To: r-sig-mac@r-project.org 
>> Subject: [R-SIG-Mac] R 4.3.1 fails on Mac OS 1
>> ATTENTION: This email originated from a sender outside of MCW. Use caution 
>> when clicking on links or opening attachments.
>> 
>> 
>> Dear Mac users of R and developers.
>> 
>> 
>> I recently updated to the Sonoma OS for Mac  (14.0)  and it has a serious 
>> problem for graphics.
>> 
>> plot(1:10) creates a graphic window but I can not switch back to the console 
>> window using either command-1 or the mouse.
>> 
>> Anybody else having this problem?  Any suggestions for a patch?
>> 
>> I am running a MacBook Pro with M1 Max.
>> 
>> Bill
>> 
>> 
>> (resent because of bad mail address)
>> William Revellepersonality-project.org/revelle.html
>> Professorpersonality-project.org
>> Department of Psychology 
>> https://urldefense.com/v3/__http://www.wcas.northwestern.edu/psych/__;!!H8mHWRdzp34!6ejyrhAkkZDmz7rI2sf4kna51unncXyvnIMc9xJ12h6pMfylTwNR8QeWq8RTUAAR7NMYOzH5OX_pOA$
>> Northwestern University
>> https://urldefense.com/v3/__http://www.northwestern.edu/__;!!H8mHWRdzp34!6ejyrhAkkZDmz7rI2sf4kna51unncXyvnIMc9xJ12h6pMfylTwNR8QeWq8RTUAAR7NMYOzE95PXdSw$
>> Use R for psychology personality-project.org/r
>> It is 90 seconds to midnight
>> https://urldefense.com/v3/__http://www.thebulletin.org__;!!H8mHWRdzp34!6ejyrhAkkZDmz7rI2sf4kna51unncXyvnIMc9xJ12h6pMfylTwNR8QeWq8RTUAAR7NMYOzFQyyeCDA$
>> 
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> 
> 
> William Revellepersonality-project.org/revelle.html
> Professorpersonality-project.org
> Department of Psychology www.wcas.northwestern.edu/psych/
> Northwestern Universitywww.northwestern.edu/
> Use R for psychology personality-project.org/r
> It is 90 seconds to midnightwww.thebulletin.org
> 
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Re: [R-SIG-Mac] R 4.3.1 fails to load

[David Winsemius]

And I forgot to ask  what's in your .Rprofile file?

On 7/22/23 13:29, Carl Witthoft wrote:

Neither R.app Gui nor R from command line will work.
This is 4.3.1 ,  MacOS 13.4  on an x86 (and yes, that's the version I 
installed).


 Heres the error traceback from the command line:

*** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
 1: as.bigz(NA)
 2: fun(libname, pkgname)
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch(fun(libname, pkgname), error = identity)
 7: runHook(".onLoad", env, package.lib, package)
 8: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck 
= vI[[j]])

 9: asNamespace(ns)
10: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)

11: loadNamespace(package, lib.loc)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch({    attr(package, "LibPath") <- which.lib.loc ns <- 
loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = 
pos, deps, exclude, include.only)}, error = function(e) {    P <- if 
(!is.null(cc <- conditionCall(e))) paste(" in", 
deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace 
load failed for %s%s:\n %s", sQuote(package), P, 
conditionMessage(e)) if (logical.return && !quietly) 
message(paste("Error:", msg), domain = NA)    else stop(msg, call. = 
FALSE, domain = NA)})

16: library(cgwtools)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace




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Re: [R-SIG-Mac] R 4.3.1 fails to load

[David Winsemius]

On 7/22/23 13:29, Carl Witthoft wrote:

Neither R.app Gui nor R from command line will work.
This is 4.3.1 ,  MacOS 13.4  on an x86 (and yes, that's the version I 
installed).


 Heres the error traceback from the command line:

*** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
 1: as.bigz(NA)



Seems you are executing a non-base function call when this cascade of 
calls leading to the segfault begins. Perhaps this is something being 
done by an out-of-date .Rdata file load? Did you remove all `.Rdata` 
files from the potential sites of auto-loading? Did you run 
`update.packages(checkBuilt=TRUE)` after the R installation.



Best of luck---

David.


 2: fun(libname, pkgname)
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch(fun(libname, pkgname), error = identity)
 7: runHook(".onLoad", env, package.lib, package)
 8: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck 
= vI[[j]])

 9: asNamespace(ns)
10: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)

11: loadNamespace(package, lib.loc)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch({    attr(package, "LibPath") <- which.lib.loc ns <- 
loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = 
pos, deps, exclude, include.only)}, error = function(e) {    P <- if 
(!is.null(cc <- conditionCall(e))) paste(" in", 
deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace 
load failed for %s%s:\n %s", sQuote(package), P, 
conditionMessage(e)) if (logical.return && !quietly) 
message(paste("Error:", msg), domain = NA)    else stop(msg, call. = 
FALSE, domain = NA)})

16: library(cgwtools)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace




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Re: [R-SIG-Mac] Serious problem with R on macOS

[David Winsemius]

On 6/8/23 09:33, DePaolis, Fernando wrote:

�well�here it goes again�it failed just now. This is the message I get when I 
try to run R from the command line on my mac



You were advised to try using Disk Utility / First Aid. Have you done so 
yet?


 (You are getting intermittent errors accessing base packages. So this 
may just be a flakey disk sector.)



--

David.




fernandodepaolis@MacBook-Pro-2 ~ % R



R version 4.3.0 (2023-04-21) -- "Already Tomorrow"

Copyright (C) 2023 The R Foundation for Statistical Computing

Platform: x86_64-apple-darwin20 (64-bit)



R is free software and comes with ABSOLUTELY NO WARRANTY.

You are welcome to redistribute it under certain conditions.

Type 'license()' or 'licence()' for distribution details.



   Natural language support but running in an English locale



R is a collaborative project with many contributors.

Type 'contributors()' for more information and

'citation()' on how to cite R or R packages in publications.



Type 'demo()' for some demos, 'help()' for on-line help, or

'help.start()' for an HTML browser interface to help.

Type 'q()' to quit R.



During startup - Warning message:

package �datasets� in options("defaultPackages") was not found

Error in loadNamespace(name) : object 'pkgInfo' not found

In addition: Warning message:

In loadNamespace(name) : package �compiler� has no 'package.rds' in Meta/

Fatal error: unable to initialize the JIT



There was no �message� of any sort when trying to run R.app. There was a brief 
flickering (like quick blinking) but nothing else.

Thank you!


Fernando DePaolis, Ph.D.
Dean of Academic Operations & Integration
Associate Professor
Middlebury Institute of International 
Studies at Monterey
--
[Sent from Outlook for Mac �MacBook Pro]
My working hours (US Pacific time zone) may not be your working hours. Please 
do not feel obligated to respond outside your normal work hours, unless 
otherwise indicated.

From: DePaolis, Fernando 
Date: Wednesday, June 7, 2023 at 9:13 PM
To: Simon Urbanek 
Cc: r-sig-mac@r-project.org 
Subject: Re: [R-SIG-Mac] Serious problem with R on macOS
Hi Simon,
You're right, I didn't post it...I'll make sure I do next time it 
happens...it's working fine for now...

Thank you.



Fernando DePaolis
Dean Of Academic Operations & Integration
Middlebury Institute of International Studies

Sent from Outlook for iOS. Apologies for any typos.


From: Simon Urbanek 
Sent: Wednesday, June 7, 2023 6:08:12 PM
To: DePaolis, Fernando 
Cc: r-sig-mac@r-project.org 
Subject: Re: [R-SIG-Mac] Serious problem with R on macOS

[You don't often get email from simon.urba...@r-project.org. Learn why this is 
important at https://aka.ms/LearnAboutSenderIdentification ]

Fernando,

I don't think you posted the error you get when running R on the command line - 
can you copy/paste what you get when running R in the Terminal? Similarly, do 
you also get an error when running the R app (in Applications)?

Cheers,
Simon




On 6/06/2023, at 6:32 AM, DePaolis, Fernando  wrote:

Uwe Ligges (from CRAN sys admin) recommended that I post this to the list.



Thank you.







Fernando DePaolis, Ph.D.
Dean of Academic Operations & Integration

Associate Professor

Middlebury Institute of International Studies at Monterey
--

[Sent from Outlook for Mac �MacBook Pro]

My working hours (US Pacific time zone) may not be your working hours. Please 
do not feel obligated to respond outside your normal work hours, unless 
otherwise indicated.



From: DePaolis, Fernando 
Date: Monday, June 5, 2023 at 10:19 AM
To: cran-sysad...@r-project.org 
Subject: Serious problem with R on macOS

Hello,

For a few months now, I�ve been having an odd and rather annoying problem. I 
use RStudio and it frequently cannot start R, producing the error message 
attached below. This is clearly not the, as I worked on it the night before or 
even just a few hours earlier. What is clear is that R is not available on my 
system, although all the files are still there (in 
/Library/Frameworks/R.framework). It could be that a critical file becomes 
corrupted, or the system can�t find it. I have not been able to determine 
whether that is the case, or which file could be affected. I might have 
re-installed R dozens of times in the last month. This is something that never 
happened in the previous more than 15 years of using R.



I�ve tried everything I can think of, and the problem persists�and haven�t 
found any satisfactory feedback online either.

Have you ever heard of a problem like this? Or do you have any suggestions?



Thank you so much for your support.












Fernando DePaolis, Ph.D.
Dean of Academic Operations & Integration

Associate Professor

Middlebury Institute of International Studies at 

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

[David Winsemius]

On 9/29/21 11:17 AM, 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 would reinstall XQuartz. The `plot(0)` command changes the focus from 
R to XQuartz, so the processing of the typed letter "a" is being handled 
by that system function rather than by R. On my 3 year-old MacAir 
running R 4.1.0 typing a letter with the system focus on a plot window 
produces a mild error tone, as does typing the delete key. (No crash 
after returning focus to the R process by mouse-clicking in the Terminal 
window.



--

David



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] checking whether the C compiler works... no

[David Winsemius]

The   C compiler aka clang is not the same as the C++ compiler. 

Why don’t you install the pre-compiled version.

— 
David

Sent from my iPhone

> On Sep 6, 2021, at 12:44 AM, Naresh Gurbuxani  
> wrote:
> When trying to install library reshape2, I get below messages.  But I do 
> have some other packages which depend upon C compiler (e.g., Rcpp).  How can 
> this problem be fixed?
> 
> Thanks,
> Naresh
> 
> Messages when trying to install reshape2:
>> install.packages("reshape2", repos = "https://cran.r-project.org;)
> Installing package into ‘/usr/local/lib/R/4.1/site-library’
> (as ‘lib’ is unspecified)
> also installing the dependencies ‘stringi’, ‘stringr’
> 
> trying URL 'https://cran.r-project.org/src/contrib/stringi_1.7.4.tar.gz'
> Content type 'application/x-gzip' length 7599762 bytes (7.2 MB)
> ==
> downloaded 7.2 MB
> 
> trying URL 'https://cran.r-project.org/src/contrib/stringr_1.4.0.tar.gz'
> Content type 'application/x-gzip' length 135777 bytes (132 KB)
> ==
> downloaded 132 KB
> 
> trying URL 'https://cran.r-project.org/src/contrib/reshape2_1.4.4.tar.gz'
> Content type 'application/x-gzip' length 37307 bytes (36 KB)
> ==
> downloaded 36 KB
> 
> * installing *source* package ‘stringi’ ...
> ** package ‘stringi’ successfully unpacked and MD5 sums checked
> ** using staged installation
> checking for R_HOME... /usr/local/Cellar/r/4.1.1/lib/R
> checking for R... /usr/local/Cellar/r/4.1.1/lib/R/bin/R
> checking for endianness... little
> checking for R >= 3.1.0 for C++11 use... yes
> checking for R < 3.4.0 for CXX1X flag use... no
> checking for cat... /bin/cat
> checking for local ICUDT_DIR... icu69/data
> checking for gcc... /usr/local/opt/llvm/bin/clang -fopenmp
> checking whether the C compiler works... no
> configure: error: in 
> `/private/var/folders/97/5377j5_d207fshvjz_pz7szwgn/T/RtmpCOKBRx/R.INSTALL64822d9c75a/stringi':
> configure: error: C compiler cannot create executables
> See `config.log' for more details
> ERROR: configuration failed for package ‘stringi’
> * removing ‘/usr/local/lib/R/4.1/site-library/stringi’
> ERROR: dependency ‘stringi’ is not available for package ‘stringr’
> * removing ‘/usr/local/lib/R/4.1/site-library/stringr’
> ERROR: dependency ‘stringr’ is not available for package ‘reshape2’
> * removing ‘/usr/local/lib/R/4.1/site-library/reshape2’
> 
> The downloaded source packages are in
>
> ‘/private/var/folders/97/5377j5_d207fshvjz_pz7szwgn/T/RtmpDOExfD/downloaded_packages’
> Warning messages:
> 1: In install.packages("reshape2", repos = "https://cran.r-project.org;) :
>  installation of package ‘stringi’ had non-zero exit status
> 2: In install.packages("reshape2", repos = "https://cran.r-project.org;) :
>  installation of package ‘stringr’ had non-zero exit status
> 3: In install.packages("reshape2", repos = "https://cran.r-project.org;) :
>  installation of package ‘reshape2’ had non-zero exit status
> 
> My session info:
>> sessionInfo()
> R version 4.1.1 (2021-08-10)
> Platform: x86_64-apple-darwin20.5.0 (64-bit)
> Running under: macOS Big Sur 11.5.2
> 
> Matrix products: default
> BLAS/LAPACK: /usr/local/Cellar/openblas/0.3.17/lib/libopenblasp-r0.3.17.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_4.1.1 tools_4.1.1 
> 
> 
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Re: [R-SIG-Mac] Difficulties with R-Studio

[David Winsemius]

Happens to me all the time on a Linux installation using Rstudio.   There’s 
some sort of mouse action that pulls up a screen to do something with the xml 
or http substrate of the IDE. The R.app IDE is much less unpredictable. 

— 
David. 

Sent from my iPhone

> On Aug 15, 2021, at 7:54 AM, Gábor Csárdi  wrote:
> 
> This has never happened to me (except when I touch the touchpad
> accidentally :), so unfortunately I don't have an answer, just some
> tips.
> 
> RStudio has an online forum. If you don't get an answer here in a
> couple of days, you might want to try to ask your question there:
> https://community.rstudio.com/
> 
> You can try the latest daily build from https://dailies.rstudio.com/
> 
> RStudio has an API that R code (including R packages) can use to
> switch panels. Is it possible that you are using some R package that
> does that?
> 
> Gabor
> 
>> On Sun, Aug 15, 2021 at 4:04 PM  wrote:
>> 
>> I use the R-Studio app, Version 1.4.1103, for my R programming work on
>> macOS Big Sur version 11.5. I find that the app switches from one window
>> to another (within the app) sometimes, without a request that it do so.
>> Sometimes I work for a long session and this does not occur, but at
>> other times it does, yet I cannot find an explanation.  I had the same
>> problem with previous versions of R. The problem is annoying, but the
>> app is so good I have been putting up with it.
>> 
>> Do others face the same problem? I suppose it is likely an issue within
>> R-Studio, since it does not occur with any other app. But is there
>> anything I can do in my macOS configuration to solve the problem?
>> 
>> Philip
>> 
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Re: [R-SIG-Mac] Some introductory questions

[David Winsemius]

> On Sep 6, 2020, at 4:31 PM, Mike Feher  wrote:
> 
> Greetings,
> 
> As I’m getting familiar with R, I have some basic questions that I thought
> of to shoot to useRs:

You should review the ListInfo material. Most of these questions have nothing 
to do with the Mac version of R.
> 
> 1. When looking up library functions, symbols, objects, etc., is there a
> Google-style “global search” capability for all that is available with my
> installation?  Or is it just all accessible via navigating the help() tree?

You should be trying help.search() or it's shortcut `??`

> 2. Are these objects, etc. stored on disk somewhere, or are they only
> accessible via the interfaces?  For example, I would be interested to see
> the source code for the demo examples to learn how to do certain things, if
> this is possible.  (It appeared as if the code for each demo that is
> executed as part of the ‘demo()’ command displayed in my R console, but I
> just want to be sure about this.)

Not sure what you are considering "interfaces". Pretty much everything is on 
disk.


> 3. How does one restore a saved session automatically?  Is that saved in a
> file or files anywhere on the local filesystem?

They are generally automagically reloaded if you exited in a manner that saved 
them and restart from the same directory. The state of the previous session is 
stored in a special .Rdata file which is invisible to Macs and Windoze machines 
by default. You need to modify your system file manage to see them. Read about 
.Rdata files and how to use them. 

> 4. I tried to read in a set of dummy space-delimited data saved in an
> absolute path on my computer, but it would not work.

Sadder words were never written, but most of the sadness derives from the 
failure to efficiently communicate what "it" actually was.

>  I tried something in
> another path that did not have a subfolder with a space in it (I.e. I plan
> on storing my data in a folder called “R Documents” or something similar)
> and that didn’t work either, so I’m still wondering whether or not (a)
> things have to be in the library location (it seems like you could
> customize that) and (b) whether R recognizes spaces in file paths.

R does recognize space on a Mac. You need to provide actual code. I cannot 
intuit what errors you are making from this description.

> 
> Please keep in mind that I am consulting the documentation first, but maybe
> not doing a global Google search for examples of these things.  I’m trying
> to remember to do both as I go along, so as not to bother everyone.
> 
> Regards and thanks in advance,
> Mike
> 
>   [[alternative HTML version deleted]]
> 
Well you are not reading the documentation for this list (or any of the several 
R-project list) since you are posting in HTML.

Hth;
David.
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Re: [R-SIG-Mac] [External] Re: crash due to rgl and base graphics conflict

[David Winsemius]

On 8/3/20 6:25 AM, Duncan Murdoch wrote:
Thanks. Looks like I should update.  I'm looking forward to the 
crashes...

Fortune candidate.


Duncan Murdoch

On 03/08/2020 9:21 a.m., Marc Schwartz wrote:

Hi,

Just installed rgl and I get the same crash and error message from 
the original post below, running R from the CLI.


If I run R from within ESS (what I normally use), I get:

   Process R abort trap: 6 at Mon Aug  3 09:15:32 2020

If I run R from R.app (the default macOS GUI), the command runs fine 
and I get the graphic.


I am running R 4.0.2 (2020-06-22) on macOS 10.15.6.

R was cleanly installed, and XQuartz (2.7.11) was updated afterwards.

Regards,

Marc Schwartz


On Aug 3, 2020, at 9:05 AM, Duncan Murdoch 
 wrote:


I just got a message from someone else using Catalina 10.15.5 who 
still gets a crash from


library(rgl)
plot(1:10)

I don't have Catalina, and haven't seen it.  Has anyone else?

Duncan Murdoch

On 31/05/2020 4:44 p.m., Richard M. Heiberger wrote:

I upgraded last night to Catalina 10.15.5 (19F96).
The crash has gone away and that example now works normally.
On Fri, May 29, 2020 at 3:25 PM Richard M. Heiberger 
 wrote:


my 12:35 email and the attached tmp.txt are from the Terminal.app,
No emacs/ESS involved.

On Fri, May 29, 2020 at 3:13 PM Duncan Murdoch 
 wrote:


On 29/05/2020 2:21 p.m., Richard M. Heiberger wrote:
I attempted to update xquartz when I updated to Catalina, and 
the same

number is still the current version number.

Here is a related issue, attached tmp2.txt is the R transcript.
The interesting thing here is that rgl.quit() prevents rgl from 
being

reattached.


Generally speaking rgl doesn't want to be reloaded in the same R
session:  detaching it doesn't clean up everything. That's not
something that I'd put any priority on fixing, whereas I would 
look at

the problems you're having on startup if I could reproduce them.

I wonder if ESS is involved somehow:  your sessionInfo listed 
ESSR on

the search list.  Do you have the same issues with plain R from the
console, or R.app?


Is there an rgl equivalent for dev.cur()?


There's rgl.cur().  rgl only supports two kinds of devices:  on a 
Mac or

Linux they'd be displayed as glX or null.  Windows also supports the
null device (which doesn't display anything), and a different one to
display within R:  I forget how the name is displayed.

It might be that you'll need to set options(rgl.useNULL) before 
starting
rgl, and only use the null device.  It won't display anything in 
R, but

allows you to call rglwidget() for a display in a browser.

Duncan Murdoch

On Fri, May 29, 2020 at 1:51 PM Duncan Murdoch 
 wrote:


On 29/05/2020 12:35 p.m., Richard M. Heiberger wrote:

I have the same Xquartz as you.


I'd guess it should be updated.  Generally XQuartz needs 
updates with
every MacOS release, and your 10.15.4 is two releases further 
along than

my 10.13.6.


I have rgl-0.100.50 from CRAN


You could update that, but I doubt if it would make any 
difference.



Apple is macOS Catalina, Version 10.15.4
Do you need hardware information?
MacBpok Air (13 -inch, Mid 2012)
Processor 2GHz Dual-Core Intel Core i7
Memory 8 GB 1600 MHz DDR3
Graphics Intel HD Graphics 4000 1536 MB


I think the XQuartz issue is most likely to help, but if it 
doesn't, I'm

not sure what I could suggest:  I don't have Catalina.

Duncan Murdoch



from the Terminal App:
The Apple Crash Report is in the attached tmp.txt
I didn't send it to Apple.

R version 4.0.0 (2020-04-24) -- "Arbor Day"

Copyright (C) 2020 The R Foundation for Statistical Computing

Platform: x86_64-apple-darwin17.0 (64-bit)


R is free software and comes with ABSOLUTELY NO WARRANTY.

You are welcome to redistribute it under certain conditions.

Type 'license()' or 'licence()' for distribution details.


 Natural language support but running in an English locale


R is a collaborative project with many contributors.

Type 'contributors()' for more information and

'citation()' on how to cite R or R packages in publications.


Type 'demo()' for some demos, 'help()' for on-line help, or

'help.start()' for an HTML browser interface to help.

Type 'q()' to quit R.



library(rgl)



plot(1:10)


2020-05-29 12:30:00.536 R[24961:3275889] *** Assertion 
failure in BOOL 
NSScreenConfigurationInvalidateIfNeededForReason(_NSScreenConfigurationUpdateReason)(), 
/AppleInternal/BuildRoot/Library/Caches/com.apple.xbs/Sources/AppKit/AppKit-1894.40.150/AppKit.subproj/NSScreenConfiguration.m:473 



2020-05-29 12:30:00.543 R[24961:3275889] *** Terminating app 
due to

uncaught exception 'NSInternalInconsistencyException', reason:
'NSScreen reconfig must only happen on the main thread.'

*** First throw call stack:

(

0   CoreFoundation 0x7fff371698d7
__exceptionPreprocess + 250

1   libobjc.A.dylib 0x7fff6ff47a9e
objc_exception_throw + 48

2   CoreFoundation 0x7fff37192bb0
+[NSException raise:format:arguments:] + 88

3   Foundation 0x7fff398de456

Re: [R-SIG-Mac] HDF4 Support for GDAL

[David Winsemius]

Have you attempted installing and using 
https://cran.r-project.org/web/packages/gdalUtils/gdalUtils.pdf

I don't have any experience with it but it says it can extract 
sub_datasets from HDF4


-- 

David.

On 6/24/20 7:00 AM, Matt Strimas-Mackey wrote:
> Hi all,
>
> The MODIS package uses gdalwarp to process MODIS data. Previously it called 
> gdalwarp via system(), however, it recently switched to using the function 
> sf::gdal_utils() to access gdalwarp, which is more portable and avoids users 
> having to install GDAL on their system. The catch is that HDF4 support is 
> required for processing MODIS data. The Windows sf binaries already come with 
> HDF4 support for GDAL, however, the Mac OS binaries do not, which makes the 
> MODIS package unusable on Mac unless sf is compiled from source, which is 
> challenging. More context on this issue is available here: 
> https://github.com/MatMatt/MODIS/issues/78
>
> In the above GH issue, Tim Salabim suggested this listserv would be a good 
> place to connect with someone that could get HDF4 support into the Mac OS 
> binaries. Any suggestions for how to proceed would be appreciated!
>
> Thanks!
>
> Matt
>
>   [[alternative HTML version deleted]]
>
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Re: [R-SIG-Mac] pdf font issue for square bracket

[David Winsemius]

On 6/3/20 6:40 AM, Koenker, Roger W wrote:

If someone could advise me on how to get the “]” and “(“ characters to look
remotely like they should in the following code, I would be eternally grateful.
Having experimented with pdf.options() and the vfont option for text() I’m at
a loss.  Rather than “]” I see only a black rectangle.



Somehow one of your your default system font has become corrupted 
probably the "Times" instance. You can often fix this by examining the 
font in Font Book.app. You often find that there is a duplicate instance 
of a system installed font and that deleting the offending instance 
withing Font Book.app will cure the problem. Look  first at the "serif" 
entry to postscriptFonts():


names( postscriptFonts() )

postscriptFonts()[ "serif" ]

--

David.




sessionInfo()

R version 3.6.2 Patched (2019-12-12 r77564)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

# PDF Font issue for "]"
v <- c(-0.59103110,0.02659437,-1.51655310,-1.36265335,
1.17848916,-0.93415132,1.32360565,0.62491779,-0.04572296,-1.00412058)
y <- c(1,1,1,0,1,0,1,0,1,0)
pdf("One.pdf", height = 2, width = 7)
plot(v[y==1],sample(c(-1,1),sum(y),replace = TRUE), type = "n",
  axes = FALSE,  xlim = range(v),xlab = "", ylab = "")
text(v[y==1],rep(0,sum(y)), "]", cex = 2)
abline(h = 0)
text(v[y==0],rep(0,n-sum(y)), "(", cex = 2, col=2)
segments(c(vo[1]-0.1,vo)[klmax],c(0,0),c(vo[1]-0.1,vo)[klmax+1],c(0,0),
 col = 2, lwd = 2)  # (use right end point to represent interval)
dev.off()

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Re: [R-SIG-Mac] Cannot compile Fortran on macOS

[David Winsemius]

On 5/19/20 1:54 PM, Kevin Ushey wrote:

The main thing that stands out to me in that error:

   Referenced from: /usr/local/lib/libquadmath.0.dylib
   Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib

R bundles its own copies of libquadmath and libgcc:

kevinushey@Kevins-MBP:/Library/Frameworks/R.framework/Resources/lib
$ ls -la
total 19120
drwxrwxr-x  11 root  admin  352 Apr 24 03:23 .
drwxrwxr-x  18 root  admin  576 Apr 29 11:46 ..
-rwxrwxr-x   1 root  admin  4070896 Apr 24 03:23 libR.dylib
drwxrwxr-x   3 root  admin   96 Apr 24 03:22 libR.dylib.dSYM
-rwxrwxr-x   1 root  admin   201472 Apr 24 03:23 libRblas.dylib
drwxrwxr-x   3 root  admin   96 Apr 24 03:22 libRblas.dylib.dSYM
-rwxrwxr-x   1 root  admin  2181472 Apr 24 03:23 libRlapack.dylib
drwxrwxr-x   3 root  admin   96 Apr 24 03:22 libRlapack.dylib.dSYM
-rw-rw-r--   1 root  admin   160624 Apr 24 03:23 libgcc_s.1.dylib
-rwxrwxr-x   1 root  admin  2851008 Apr 24 03:23 libgfortran.5.dylib
-rwxrwxr-x   1 root  admin   309648 Apr 24 03:23 libquadmath.0.dylib

  which should normally be used during the link step. However, versions in
/usr/local/lib are being discovered instead, which presumably aren't
compatible.



Kevin;


Is that the sort of situation that might be cause by mixing 
homebrew-compiled and R.Framework-compiled packages?



David.



The simplest fix is (likely) to move those files out of the way. Otherwise,
you'd likely have to muck around with Makevars / Makeconf to adjust the
linker flags so the correct versions of these libraries are found.

Best,
Kevin

On Tue, May 19, 2020 at 6:46 AM Adelchi Azzalini 
wrote:


Hi.
In essence, my problem is that I cannot install a package which requires
Fortran-77 compilation on my Mac.

More in detail, this is my own package 'mnormt' which exists on CRAN since
2006; it is currently at version 1.5-7. It has been developed in successive
versions on a Linux machine, where it compiles with no problems. The macOS
and MS-windows versions are created on CRAN, where it passes all pertaining
checks.

Now, in the new pandemic world, I need create a new version of the
package, but working from home, hence using my Mac laptop instead of the
Linux desktop as in the past. Unfortunately, compilation or loading does
not work. If I run

  R CMD check mnormt_1.5-7.tar.gz

first I get a bunch of warning messages such as

Warning: Possible change of value in conversion from REAL(8) to INTEGER(4)
  [-Wconversion]
Warning: ‘lxchng’ may be used uninitialized in this function
[-Wmaybe-uninitialized]
Warning: Label 10 at (1) defined but not used [-Wunused-label]

and finally it crashes with

Error: package or namespace load failed for ‘mnormt’:
  .onLoad failed in loadNamespace() for 'mnormt', details:
   call: dyn.load(file, DLLpath = DLLpath, ...)
   error: unable to load shared object
'/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so':

dlopen(/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so,
6): Symbol not found: ___addtf3
   Referenced from: /usr/local/lib/libquadmath.0.dylib
   Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib
  in /usr/local/lib/libquadmath.0.dylib
Error: loading failed

Needless to say, I have no idea what this "addtf3" is or it should be.
There is no such a symbol in the Fortran code.

I believe to have installed all ingredients indicated at
https://mac.r-project.org/tools/
See the list below with details about my system and other installed tools.

Any suggestions for sorting this out?

Adelchi Azzalini


---
Installation info:

R> R.version
_
platform   x86_64-apple-darwin17.0
arch   x86_64
os darwin17.0
system x86_64, darwin17.0
status
major  4
minor  0.0
year   2020
month  04
day24
svn rev78286
language   R
version.string R version 4.0.0 (2020-04-24)
nickname   Arbor Day

--- macOS Mojave 10.14.6

--- Xcode version 11.3.1

--- Fortran

[aa@mac-2013:~] gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran

COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin18/8.2.0/lto-wrapper
Target: x86_64-apple-darwin18
Configured with: ../gcc-8.2.0/configure --prefix=/usr/local/gfortran
--with-gmp=/Users/fx/devel/gcc/build_package/deps
--enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin18
--disable-multilib --with-native-system-header-dir=/usr/include
--with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
Thread model: posix
gcc version 8.2.0 (GCC)

[aa@mac-2013:~] echo $PATH

.:/Users/aa/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin/:/usr/X11R6/bin:/opt/local/bin:/Library/TeX/texbin:/usr/local/gfortran/bin

-- other tools indicated at https://mac.r-project.org/tools/
xz-5.2.5/  is installed
PCRE2 10.34 built with --disable-jit
bzip2 Version 1.0.6 is installed

Re: [R-SIG-Mac] Cannot compile Fortran on macOS

[David Winsemius]

On 5/19/20 1:46 PM, Yoshihiko Baba via R-SIG-Mac wrote:
> Adelchi,
>
> Why don’t you try Fink version of R?
>
> Fink build mnormt on R 4.0 as well (although it is experimental).
> https://github.com/fink/fink-distributions/issues/623


This should be considered contrary to recommended practice: From the 
page for macOS tools that was cited by the OP we see:


"Although it is possible to compile R using tools from other package 
managers such as Homebrew, MacPorts or Fink, such binaries are by 
definition incompatible with macOS native libraries and applications. If 
you choose one of those package managers, make sure you 
compile/everything/using those tools including R and all packages and 
libraries you intend to use."


I think it should have been offered as advice to only be followed by 
persons with great experience in compiling and building packages on Macs.

Best;

David

>
> Fink allows you to install different versions of R (3.6, 3.5, 3.4, 3.3, 3.2 
> and 3.1).
>
> For different versions, CRAN packages are separately installed 
> (/sw/lib/R/3.6/site-library  and so on).
>
>
>> 2020/05/19 22:45、Adelchi Azzalini のメール:
>>
>> Hi.
>> In essence, my problem is that I cannot install a package which requires 
>> Fortran-77 compilation on my Mac.
>>
>> More in detail, this is my own package 'mnormt' which exists on CRAN since 
>> 2006; it is currently at version 1.5-7. It has been developed in successive 
>> versions on a Linux machine, where it compiles with no problems. The macOS 
>> and MS-windows versions are created on CRAN, where it passes all pertaining 
>> checks.
>>
>> Now, in the new pandemic world, I need create a new version of the package, 
>> but working from home, hence using my Mac laptop instead of the Linux 
>> desktop as in the past. Unfortunately, compilation or loading does not work. 
>> If I run
>>
>> R CMD check mnormt_1.5-7.tar.gz
>>
>> first I get a bunch of warning messages such as
>>
>> Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) 
>>   [-Wconversion]
>> Warning: ‘lxchng’ may be used uninitialized in this function 
>> [-Wmaybe-uninitialized]
>> Warning: Label 10 at (1) defined but not used [-Wunused-label]
>>
>> and finally it crashes with
>>
>> Error: package or namespace load failed for ‘mnormt’:
>> .onLoad failed in loadNamespace() for 'mnormt', details:
>>   call: dyn.load(file, DLLpath = DLLpath, ...)
>>   error: unable to load shared object 
>> '/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so':
>>   
>> dlopen(/Users/aa/SW-aa/Pkg-mnormt/mnormt.Rcheck/00LOCK-mnormt/00new/mnormt/libs/mnormt.so,
>>  6): Symbol not found: ___addtf3
>>   Referenced from: /usr/local/lib/libquadmath.0.dylib
>>   Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib
>> in /usr/local/lib/libquadmath.0.dylib
>> Error: loading failed
>>
>> Needless to say, I have no idea what this "addtf3" is or it should be. There 
>> is no such a symbol in the Fortran code.
>>
>> I believe to have installed all ingredients indicated at 
>> https://mac.r-project.org/tools/
>> See the list below with details about my system and other installed tools.
>>
>> Any suggestions for sorting this out?
>>
>> Adelchi Azzalini
>>
>>
>> ---
>> Installation info:
>>
>> R> R.version
>>_
>> platform   x86_64-apple-darwin17.0
>> arch   x86_64
>> os darwin17.0
>> system x86_64, darwin17.0
>> status
>> major  4
>> minor  0.0
>> year   2020
>> month  04
>> day24
>> svn rev78286
>> language   R
>> version.string R version 4.0.0 (2020-04-24)
>> nickname   Arbor Day
>>
>> --- macOS Mojave 10.14.6
>>
>> --- Xcode version 11.3.1
>>
>> --- Fortran
>>
>> [aa@mac-2013:~] gfortran -v
>> Using built-in specs.
>> COLLECT_GCC=gfortran
>> COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin18/8.2.0/lto-wrapper
>> Target: x86_64-apple-darwin18
>> Configured with: ../gcc-8.2.0/configure --prefix=/usr/local/gfortran 
>> --with-gmp=/Users/fx/devel/gcc/build_package/deps 
>> --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin18 
>> --disable-multilib --with-native-system-header-dir=/usr/include 
>> --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
>> Thread model: posix
>> gcc version 8.2.0 (GCC)
>>
>> [aa@mac-2013:~] echo $PATH
>> .:/Users/aa/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin/:/usr/X11R6/bin:/opt/local/bin:/Library/TeX/texbin:/usr/local/gfortran/bin
>>
>> -- other tools indicated at https://mac.r-project.org/tools/
>>xz-5.2.5/  is installed
>>PCRE2 10.34 built with --disable-jit
>>bzip2 Version 1.0.6 is installed
>>
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Re: [R-SIG-Mac] mac.r-project.org links are broken

[David Winsemius]

On 1/25/20 2:05 PM, Jonathon Love wrote:

in the interim - does anyone know if this content is mirrored somewhere?



They appear functional. Have you checked recently?


--

David



with thanks


On 26/1/20 05:31, peter dalgaard wrote:

Yes, they are on a plane to New Zealand... (more or less, anyway)

Expect things to get tidied up during next week.

-pd


On 25 Jan 2020, at 12:08 , Jonathon Love  wrote:

hi,

in case no-one had noticed yet, the following links are broken:

http://mac.r-project.org/src/

http://mac.r-project.org/libs/

as linked from:

https://cran.r-project.org/bin/macosx/tools/

earlier today, the SSL on mac.r-project.org was broken too, but that 
appears to be working now.


cheers

jonathon

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Re: [R-SIG-Mac] segfault with raster package

[David Winsemius]

You should realize that postings on Nabble are not necessarily going to have 
reached the “true” mailing list. 

— 
David. 

Sent from my iPhone

> On Dec 16, 2019, at 1:53 PM, Duncan Murdoch  wrote:
> 
>> On 16/12/2019 4:34 p.m., Marc Girondot via R-SIG-Mac wrote:
>> When I load the last version of raster package in MacOS, I get a segfault:
>> This is similar to the problem described here:
>> https://r.789695.n4.nabble.com/Raster-package-crash-with-segmentation-fault-td4759487.html
>> or here
>> https://github.com/rspatial/raster/issues/63
>> The last working version for me is the 2.5-8 installed with:
>> require(devtools)
>> install_version("raster", version = "2.5-8", repos
>> ="http://cran.us.r-project.org;)
>> I would like know if the problem with the raster package is common in
>> macOSX or if there is something special for me.
> 
> library(raster) works fine for me.  This loads 3.0-7.  I'm on MacOS 10.13.6, 
> likely older than whatever you are using.
> 
> Duncan Murdoch
> 
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Re: [R-SIG-Mac] Installing the "jpeg" package?

[David Winsemius]

On 11/1/19 8:03 PM, Spencer Graves wrote:

Hello, All:


  How can I get the dev files for libjpeg installed under macOS 
10.15.1 Catalina?



You probably have the right tools, but it wouldn't hurt to check:


https://cran.r-project.org/bin/macosx/tools/


And have you installed the libjpeg library from the /libs/ directory?


http://mac.r-project.org/libs/

The directions for installation from a Terminal session are at the 
bottom of the page.


I have not updated to Catalina, but the error message suggested that 
jpeglib.h could not be found.



Hope this helps;

David






  Simon Urbanek, the maintainer for the "jpeg" package, said I 
need them to install the "jpeg" package from sources.  I'm unable to 
get that package to install either as a binary or from sources;  see 
below.



  Suggestions?
  Thanks,
  Spencer Graves


> update.packages()
jpeg :
 Version 0.1-8 installed in 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library

 Version 0.1-8.1 available at https://cran.rstudio.com
Update? (Yes/no/cancel) y

  There is a binary version available but the
  source version is later:
 binary  source needs_compilation
jpeg  0.1-8 0.1-8.1  TRUE

Do you want to install from sources the package which needs 
compilation? (Yes/no/cancel) y

installing the source package ‘jpeg’

trying URL 'https://cran.rstudio.com/src/contrib/jpeg_0.1-8.1.tar.gz'
Content type 'application/x-gzip' length 18116 bytes (17 KB)
==
downloaded 17 KB

* installing *source* package ‘jpeg’ ...
** package ‘jpeg’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   
-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk 
-I/usr/local/include  -fPIC  -Wall -g -O2  -c read.c -o read.o

In file included from read.c:1:
./rjcommon.h:11:10: fatal error: 'jpeglib.h' file not found
#include 
 ^~~
1 error generated.
make: *** [read.o] Error 1
ERROR: compilation failed for package ‘jpeg’
* removing 
‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/jpeg’
* restoring previous 
‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/jpeg’


The downloaded source packages are in
‘/private/var/folders/mh/mrm_14nx19g13lsnj9zmvwjrgn/T/Rtmp8GMSE7/downloaded_packages’ 


Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘jpeg’ had non-zero exit status

> update.packages()
jpeg :
 Version 0.1-8 installed in 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library

 Version 0.1-8.1 available at https://cran.rstudio.com
Update? (Yes/no/cancel) y

  There is a binary version available but the
  source version is later:
 binary  source needs_compilation
jpeg  0.1-8 0.1-8.1  TRUE

Do you want to install from sources the package which needs 
compilation? (Yes/no/cancel) n
trying URL 
'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/jpeg_0.1-8.tgz'

Content type 'application/x-gzip' length 389601 bytes (380 KB)
==
downloaded 380 KB


The downloaded binary packages are in
/var/folders/mh/mrm_14nx19g13lsnj9zmvwjrgn/T//Rtmp8GMSE7/downloaded_packages 



> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.1

Matrix products: default
BLAS: 
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.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
[6] methods   base

other attached packages:
[1] bssm_0.1.8

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2   lattice_0.20-38  assertthat_0.2.1
 [4] dplyr_0.8.3  crayon_1.3.4 R6_2.4.0
 [7] grid_3.6.1   gtable_0.3.0 magrittr_1.5
[10] coda_0.19-3  scales_1.0.0 ggplot2_3.2.1
[13] pillar_1.4.2 rlang_0.4.1  lazyeval_0.2.2
[16] rstudioapi_0.10  diagis_0.1.3-1   tools_3.6.1
[19] glue_1.3.1   purrr_0.3.3  munsell_0.5.0
[22] compiler_3.6.1   pkgconfig_2.0.3  colorspace_1.4-1
[25] tidyselect_0.2.5 gridExtra_2.3    tibble_2.1.3

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Re: [R-SIG-Mac] Problems running rJava in MacOS

[David Winsemius]

Was there a reason to refuse the system's offer to override?


--

David.

On 9/4/19 4:30 PM, Manuel Spínola wrote:

Dear list members,

I am having troubles running rJava.

MacOS 10.14.6
R 3.6.1
rJava 0.9-11
jdk 11.0.4


library(rJava)

Error: package or namespace load failed for ‘rJava’:
  .onLoad failed in loadNamespace() for 'rJava', details:
   call: dyn.load(file, DLLpath = DLLpath, ...)
   error: unable to load shared object
'/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so':

dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so,
6): Library not loaded:
/Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
   Referenced from:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so
   Reason: image not found

I run in terminal

(base) Manuels-MacBook-Pro:~ manuelspinola$ R CMD javareconf

Java interpreter : /usr/bin/java

Java version : 11.0.4

Java home path   :
/Library/Java/JavaVirtualMachines/jdk-11.0.4.jdk/Contents/Home

Java compiler: /usr/bin/javac

Java headers gen.: /usr/bin/javah

Java archive tool: /usr/bin/jar


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

clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/Library/Java/JavaVirtualMachines/jdk-11.0.4.jdk/Contents/Home/include
-I/Library/Java/JavaVirtualMachines/jdk-11.0.4.jdk/Contents/Home/include/darwin
-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-I/usr/local/include  -fPIC  -Wall -g -O2  -c conftest.c -o conftest.o

clang -dynamiclib -Wl,-headerpad_max_install_names -undefined
dynamic_lookup -single_module -multiply_defined suppress
-L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
conftest.so conftest.o
-L/Library/Java/JavaVirtualMachines/jdk-11.0.4.jdk/Contents/Home/lib/server
-ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation



JAVA_HOME:
/Library/Java/JavaVirtualMachines/jdk-11.0.4.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 : -L$(JAVA_HOME)/lib/server -ljvm

Updating Java configuration in /Library/Frameworks/R.framework/Resources

override rw-r--r--  root/admin for
/Library/Frameworks/R.framework/Resources/etc/Makeconf? (y/n [n])




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Re: [R-SIG-Mac] Problem generating an SVG file from a CSV file on the Mac - updated with test script and test data

[David Winsemius]

Run (in an R console session)


update.packages(checkBuilt=TRUE, ask=FALSE)


On a Mac the .Rprofile file would normally be invisible (to the Finder 
anyway) and you would need to tell Finder to display "dot-files". 
(Search with Google for how to do that.).



--

David

On 8/20/19 8:35 PM, Richard Fuhr wrote:

I am an R newbie and when I upgraded to 3.6 I did nothing in addition (and I 
didn’t reinstall any packages).
I don’t have a file in my home directory named .Rprofile or anything similar to 
that name.
---
Richard Fuhr
206-524-8049  land line
206-491-5640  cell phone
https://richardfuhr.neocities.org 






On Aug 20, 2019, at 8:31 PM, Roy Mendelssohn - NOAA Federal 
 wrote:

Looks similar to mine.  I am just guessing here,  but did you upgrade to 3.6 
and not reinstall all of your packages?  Or have you checked if you have 
something in .Rprofile or the like that is setting the path to something that 
conflicts?

-Roy



On Aug 20, 2019, at 8:20 PM, Richard Fuhr  wrote:

Roy,

Thanks for testing it.

I am running MacOS Mojave 10.14.6

When I invoke the commands interactively from within R, the system also hangs 
when I try to create the SVG file.

I don’t see an error message; it just hangs.

Invoking sessionInfo() yields the following:



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

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

Random number generation:
RNG: Mersenne-Twister
Normal:  Inversion
Sample:  Rounding

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_3.6.1
Thanks,

Richard








On Aug 20, 2019, at 8:11 PM, Roy Mendelssohn - NOAA Federal 
 wrote:

Worked on my machine.  I think you need to give more info,  including what 
version of the OS you are running,  and from within R the result of 
'sessionInfo()',  also what happens if you run it from within R,  rather than 
from RScript.

HTH,

-Roy



On Aug 20, 2019, at 7:27 PM, Richard Fuhr  wrote:

I am sending this message again to the distribution list, and this time I am
* making this message plain text
* attaching an R file called FuhrTest.R
* attaching an input file called FuhrTest.csv ( a small file but it does 
duplicate the problem)

The purpose of the code is to read the csv file, which consists of a few dates 
and weights and to generate plots of the data using various formats.

The formats PDF, JPG, PNG and SVG get successfully generated on my Linux 
machine running the Pop!_OS distribution.

However, on my Mac, using the identical R script, the system hangs when trying 
to generate an SVG plot.

I have also duplicated the problem interactively.

If the lines to generate an SVG file are commented out on the Mac, then the R 
code runs as desired.

I invoked the script via the command

Rscript FuhrTest.R

So if someone can take a look at this case when running R on a Mac, that would 
be very helpful.

It would be nice to be able to generate SVG files using R on my Mac that 
represent data plots


Thanks,



Richard Fuhr
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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 Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.


**
"The contents of this message do not reflect any position of the U.S. Government or 
NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.



[[alternative HTML version deleted]]

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Re: [R-SIG-Mac] point size in svg

[David Winsemius]

> On Jun 23, 2019, at 10:04 PM, Spencer Graves  
> wrote:
> 
> Hello, All:
> 
> 
>   I'm unable to control font size in plots created by "svg" in R 3.6.0 on 
> macOS Mojave 10.14.5.  Consider the following:
> 
> 
> svg('cex-svg.svg')
> cex. <- 5
> plot(1:2, cex.axis=cex.)
> text(1:2, 1:2, c('as', 'DF'),
>   cex=cex.)
> dev.off()
> 
> 
>   When I run this in R 3.5.2 under Windows 7, it works fine.  In R 3.6.0 
> under macOS 10.14.5, I get tiny fonts.  Changing "cex." has no impact on the 
> result.  A question about this to R-Devel generated replies from Peter 
> Langfelder and David Winsemius, who noted that it worked fine under Ubuntu 
> 18.04 (supposedly with R 3.15.2 -- probably R 3.5.2, but I'm not sure).

You should be sure.

>  I experimented with the width, height, pointsize and family arguments for 
> "svg", without solving this problem.

With R version 3.5.1 (2018-07-02) -- "Feather Spray" on OS X 10.11.6 I am 
unable to reproduce. My Mac hardware is considered well past (Apple) end of 
life despite its functionality, so I cannot upgrade my OS. I'm attaching the 
file that is the result so Spencer can view it, although I suspect it will be 
scrubbed by the mail-server.



-- 
David.

> 
> 
>   I believe this problem is fairly recent:  I just looked at svg files I 
> created with R on this same computer probably last fall, and the font size 
> looks reasonable -- better than what I get today.  I'm not 100 percent sure, 
> but I think I was able to control the font size with the cex and cex.axis 
> arguments with those earlier versions of R and macOS.
> 
> 
>   Suggestions?
>   Thanks,
>   Spencer Graves
> 
> 
> #  This script worked as expected on Windows:
> sessionInfo()
> R version 3.5.2 (2018-12-20)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 7 x64 (build 7601) Service Pack 1
> 
> Matrix products: default
> 
> locale:
>   [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
> 
> attached base packages:
>   [1] stats graphics  grDevices utils datasets
> [6] methods   base
> 
> loaded via a namespace (and not attached):
>   [1] compiler_3.5.2 tools_3.5.2yaml_2.2.0
> 
> 
> # It failed on macOS:
> 
> 
>>> sessionInfo()
>>> R version 3.6.0 (2019-04-26)
>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>> Running under: macOS Mojave 10.14.5
>>> 
>>> Matrix products: default
>>> BLAS: 
>>> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.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
>>> [6] methods   base
>>> 
>>> other attached packages:
>>> [1] Ecdat_0.3-2 Ecfun_0.2-1
>>> 
>>> ______
>>> r-de...@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> 
>> __
>> r-de...@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> 
> 
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David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law





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Re: [R-SIG-Mac] CRAN OSX rgdal binaries 1.3-3 and 1.3-4

[David Winsemius]

> On Aug 5, 2018, at 6:28 AM, Roger Bivand  wrote:
> 
> The CRAN OSX rgdal binaries 1.3-3 and 1.3-4 do not include PROJ datum 
> metadata files. To check whether your OSX binary rgdal has the PROJ datum 
> metadata files, try:
> 
> library(rgdal)
> projNAD()
> 
> If they are not present, consider running this snippet:
> 
> pkg <- "rgdal"
> exdir <- file.path(system.file(package=pkg), "proj")
> list.files(exdir)
> tf <- tempfile()
> fl <- "http://download.osgeo.org/proj/proj-datumgrid-1.7.zip;
> download.file(fl, tf)
> unzip(tf, exdir=exdir)
> list.files(exdir)
> 
> Hope this helps,

I think a lot of us Mac useRs install the KyngChaos super-package (GDAL, GEOS, 
PROJ, SQLite and UnixImageIO framework described and linked to at:

https://www.kyngchaos.com/software/frameworks

I see that another version was released earlier this year which I had not 
installed, so I only had GDAL 2.1. I got this when loading `rgdal` version 
1.3-1 (and I see that I'm a couple of minor versions behind. so I'll update) I 
did wonder that the message about linking to `sp` ver 1.2-7 didn't match my 
current version of `sp` which is 1.3-1

library(rgdal)
Loading required package: sp
rgdal: version: 1.3-1, (SVN revision 747)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
 Path to GDAL shared files: 
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rgdal/gdal
 GDAL binary built with GEOS: FALSE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: 
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rgdal/proj
 Linking to sp version: 1.2-7 

# When I updated rgdal the startup message from rgdal now says:

Linking to sp version: 1.3-1 

# ... despite the fact that I installed 1.3-4

That's never cause a problem that I've noticed, but I'm not even a moderate 
user of GIS so am not stressing the interlocking programs very hard. 

I then mounted the newer super-package 2.2 disk image from KyngChaos and ran 
the pkg-installer to see if I could break anything. Nothing seems to be broken, 
but the rgdal package still reports loading GDAL 2.1.3, despite GDAL 2.2 being 
the more recent version and the one to which the 'Current' folder-symlink is 
pointing. The PROJ framework now has a new 4B directory but the startup message 
for the PROJ.4 runtime is also unchanged.

> 

> Roger
> 
> -- 
> Roger Bivand
> Department of Economics, Norwegian School of Economics,
> Helleveien 30, N-5045 Bergen, Norway.
> voice: +47 55 95 93 55; e-mail: roger.biv...@nhh.no
> http://orcid.org/-0003-2392-6140
> https://scholar.google.no/citations?user=AWeghB0J=en
> 
> _______
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David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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[R-SIG-Mac] SOLVED Re: java version, perhaps related to ggplot2

[David Winsemius]

> On May 24, 2018, at 8:45 PM, David Winsemius  wrote:
> 
> 
> 
>> On May 24, 2018, at 1:47 PM, Simon Urbanek  
>> wrote:
>> 
>> You need to configure R to match your Java using R CMD javareconf.
>> 
>> The CRAN machine uses JDK 1.9 which was the default until Java 10 was 
>> released recently. If you use something else, you have to configure R 
>> accordingly.
>> 
>> Also I strongly recommend using rJava 0.9-10 since it works around some 
>> issue with Java on macOS and with Java 10.
> 
> Oracle has pulled the JDK 1.9 and only is only offering version 10:
> 
> http://www.oracle.com/technetwork/java/javase/downloads/index.html

 
Today I accepted the Oracle offer to update my installation of Java on my High 
Sierra machine to their version 10.0.2 (build 10.0.2-13  ( from their build 
10.0.2-10 ) and after 

user$ sudo R CMD javareconf 

... rJava 0.9-10 loads without complaint.

-- 
David.


> 
> 
> -- 
> David
>> 
>> Cheers,
>> Simon
>> 
>> 
>> 
>> 
>> 
>>> On May 23, 2018, at 7:50 PM, David Winsemius  wrote:
>>> 
>>> 
>>> 
>>>> On May 22, 2018, at 1:36 AM, Richard M. Heiberger  wrote:
>>>> 
>>>> sI have Macintosh High Sierra 10.13.4
>>>> and R_3.5.0
>>>> 
>>>> I am attempting to R CMD build and check my package microplot against
>>>> the imminent ggplot2_2.2.1.9000
>>>> 
>>> 
>>> I have a new High Sierra Machine with a System that was ported over from an 
>>> earlier version of the OS. I've installed R 3.5.0.  I tried installing 
>>> micro plot from binary without error, but when I try to load the rJava 
>>> library I was getting an error with the old Java version 151, so I accepted 
>>> the Oracle offer of installing version 171 downloaded from the Java 
>>> website, but I'm also seeing:
>>> 
>>> library(rJava)
>>> Error: package or namespace load failed for ‘rJava’:
>>> .onLoad failed in loadNamespace() for 'rJava', details:
>>> call: dyn.load(file, DLLpath = DLLpath, ...)
>>> error: unable to load shared object 
>>> '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
>>> dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so,
>>>  6): Library not loaded: 
>>> /Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home/lib/server/libjvm.dylib
>>> Referenced from: 
>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
>>> Reason: image not found
>>> 
>>> 
>>> There is a folder  /Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk, but 
>>> nothing named with a jdk-9 prefix
>>> 
>>> 
>>> S
>>> Best;
>>> 
>>> David.
>>> 
>>>> The build fails with messages
>>>> 
>>>> ** byte-compile and prepare package for lazy loading
>>>> Error : .onLoad failed in loadNamespace() for 'rJava', details:
>>>> call: dyn.load(file, DLLpath = DLLpath, ...)
>>>> error: unable to load shared object
>>>> '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
>>>> dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so,
>>>> 6): Library not loaded:
>>>> /Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home/lib/server/libjvm.dylib
>>>> Referenced from:
>>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
>>>> Reason: image not found
>>>> ERROR: lazy loading failed for package ‘microplot’
>>>> 
>>>> Indeed I do not have Java 9, I have Java 8, which the Java updater
>>>> says is current (171).
>>>> The java site
>>>> http://www.oracle.com/technetwork/java/javase/overview/index.html
>>>> seems to want to give me Java 10 (not Java 9), and the discussion on
>>>> this R-sig-mac list
>>>> [R-SIG-Mac] R and Java 10 ➜ rJava not able to build
>>>> beginning March 29 seems to say 8 is still correct.  As suggested
>>>> there I looked at R-admin for 3.5.0
>>>> and discover "The situation with Java support on macOS is messy".
>>>> I attempted the suggested workaround
>>>> JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk/Contents/Home
>>>> and got the same message as above.
>>>> 
>>>> I need guidance as to the next steps I should take.
>>>> 
>>>> Rich
>>>> 
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>>> 
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>>> 
>> 
> 
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'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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Re: [R-SIG-Mac] java version, perhaps related to ggplot2

[David Winsemius]

> On May 24, 2018, at 1:47 PM, Simon Urbanek <simon.urba...@r-project.org> 
> wrote:
> 
> You need to configure R to match your Java using R CMD javareconf.
> 
> The CRAN machine uses JDK 1.9 which was the default until Java 10 was 
> released recently. If you use something else, you have to configure R 
> accordingly.
> 
> Also I strongly recommend using rJava 0.9-10 since it works around some issue 
> with Java on macOS and with Java 10.

Oracle has pulled the JDK 1.9 and only is only offering version 10:

http://www.oracle.com/technetwork/java/javase/downloads/index.html


-- 
David
> 
> Cheers,
> Simon
> 
> 
> 
> 
> 
>> On May 23, 2018, at 7:50 PM, David Winsemius <dwinsem...@comcast.net> wrote:
>> 
>> 
>> 
>>> On May 22, 2018, at 1:36 AM, Richard M. Heiberger <r...@temple.edu> wrote:
>>> 
>>> sI have Macintosh High Sierra 10.13.4
>>> and R_3.5.0
>>> 
>>> I am attempting to R CMD build and check my package microplot against
>>> the imminent ggplot2_2.2.1.9000
>>> 
>> 
>> I have a new High Sierra Machine with a System that was ported over from an 
>> earlier version of the OS. I've installed R 3.5.0.  I tried installing micro 
>> plot from binary without error, but when I try to load the rJava library I 
>> was getting an error with the old Java version 151, so I accepted the Oracle 
>> offer of installing version 171 downloaded from the Java website, but I'm 
>> also seeing:
>> 
>> library(rJava)
>> Error: package or namespace load failed for ‘rJava’:
>> .onLoad failed in loadNamespace() for 'rJava', details:
>> call: dyn.load(file, DLLpath = DLLpath, ...)
>> error: unable to load shared object 
>> '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
>> dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so,
>>  6): Library not loaded: 
>> /Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home/lib/server/libjvm.dylib
>> Referenced from: 
>> /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
>> Reason: image not found
>> 
>> 
>> There is a folder  /Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk, but 
>> nothing named with a jdk-9 prefix
>> 
>> 
>> S
>> Best;
>> 
>> David.
>> 
>>> The build fails with messages
>>> 
>>> ** byte-compile and prepare package for lazy loading
>>> Error : .onLoad failed in loadNamespace() for 'rJava', details:
>>> call: dyn.load(file, DLLpath = DLLpath, ...)
>>> error: unable to load shared object
>>> '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
>>> dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so,
>>> 6): Library not loaded:
>>> /Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home/lib/server/libjvm.dylib
>>> Referenced from:
>>> /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
>>> Reason: image not found
>>> ERROR: lazy loading failed for package ‘microplot’
>>> 
>>> Indeed I do not have Java 9, I have Java 8, which the Java updater
>>> says is current (171).
>>> The java site
>>> http://www.oracle.com/technetwork/java/javase/overview/index.html
>>> seems to want to give me Java 10 (not Java 9), and the discussion on
>>> this R-sig-mac list
>>>  [R-SIG-Mac] R and Java 10 ➜ rJava not able to build
>>> beginning March 29 seems to say 8 is still correct.  As suggested
>>> there I looked at R-admin for 3.5.0
>>> and discover "The situation with Java support on macOS is messy".
>>> I attempted the suggested workaround
>>> JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk/Contents/Home
>>> and got the same message as above.
>>> 
>>> I need guidance as to the next steps I should take.
>>> 
>>> Rich
>>> 
>>> ___
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>>> R-SIG-Mac@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
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>> 
> 

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Re: [R-SIG-Mac] java version, perhaps related to ggplot2

[David Winsemius]

> On May 22, 2018, at 1:36 AM, Richard M. Heiberger  wrote:
> 
> sI have Macintosh High Sierra 10.13.4
> and R_3.5.0
> 
> I am attempting to R CMD build and check my package microplot against
> the imminent ggplot2_2.2.1.9000
> 

I have a new High Sierra Machine with a System that was ported over from an 
earlier version of the OS. I've installed R 3.5.0.  I tried installing micro 
plot from binary without error, but when I try to load the rJava library I was 
getting an error with the old Java version 151, so I accepted the Oracle offer 
of installing version 171 downloaded from the Java website, but I'm also seeing:

library(rJava)
Error: package or namespace load failed for ‘rJava’:
 .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object 
'/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
  
dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so,
 6): Library not loaded: 
/Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home/lib/server/libjvm.dylib
  Referenced from: 
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
  Reason: image not found


There is a folder  /Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk, but 
nothing named with a jdk-9 prefix


S
Best;

David.

> The build fails with messages
> 
> ** byte-compile and prepare package for lazy loading
> Error : .onLoad failed in loadNamespace() for 'rJava', details:
>  call: dyn.load(file, DLLpath = DLLpath, ...)
>  error: unable to load shared object
> '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
>  
> dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so,
> 6): Library not loaded:
> /Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home/lib/server/libjvm.dylib
>  Referenced from:
> /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
>  Reason: image not found
> ERROR: lazy loading failed for package ‘microplot’
> 
> Indeed I do not have Java 9, I have Java 8, which the Java updater
> says is current (171).
> The java site
> http://www.oracle.com/technetwork/java/javase/overview/index.html
> seems to want to give me Java 10 (not Java 9), and the discussion on
> this R-sig-mac list
>[R-SIG-Mac] R and Java 10 ➜ rJava not able to build
> beginning March 29 seems to say 8 is still correct.  As suggested
> there I looked at R-admin for 3.5.0
> and discover "The situation with Java support on macOS is messy".
> I attempted the suggested workaround
> JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk/Contents/Home
> and got the same message as above.
> 
> I need guidance as to the next steps I should take.
> 
> Rich
> 
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Re: [R-SIG-Mac] Generating R .pkg file for Mac Distribution

[David Winsemius]

> On May 16, 2018, at 2:40 PM, Nigel Delaney  wrote:
> 
> Hi,
> 
> Mac binaries on R are distributed as .pkg files available from CRAN
> for installation.  Does anyone know if the source script (assuming a
> script is used) that generates this pkg file is available anywhere?
> The pkg seems to contain a few elements like a postflight/postinstall
> script that I could not find in any open source repository and are not
> part of the R binaries.
> 
> We have a few users who are dealing with the fortran compiler issues
> on Mac, and were hoping to just modify the current .pkg to contain a
> few more packages, was hoping to avoid reinventing the wheel on the
> packaging scripts.
> 

Are their clang and gfortran installations up-to-date:

https://cran.r-project.org/bin/macosx/tools/


> Thanks for any help,
> Nigel
> 
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Re: [R-SIG-Mac] R 3.5.0

[David Winsemius]

It was my experience yesterday with using the old method (copy folders to new 
../library/ and use update.packages(checkBuilt=TRUE) ) that I was given the 
option to have packages with more recent updates compiled from source. I had 
anticipated the issue (time) mentioned by Simon, so I only copied over perhaps 
a third of my full complement of packages. 

Sent from my iPhone

> On Apr 25, 2018, at 11:20 AM, Roy Mendelssohn - NOAA Federal 
>  wrote:
> 
> Hi Simon:
> 
> Perfect,  thank you for the info.  One of the reasons I was asking is in 
> ~/Library/R i have a umber of packages that in fact are in CRAN but what I 
> have are the development versions.  Everything I have in 
> /Library/Frameworks/R are the CRAN versions.  It is easier for me to do the 
> ~/Library//R update myself through a script so I keep the development 
> versions.
> 
> Mostly also thanks for all of your work on the Mac version.  Much appreciated.
> 
> -Roy
> 
>> On Apr 25, 2018, at 11:10 AM, Simon Urbanek  
>> wrote:
>> 
>> Roy,
>> 
>> first, I'd recommend holding off with updating packages. Due to the number 
>> of packages, updating all of them takes quite some time, so in order to use 
>> the binaries that are built with the release version of R it will probably 
>> take at least until tomorrow that they are propagated through the mirror 
>> network. Hence you'll have to re-install them anyway if you do it now. 
>> 
>> That said, the "select packages from previous version" search function only 
>> applies to the system library - the use library is not in scope. However, 
>> where you install those packages is up to you depending on the selection in 
>> the Package Installer - the two steps are separate in the GUI.
>> 
>> Cheers,
>> Simon
>> 
>> 
>> 
>>> On Apr 25, 2018, at 11:26 AM, Roy Mendelssohn - NOAA Federal 
>>>  wrote:
>>> 
>>> Hi All:
>>> 
>>> If I remember correctly how R release numbers work,  R 3.5.0 would mean 
>>> best practice would be to re-install all packages,  is this correct?  The 
>>> Mac version has had a mechanism that does helps automate this process,  but 
>>> I have a few questions as to how this works.  Specifically:
>>> 
>>> 1.  In looking for packages to re-install, does it look just in the 
>>> /LIbrary/Frameworks/R location for packages,  or does it look in 
>>> ~/username/Library/R also?
>>> 
>>> 2.  If it does look at both locations,  does the re-install then put 
>>> everything into  /LIbrary/Frameworks/R or is present location maintained?
>>> 
>>> I ask because I have a lot of packages in ~/username/Library/R and want to 
>>> maintain things that way, so I want to be certain that I know what will 
>>> happen fi I use the built-in mechanism.
>>> 
>>> Thanks,
>>> 
>>> -Roy
>>> 
>>> 
>>> 
>>> **
>>> "The contents of this message do not reflect any position of the U.S. 
>>> Government or NOAA."
>>> **
>>> Roy Mendelssohn
>>> Supervisory Operations Research Analyst
>>> NOAA/NMFS
>>> Environmental Research Division
>>> Southwest Fisheries Science Center
>>> ***Note new street address***
>>> 110 McAllister Way
>>> Santa Cruz, CA 95060
>>> Phone: (831)-420-3666
>>> Fax: (831) 420-3980
>>> e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/
>>> 
>>> "Old age and treachery will overcome youth and skill."
>>> "From those who have been given much, much will be expected" 
>>> "the arc of the moral universe is long, but it bends toward justice" -MLK 
>>> Jr.
>>> 
>>> ___
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>> 
> 
> **
> "The contents of this message do not reflect any position of the U.S. 
> Government or NOAA."
> **
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
> ***Note new street address***
> 110 McAllister Way
> Santa Cruz, CA 95060
> Phone: (831)-420-3666
> Fax: (831) 420-3980
> e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/
> 
> "Old age and treachery will overcome youth and skill."
> "From those who have been given much, much will be expected" 
> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
> 
> ___
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> R-SIG-Mac@r-project.org
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Re: [R-SIG-Mac] HELP

[David Winsemius]

> On Mar 20, 2018, at 8:35 AM, Keith O'Hara <keith.oh...@nyu.edu> wrote:
> 
> Did you try reinstalling the mvtnorm package?
> 
> Keith
> 
>> On Mar 19, 2018, at 10:56 PM, Yonabeth Nava de Escalante 
>> <yonabet...@gmail.com> wrote:
>> 
>> I am trying to install the ‘rms’ package in my Mac OS X Yosemite 10.10.5. 
>> When I try to load the library I get this error:
>> 
>>> library(rms)
>> Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
>> there is no package called ‘mvtnorm’
>> Error: package or namespace load failed for ‘rms’
>> 
>> I tried installing the dependencies with 
>> 
>> install.packages("rms",dependencies = TRUE)
>> 
>> I also tried
>> 
>> install.packages("rms", repos=c("http://rstudio.org/_packages;, 
>> "http://cran.rstudio.com”))
>> 
>> However, I keep getting the same error. 
>>  [[alternative HTML version deleted]]

I can confirm this behavior. I load rms from startup in my .Rprofile file and 
if mvtrnorm is missing I also get:

Error: package or namespace load failed for ‘rms’ in loadNamespace(i, 
c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘mvtnorm’

To me it signals a needt to let the package maintainer know about the issue.

> maintainer("rms")
[1] "Frank E Harrell Jr <f.harr...@vanderbilt.edu>"

>> 
>> ___
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> 
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David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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Re: [R-SIG-Mac] EXT: Continuous loop when using R on MacOS Sierra with 3.4.4 GUI 1.70 El Capitan build (7507)

[David Winsemius]

> On Mar 18, 2018, at 12:19 PM, Gero, Eric (GE Digital) <eric.g...@ge.com> 
> wrote:
> 
> I have the exact same problem.  It works fine on my Mac at home, but scrolls 
> the same error message on my MacBook Pro from work.  RStudio does work fine 
> though. 

Have you tried deleting /Users/andrewb/.Rapp.history as well as 
/Users/andrewb/.Rdata?

-- 
David.
> 
> Thank you, 
> Eric
> 
> Sent from my iPhone
> 
>> On Mar 18, 2018, at 10:46 AM, Andrew Beckett <andr...@cadence.com> wrote:
>> 
>> Dear All,
>> 
>> I've been using R on my home MacBook Air for the last 3 years, but recently 
>> installed on my work MacBook Pro. Both with 3.4.3 and 3.4.4 (version in 
>> subject line) I get a continuous stream of messages (in red) in the R 
>> console when I start R:
>> 
>> 2018-03-18 11:57:25.151 R[23446:1805525] action changeColor:
>> 2018-03-18 11:57:25.151 R[23446:1805525] action changeColor:
>> 2018-03-18 11:57:25.152 R[23446:1805525] action changeColor:
>> 2018-03-18 11:57:25.153 R[23446:1805525] action changeColor:
>> 2018-03-18 11:57:25.154 R[23446:1805525] action changeColor:
>> 2018-03-18 11:57:25.154 R[23446:1805525] action changeColor:
>> 2018-03-18 11:57:25.186 R[23446:1805525] action changeColor:
>> 2018-03-18 11:57:25.186 R[23446:1805525] action changeColor:
>> 2018-03-18 11:57:25.187 R[23446:1805525] action changeColor:
>> 2018-03-18 11:57:25.188 R[23446:1805525] action changeColor:
>> 2018-03-18 11:57:25.222 R[23446:1805525] action changeColor:
>> 2018-03-18 11:57:25.222 R[23446:1805525] action changeColor:
>> 2018-03-18 11:57:25.255 R[23446:1805525] action changeColor:
>> 2018-03-18 11:57:25.255 R[23446:1805525] action changeColor:
>> 2018-03-18 11:57:25.288 R[23446:1805525] action changeColor:
>> 2018-03-18 11:57:25.288 R[23446:1805525] action changeColor:
>> 2018-03-18 11:57:25.328 R[23446:1805525] action _forceClickMonitorDidChange:
>> 2018-03-18 11:57:25.442 R[23446:1805525] action _forceClickMonitorDidChange:
>> 2018-03-18 11:57:25.442 R[23446:1805525] action _forceClickMonitorDidChange:
>> 2018-03-18 11:57:25.442 R[23446:1805525] action _forceClickMonitorDidChange:
>> 
>> Any idea what is causing this or how to fix it? I've searched with Google 
>> and also using the FAQ, plus the GitHub issues, and not found anything. It 
>> makes R unusable because any output I produce from any R commands just gets 
>> lost amongst the continuous stream of red messages. There's no clue at the 
>> top of the console - it just looks like this:
>> 
>> R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
>> Copyright (C) 2018 The R Foundation for Statistical Computing
>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>> 
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>> 
>> Natural language support but running in an English locale
>> 
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>> 
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>> 
>> [R.app GUI 1.70 (7507) x86_64-apple-darwin15.6.0]
>> 
>> [History restored from /Users/andrewb/.Rapp.history]
>> 
>> 2018-03-18 12:10:08.485 R[26425:1835450] action changeColor:
>> 2018-03-18 12:10:08.485 R[26425:1835450] action changeColor:
>> 2018-03-18 12:10:08.512 R[26425:1835450] action changeColor:
>> 2018-03-18 12:10:08.512 R[26425:1835450] action changeColor:
>> 2018-03-18 12:10:08.512 R[26425:1835450] action changeColor:
>> 2018-03-18 12:10:08.512 R[26425:1835450] action changeColor:
>> 
>> Regards,
>> 
>> Andrew.
>> 
>>   [[alternative HTML version deleted]]
>> 
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'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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Re: [R-SIG-Mac] OS X builds for R-devel

[David Winsemius]

> On Feb 27, 2018, at 1:45 AM, Alexey Sergushichev <alserg...@gmail.com> wrote:
> 
> Hi David,
> 
> My question was not about installing r-devel on Mac, but whether there are 
> plans on having the packages available on CRAN web-site. I'm asking this, 
> because Bioconductor build system depends on availability of OS X binaries of 
> some packages on CRAN.

You should specify which packages you feel are not available that should be 
available. The two references you made were to two efforts at building 
packages. One of them (re: ChemmineR) was a warning, not a report of failure. 
And it was not a warning about a missing CRAN hosted package but rather a 
warning about C code in the package itself:

---
* checking whether package ‘ChemmineR’ can be installed ... WARNING
Found the following significant warnings:
  r_wrap.cc:1689:14: warning: explicitly assigning value of variable of type 
'void *' to itself [-Wself-assign]
See ‘/Users/biocbuild/bbs-3.7-bioc/meat/ChemmineR.Rcheck/00install.out’ for 
details.
---

The other  ( re: cbaf) was a report of error, but the error was the absence on 
the build machine of the 'xlsx'-package. Why that package is missing on that 
particular machine is surely not something that the maintainers of the Mac fork 
can be expected to know. That package has been available on CRAN for many years 
and continues to be available. Its Package Description file does not indicate 
any need for compilation.


-- 
David.


> 
> --
> Alexey
> 
> On Fri, Feb 23, 2018 at 8:01 PM, David Winsemius <dwinsem...@comcast.net> 
> wrote:
> 
> > On Feb 19, 2018, at 12:27 PM, Alexey Sergushichev <alserg...@gmail.com> 
> > wrote:
> >
> > Dear all,
> >
> > Are there any plans on having package build for r-devel on CRAN? I
> > understand it's far from the highest priority but it would be good to have
> > any estimates. I'm aware of several packages on Bioconoductor-devel that
> > fail builds due to absence of binary versions of some packages (
> > http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-buildsrc.html
> > http://bioconductor.org/checkResults/devel/bioc-LATEST/cbaf/merida2-buildsrc.html
> > ).
> >
> > Thanks,
> > Alexey Sergushichev
> >
> >   [[alternative HTML version deleted]]
> 
> The fact that you post in HTML and make no effort to describe your setup 
> makes me suspect you may also have missed the instructions about installing 
> XCode and configuring R for compiling source packages. This can still be done 
> with the binary distribution versions of R and R.app, and do not require that 
> you build R from sources. See the CRAN-Mac-tools page:
> 
> https://cran.r-project.org/bin/macosx/tools/
> 
> It used to be the case that one needed Xcode and Command Line Tools 
> installed. (I do have them.) I cannot tell from the current Mac-devel page 
> whether that is still the case. I have a current version of R running in El 
> Capitan. This is my ~/.R/Makevars file:
> 
> # created by rstan at Thu Mar 19 11:26:15 2015
> CXXFLAGS = -mtune=core2 -O3 $(LTO)  #set_by_rstan
> R_XTRA_CPPFLAGS =  -I$(R_INCLUDE_DIR)   #set_by_rstan
> CC=/usr/local/clang4/bin/clang
> CXX=/usr/local/clang4/bin/clang++
> LDFLAGS=-L/usr/local/clang4/libI
> 
> I just executed the following commands in the R.app environment.
> 
> source("https://bioconductor.org/biocLite.R;)
> biocLite()
> # declined the offer to update packages
>  biocLite(c("ChemmineR"), type="source", dependencies=TRUE)
> 
> It then tried to install all the dependencies (failing for ChemmineOB because 
> the OpenBabel system requirement was not met) and got a  report of success 
> with ChemmineR and the package was capable of loading. So I've successfully 
> tested my theory that the only barriers to successful compilation of 
> ChemmineR from source are lack of knowledge of the R and Bioconductor 
> ecosystem (and lack of one external package.) I'm not that interested in 
> getting a full package installed, so haven't taken the time to install 
> OpenBabel and recompile ChemmineOB.
> 
> 
> Hope this helps;
> David.
> 
> >
> > _______
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> David Winsemius
> Alameda, CA, USA
> 
> 'Any technology distinguishable from magic is insufficiently advanced.'   
> -Gehm's Corollary to Clarke's Third Law
> 
> 
> 
> 
> 
> 

David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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Re: [R-SIG-Mac] OS X builds for R-devel

[David Winsemius]

> On Feb 19, 2018, at 12:27 PM, Alexey Sergushichev <alserg...@gmail.com> wrote:
> 
> Dear all,
> 
> Are there any plans on having package build for r-devel on CRAN? I
> understand it's far from the highest priority but it would be good to have
> any estimates. I'm aware of several packages on Bioconoductor-devel that
> fail builds due to absence of binary versions of some packages (
> http://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineR/merida2-buildsrc.html
> http://bioconductor.org/checkResults/devel/bioc-LATEST/cbaf/merida2-buildsrc.html
> ).
> 
> Thanks,
> Alexey Sergushichev
> 
>   [[alternative HTML version deleted]]

The fact that you post in HTML and make no effort to describe your setup makes 
me suspect you may also have missed the instructions about installing XCode and 
configuring R for compiling source packages. This can still be done with the 
binary distribution versions of R and R.app, and do not require that you build 
R from sources. See the CRAN-Mac-tools page:

https://cran.r-project.org/bin/macosx/tools/

It used to be the case that one needed Xcode and Command Line Tools installed. 
(I do have them.) I cannot tell from the current Mac-devel page whether that is 
still the case. I have a current version of R running in El Capitan. This is my 
~/.R/Makevars file:

# created by rstan at Thu Mar 19 11:26:15 2015 
CXXFLAGS = -mtune=core2 -O3 $(LTO)  #set_by_rstan
R_XTRA_CPPFLAGS =  -I$(R_INCLUDE_DIR)   #set_by_rstan
CC=/usr/local/clang4/bin/clang
CXX=/usr/local/clang4/bin/clang++
LDFLAGS=-L/usr/local/clang4/libI 

I just executed the following commands in the R.app environment.

source("https://bioconductor.org/biocLite.R;)
biocLite()
# declined the offer to update packages
 biocLite(c("ChemmineR"), type="source", dependencies=TRUE)

It then tried to install all the dependencies (failing for ChemmineOB because 
the OpenBabel system requirement was not met) and got a  report of success with 
ChemmineR and the package was capable of loading. So I've successfully tested 
my theory that the only barriers to successful compilation of ChemmineR from 
source are lack of knowledge of the R and Bioconductor ecosystem (and lack of 
one external package.) I'm not that interested in getting a full package 
installed, so haven't taken the time to install OpenBabel and recompile 
ChemmineOB.


Hope this helps;
David.

> 
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David Winsemius
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'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 180, Issue 6

[David Winsemius]

> On Feb 16, 2018, at 11:15 AM, Ossenbruggen, Paul <paul.ossenbrug...@unh.edu> 
> wrote:
> 
> First of all, I want to thank David Wensemius and Brandon Hurr.
> 
> Next, I want to say that my problem was more complicated than removing the 
> invisible file, .RData. After removal and startup of RStudio, I received:
> 
> Error: object 'CF.mb' not found.
> 
> I removed the following files: .Rhistory .Rprfile .Rprofile .Rdata. After 
> removing them, my error message went away.

That makes sense. The history files can get corrupted as well. You can also get 
a clean load of R by running from the command line with the --vanilla flag.

For those using the R.app GUI, the history file in use is .Rapp.history rather 
than .Rhistory. See the R-MAC-FAQ.

David.
> 
> Paul
> 
> 
> 
> On Feb 16, 2018, at 6:00 AM, 
> r-sig-mac-requ...@r-project.org<mailto:r-sig-mac-requ...@r-project.org> wrote:
> 
> 
> 
> 
> Send R-SIG-Mac mailing list submissions to
> r-sig-mac@r-project.org<mailto:r-sig-mac@r-project.org>
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dmac=DwIGaQ=c6MrceVCY5m5A_KAUkrdoA=vXaWf90_eNvgohBfU4b0GVo02vigVp6lPSTKMqr0RwQ=S86paWuTkKAFxU7d9pmaDrGf5fQvUDN4lTfSAFihUSI=5USUZGu_N566kZFSUUNPm__bJ6mBMkTahr2mCeIwDXw=
> or, via email, send a message with subject or body 'help' to
> r-sig-mac-requ...@r-project.org
> 
> You can reach the person managing the list at
> r-sig-mac-ow...@r-project.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of R-SIG-Mac digest..."
> 
> 
> Today's Topics:
> 
>  1. Re:  R-SIG-Mac Digest, Vol 180, Issue 5 (Ossenbruggen, Paul)
>  2. Re:  R-SIG-Mac Digest, Vol 180, Issue 5 (David Winsemius)
>  3. Re:  R-SIG-Mac Digest, Vol 180, Issue 5 (Brandon Hurr)
> 
> --
> 
> Message: 1
> Date: Thu, 15 Feb 2018 14:18:45 +
> From: "Ossenbruggen, Paul" <paul.ossenbrug...@unh.edu>
> To: "r-sig-mac@r-project.org" <r-sig-mac@r-project.org>
> Subject: Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 180, Issue 5
> Message-ID: <e70bf2ce-f724-4d3b-aaa4-276387e68...@unh.edu>
> Content-Type: text/plain; charset="utf-8"
> 
> Given David Winsemius’ reply, I obtained the following information:
> 
> 
> PJO:SDE PJO$ find /Users/PJO/Library/R/3.4/library/CF/ -type f -iname ".*" -ls
> 
> 52645352   24 -rw-r--r--1 PJO  staff8196 
> Feb  9 13:20 /Users/PJO/Library/R/3.4/library/CF//.DS_Store
> 
> 52645353   16 -rw-r--r--1 PJO  staff6148 
> Feb  9 13:20 /Users/PJO/Library/R/3.4/library/CF//extdata/.DS_Store
> 
> The following
> PJO:SDE PJO$ find /Users/PJO/Library/R/3.4/library/CF/ -type f -iname 
> "CF.Rdata" -ls
> PJO:SDE PJO$ find /Users/PJO/Library/R/3.4/library/CF/ -type f -iname "CF.mb" 
> -ls
> PJO:SDE PJO$ find /Users/PJO/Library/R/3.4/library/CF/ -type f -iname ".mb" 
> -ls
> return nothing or
> PJO:SDE PJO$
> 
> I hope this information is of some use.
> 
> Thanks,
> Paul
> 
> On Feb 15, 2018, at 6:00 AM, r-sig-mac-requ...@r-project.org wrote:
> 
> Caution - External Email;
> 
> 
> Send R-SIG-Mac mailing list submissions to
> r-sig-mac@r-project.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dmac=DwIGaQ=c6MrceVCY5m5A_KAUkrdoA=vXaWf90_eNvgohBfU4b0GVo02vigVp6lPSTKMqr0RwQ=cb_FXbPhkXtSllNWIRAvnjDKHGCFqirdYqn2-fCXn3E=lWzj9K1TzXbvPZJx5dD70IvjNFcxTS-iuZY36R4qlDo=
> or, via email, send a message with subject or body 'help' to
> r-sig-mac-requ...@r-project.org
> 
> You can reach the person managing the list at
> r-sig-mac-ow...@r-project.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of R-SIG-Mac digest..."
> 
> 
> Today's Topics:
> 
> 1.  R installation error caused by a bogus file. (Ossenbruggen, Paul)
> 2. Re:  Update of RcppParallel failed (Marc Girondot)
> 3. Re:  R installation error caused by a bogus file.
>(David Winsemius)
> 
> --
> 
> Message: 1
> Date: Wed, 14 Feb 2018 15

Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 180, Issue 5

[David Winsemius]

> On Feb 15, 2018, at 6:18 AM, Ossenbruggen, Paul <paul.ossenbrug...@unh.edu> 
> wrote:
> 
> Given David Winsemius’ reply, I obtained the following information:
> 
> 
> PJO:SDE PJO$ find /Users/PJO/Library/R/3.4/library/CF/ -type f -iname ".*" -ls
> 
> 52645352   24 -rw-r--r--1 PJO  staff8196 
> Feb  9 13:20 /Users/PJO/Library/R/3.4/library/CF//.DS_Store
> 
> 52645353   16 -rw-r--r--1 PJO  staff6148 
> Feb  9 13:20 /Users/PJO/Library/R/3.4/library/CF//extdata/.DS_Store
> 
> The following
> PJO:SDE PJO$ find /Users/PJO/Library/R/3.4/library/CF/ -type f -iname 
> "CF.Rdata" -ls
> PJO:SDE PJO$ find /Users/PJO/Library/R/3.4/library/CF/ -type f -iname "CF.mb" 
> -ls
> PJO:SDE PJO$ find /Users/PJO/Library/R/3.4/library/CF/ -type f -iname ".mb" 
> -ls
> return nothing or
> PJO:SDE PJO$ 
> 
> I hope this information is of some use.

1) When you reply to a posting you get from mailing list you should 
aggressively trim the stuff that is not needed to understand you query.

2) My approach to managing my invisible files in the MacOS is to make thm 
visible with this at a Terminal session:

defaults write com.apple.finder AppleShowAllFiles YES

Then you can find .Rdata files in whatever directory they might reside. I say 
"they" becaus you might have one in any directory that was your working 
directory at the time of a shutdown where you accept the R.app's offer to save 
work.

So, don't just look at your Library sub directory, which is not a typical place 
to house a working directory. Instead look everywhere:

find /Users/username/ -iname ".R*"




> 
> Thanks,
> Paul
> 
>> 

David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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Re: [R-SIG-Mac] R installation error caused by a bogus file.

[David Winsemius]

> On Feb 14, 2018, at 7:01 AM, Ossenbruggen, Paul <paul.ossenbrug...@unh.edu> 
> wrote:
> 
> I receive the following error whenever I restart R and reload R onto my 
> computer:
> 
> Error: object 'CF.mb' not found
> [R.app GUI 1.70 (7463) x86_64-apple-darwin15.6.0]
> 
> The object 'CF.mb’ file is a bogus file. In actually, it does not and should 
> not exist and R should not attempting to load it.
> 
> I suspect that I created it by mistake when I worked with RStudio in creating 
> a R package called “CF”. Most likely I typed “CF.mb" instead of “CF.md.” The 
> extension “.md” makes sense. It is extension for a Markdown file. “.mb” 
> stands for some animation program extension, which I am not using. 
> 
> QUESTION: How do I stop R from looking for this object?
> 
> Apparently, R has saved a call to the 'CF.mb’  file somewhere in its memory. 
> My guess if I erase this call, I will be running R the way it is designed.
> 

Have you deleted your `.Rdata` file? It's an invisible file and you may need to 
use Terminal.app to remove it from you startup directory. Where exactly that 
might be depends on how Rstudio is configured.

--
David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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Re: [R-SIG-Mac] [SOLVED] Persistent inability to load rgl (spinning beachball hang)

[David Winsemius]

> On Dec 30, 2017, at 5:51 PM, David Winsemius <dwinsem...@comcast.net> wrote:
> 
> After successfully installing RQuantLib from sources, I went to run its demos 
> and got a fatal "beachball". 
> 
> Tried running R from Terminal with R --vanilla
> 
> The demos() panel says that rgl is required and that seemed not to be a 
> difficulty since I had used it many times in the past.
> 
> Tried loading rgl ... beachball.
> 
> Tried reinstalling XQuartz (and restarting Mac)
> 
> Tried Launching XQuartz and got an apple  error saying:

Actually was the libTIFF sectoion that applied and succeeded:


# Fix libTIFF

dyld: Symbol not found: __cg_TIFFClientOpen
  Referenced from: 
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/ImageIO
  Expected in: /usr/local/lib/libTIFF.dylib
 in 
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/ImageIO
Trace/BPT trap

sudo cp 
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Resources/libTIFF.dylib
 /usr/local/lib/

> 

> 
> dyld: Symbol not found: __cg_jpeg_resync_to_restart
>  Referenced from: 
> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib
>  Expected in: /usr/local/lib/libJPEG.dylib
> 
> So searched on the error message and tried this fix from 
> https://gist.github.com/leonardoborges/2549670
> 
> 
> sudo cp 
> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Resources/libJPEG.dylib
>  /usr/local/lib/libJPEG.dylib
> 
> 
> Voila! No further difficulties.
> 
> -- 
> David Winsemius
> Alameda, CA, USA
> 
> 'Any technology distinguishable from magic is insufficiently advanced.'   
> -Gehm's Corollary to Clarke's Third Law
> 
> _______
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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[R-SIG-Mac] [SOLVED] Persistent inability to load rgl (spinning beachball hang)

[David Winsemius]

After successfully installing RQuantLib from sources, I went to run its demos 
and got a fatal "beachball". 

Tried running R from Terminal with R --vanilla

The demos() panel says that rgl is required and that seemed not to be a 
difficulty since I had used it many times in the past.

Tried loading rgl ... beachball.

Tried reinstalling XQuartz (and restarting Mac)

Tried Launching XQuartz and got an apple  error saying:


dyld: Symbol not found: __cg_jpeg_resync_to_restart
  Referenced from: 
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib
  Expected in: /usr/local/lib/libJPEG.dylib

So searched on the error message and tried this fix from 
https://gist.github.com/leonardoborges/2549670


sudo cp 
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Resources/libJPEG.dylib
 /usr/local/lib/libJPEG.dylib


Voila! No further difficulties.

-- 
David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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Re: [R-SIG-Mac] .libPaths

[David Winsemius]

> On Dec 25, 2017, at 2:36 PM, Michael Hall <mik3h...@gmail.com> wrote:
> 
> 
>> On Dec 25, 2017, at 4:31 PM, David Winsemius <dwinsem...@comcast.net> wrote:
>> 
>> 
>>> On Dec 25, 2017, at 1:39 PM, Michael Hall <mik3h...@gmail.com> wrote:
>>> 
>>> 
>>>> On Dec 25, 2017, at 3:37 PM, David Winsemius <dwinsem...@comcast.net> 
>>>> wrote:
>>>> 
>>>> .libPaths() <- 
>>>> "/Library/Frameworks/R.framework/Versions/3.4/Resources/library"
>>> 
>>> .libPaths() <- 
>>> "/Library/Frameworks/R.framework/Versions/3.4/Resources/library"
>>> Error in .libPaths() <- 
>>> "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" : 
>>> invalid (NULL) left side of assignment
>> 
>> Sorry. Make that:
>> 
>> .libPaths("/Library/Frameworks/R.framework/Versions/3.4/Resources/library”)
> 
> I think that works for the session but it’s not persistent.
> Given .libPaths as…
> 
> .libPaths
> function (new) 
> {
>if (!missing(new)) {
>new <- Sys.glob(path.expand(new))
>paths <- c(new, .Library.site, .Library)
>paths <- paths[dir.exists(paths)]
>.lib.loc <<- unique(normalizePath(paths, "/"))
>}
>else .lib.loc
> }
> 
> You might notice 
> paths <- c(new, .Library.site, .Library) 
> always tacks that on anyhow.
> 
> .Library
> [1] "/Library/Frameworks/R.framework/Resources/library”
> 
> so that
> .libPaths(“”)
> might make more sense and also works.
> But it is still not persistent. Leave the app and get back in and it’s back 
> to including the user lib.
> How do I persistently get rid of that?

My guess is that you are running the R.app GUI and have not unchecked the 
default settings in the Startup panel of Preferences:



> 
> 

David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law





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Re: [R-SIG-Mac] .libPaths

[David Winsemius]

> On Dec 25, 2017, at 1:39 PM, Michael Hall <mik3h...@gmail.com> wrote:
> 
> 
>> On Dec 25, 2017, at 3:37 PM, David Winsemius <dwinsem...@comcast.net> wrote:
>> 
>> .libPaths() <- 
>> "/Library/Frameworks/R.framework/Versions/3.4/Resources/library"
> 
> .libPaths() <- 
> "/Library/Frameworks/R.framework/Versions/3.4/Resources/library"
> Error in .libPaths() <- 
> "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" : 
>   invalid (NULL) left side of assignment

Sorry. Make that:

.libPaths("/Library/Frameworks/R.framework/Versions/3.4/Resources/library")


-- 
David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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Re: [R-SIG-Mac] odd warning looking up Bioconductor packages

[David Winsemius]

> On Dec 11, 2017, at 6:11 AM, Federico Calboli <federico.calb...@kuleuven.be> 
> wrote:
> 
> Hi All,
> 
> I am using R version 3.4.3 Patched (2017-12-05 r73849) R.app GUI 1.70 (7463) 
> x86_64-apple-darwin15.6.0 on MacOS 10.13.2.  Using R.app I am looking for 
> Bioconductor packages, and using the package installer I get the following 
> warning:
> 
> Warning: unable to access index for repository 
> http://www.bioconductor.org/packages/3.6/extra/bin/macosx/el-capitan/contrib/3.4:
>   cannot open URL 
> 'http://www.bioconductor.org/packages/3.6/extra/bin/macosx/el-capitan/contrib/3.4/PACKAGES’
> 
> despite the fact I do get a list of available packages (screenshot attached).
> 
> I emailed the bioconductor devs but it is not clear what is going on, aside 
> than my R is looking for a webpage that is a 404.  I was wondering whether 
> this is a peculiarity of my own machine or whether it has been encountered 
> elsewhere.  Assuming it is my machine, is there a way of making said warning 
> go away?

I've been getting the same warning for a while. The BioConductor approved way 
is to use `source("https://bioconductor.org/biocLite.R;); 
biocLite(c("pkg_name")). It has not affected my ability to install BioC 
packages, so I've been ignoring it. The other reason I've been ignoring it is 
that I'm not using the approved method. I thought it is from R.app using an old 
address with the "http" not being "https" some place in the Package Installer 
script.

I can get it just by clicking on the "Get List" button of the GUI Package 
Installer panel with Bioconductor (binaries) selected. If I choose to reinstall 
pkg:"a4" is get the warning again then 

trying URL 
'http://www.bioconductor.org/packages/3.6/bioc/bin/macosx/el-capitan/contrib/3.4/a4_1.26.0.tgz'
Content type 'application/x-gzip' length 966139 bytes (943 KB)

 followed by the reports of success and then another warning. So maybe it's 
not the "http" but rather the target website.

-- 
David.


> sessionInfo()
R version 3.4.2 Patched (2017-10-04 r73465)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.4/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] grDevices utils datasets  graphics  stats methods   base 

other attached packages:
[1] rms_5.1-1   SparseM_1.77Hmisc_4.0-3 ggplot2_2.2.1   
Formula_1.2-2   survival_2.41-3
[7] sos_2.0-0   brew_1.0-6  lattice_0.20-35

loaded via a namespace (and not attached):
 [1] viridis_0.4.0   tidyr_0.7.2 jsonlite_1.5
viridisLite_0.2.0   splines_3.4.2  
 [6] assertthat_0.2.0latticeExtra_0.6-28 gamlss_5.0-5
backports_1.1.1 quantreg_5.34  
[11] glue_1.2.0  downloader_0.4  digest_0.6.12   
RColorBrewer_1.1-2  checkmate_1.8.5
[16] minqa_1.2.4 colorspace_1.3-2sandwich_2.4-0  
htmltools_0.3.6 Matrix_1.2-12  
[21] plyr_1.8.4  XML_3.98-1.9pkgconfig_2.0.1 
DiagrammeR_0.9.2purrr_0.2.4
[26] mvtnorm_1.0-6   scales_0.5.0gamlss.data_5.0-0   lme4_1.1-14
 MatrixModels_0.4-1 
[31] htmlTable_1.11.0tibble_1.3.4influenceR_0.1.0TH.data_1.0-8  
 nnet_7.3-12
[36] lazyeval_0.2.1  rgexf_0.15.3magrittr_1.5
polspline_1.1.12nlme_3.1-131   
[41] MASS_7.3-47 foreign_0.8-69  mxnet_0.10.1Rook_1.1-1 
 tools_3.4.2
[46] data.table_1.10.4-3 hms_0.4.0   multcomp_1.4-8  stringr_1.2.0  
 munsell_0.4.3  
[51] cluster_2.0.6   bindrcpp_0.2gamlss.dist_5.0-3   compiler_3.4.2 
 rlang_0.1.4
[56] nloptr_1.0.4grid_3.4.2  rstudioapi_0.7  
htmlwidgets_0.9 visNetwork_2.0.1   
[61] igraph_1.1.2base64enc_0.1-3 gtable_0.2.0
codetools_0.2-15R6_2.2.2   
[66] gridExtra_2.3   zoo_1.8-0   knitr_1.17  dplyr_0.7.4
 bindr_0.1  
[71] readr_1.1.1 stringi_1.1.6   parallel_3.4.2  Rcpp_0.12.14   
 rpart_4.1-11   
[76] acepack_1.4.1  



> 
> Cheers
> 
> F
> 
> 
> 
> --
> Federico Calboli
> LBEG - Laboratory of Biodiversity and Evolutionary Genomics
> Charles Deberiotstraat 32 box 2439
> 3000 Leuven
> +32 16 32 87 67
> 
> 
> 
> 
> 
> ___
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David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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Re: [R-SIG-Mac] illegal operation on vignette("xkcd-intro"): pdf viewer perhaps?

[David Winsemius]

> On Nov 13, 2017, at 5:45 AM, Tim Bates <timothy.c.ba...@gmail.com> wrote:
> 
> On R version: R version 3.4.2 (2017-09-28) (Platform: 
> x86_64-apple-darwin15.6.0, MacOS: 10.13.1)
> 
> load library(xkcd), and then try and run the vignette:
> 
> vignette("xkcd-intro")
> 
> *** caught illegal operation ***
> address 0x7fff7429b5e2, cause 'illegal opcode'
> 
> Traceback:
> 1: system2(pdfviewer, shQuote(out), wait = FALSE)
> 2: print.vignette(x)
> 3: function (x, ...) UseMethod("print")(x)
> 
> Possible actions...

I suppose it's a bug by definition, but whether it is the sign of a flakey 
system at your end or a more widespread (reproducible) issue is open to 
question... since you have not followed the bug-reporting guidelines in the 
Posting Guide. I'm unable to reproduce. Did you load the several dependencies?


My guess is that you should be examining your Adobe Acrobat Reader setup. I see 
this when I look for system level pdfviewer info:

/Library/Preferences/com.adobe.acrobat.pdfviewer.plist


When installing the package with dependencies I get:

also installing the dependencies ‘extrafontdb’, ‘Rttf2pt1’, ‘extrafont’

trying URL 
'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.4/extrafontdb_1.0.tgz'
Content type 'application/x-gzip' length 6855 bytes
==
downloaded 6855 bytes

trying URL 
'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.4/Rttf2pt1_1.3.4.tgz'
Content type 'application/x-gzip' length 104961 bytes (102 KB)
==
downloaded 102 KB

trying URL 
'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.4/extrafont_0.17.tgz'
Content type 'application/x-gzip' length 33006 bytes (32 KB)
==
downloaded 32 KB

trying URL 
'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.4/xkcd_0.0.5.tgz'
Content type 'application/x-gzip' length 372586 bytes (363 KB)
==
downloaded 363 KB

> sessionInfo()
R version 3.4.2 Patched (2017-10-04 r73465)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.4/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] grDevices utils datasets  graphics  stats methods   base 

other attached packages:
 [1] xkcd_0.0.5  extrafont_0.17  rms_5.1-1   SparseM_1.77
Hmisc_4.0-3 ggplot2_2.2.1  
 [7] Formula_1.2-2   survival_2.41-3 sos_2.0-0   brew_1.0-6  
lattice_0.20-35

loaded via a namespace (and not attached):
 [1] viridis_0.4.0   tidyr_0.7.2 jsonlite_1.5
viridisLite_0.2.0  
 [5] splines_3.4.2   assertthat_0.2.0latticeExtra_0.6-28 Rttf2pt1_1.3.4 

 [9] gamlss_5.0-4backports_1.1.1 quantreg_5.34   glue_1.2.0 

[13] downloader_0.4  extrafontdb_1.0 digest_0.6.12   
RColorBrewer_1.1-2 
[17] checkmate_1.8.5 minqa_1.2.4 colorspace_1.3-2sandwich_2.4-0 

[21] htmltools_0.3.6 Matrix_1.2-11   plyr_1.8.4  XML_3.98-1.9   

[25] pkgconfig_2.0.1 DiagrammeR_0.9.2purrr_0.2.4 mvtnorm_1.0-6  

[29] scales_0.5.0gamlss.data_5.0-0   lme4_1.1-14 
MatrixModels_0.4-1 
[33] htmlTable_1.9   tibble_1.3.4influenceR_0.1.0TH.data_1.0-8  

[37] nnet_7.3-12 lazyeval_0.2.1  rgexf_0.15.3magrittr_1.5   

[41] polspline_1.1.12nlme_3.1-131MASS_7.3-47 foreign_0.8-69 

[45] mxnet_0.10.1Rook_1.1-1  tools_3.4.2 
data.table_1.10.4-3
[49] hms_0.3 multcomp_1.4-7  stringr_1.2.0   munsell_0.4.3  

[53] cluster_2.0.6   bindrcpp_0.2gamlss.dist_5.0-3   compiler_3.4.2 

[57] rlang_0.1.2 grid_3.4.2  nloptr_1.0.4rstudioapi_0.7 

[61] htmlwidgets_0.9 visNetwork_2.0.1igraph_1.1.2
base64enc_0.1-3
[65] gtable_0.2.0codetools_0.2-15R6_2.2.2gridExtra_2.3  

[69] zoo_1.8-0   knitr_1.17  dplyr_0.7.4 bindr_0.1  

[73] readr_1.1.1 stringi_1.1.5   parallel_3.4.2  Rcpp_0.12.13   

[77] rpart_4.1-11acepack_1.4.1  

> 
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David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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Re: [R-SIG-Mac] Macports installation problem

[David Winsemius]

> On Oct 21, 2017, at 5:47 AM, clark richards <clark.richa...@gmail.com> wrote:
> 
> Interesting discussion, even if it is technically off-topic (i.e. is about a 
> Macports issue rather than an R issue).
> 
> For myself, I have found instances where I needed to install R through 
> non-standard channels (my choice lately has been homebrew). This was largely 
> related to having the required system tools necessary for a package 
> development environment that permits the compilation of C/fortran code and 
> some system libraries (gdal, etc). As Don and others pointed out many such 
> dependencies should be available through the OSX R develop page (forget the 
> address right now ...), I have some older machines for which those 
> precompiled binaries do not install, including a 9 year old Macbook which 
> will run OSX up to ElCapitan but is not compatible with the newer binaries. 
> In that case, in order to have an R and gfortran that played together I had 
> to use homebrew as I could not find a binary gfortran that would work for my 
> architecture.

I have two older Macs of roughly the same vintage, both running El Cap. 
Regarding gfortran for package devel, I wondered if you had noticed that advice 
at the top of the CRAN Tools page to add some locations to a Makevars file:

https://cran.r-project.org/bin/macosx/tools/

I was having difficulties until someone gently reminded me to "read the manual".

GDAL (and associated packages) are generally obtained from Kyngchaos and that 
has been the case for as long as I remember.

-- 
David.


> 
> I love working on OSX, though I have often lamented the difficulties in 
> getting a suitable package development environment configured -- at least 
> compared to Windows (just install Rtools.exe) and Linux (everything required 
> is easily installed from the distro package manager).
> 
> Clark
> 
> 
> Message: 2
> Date: Fri, 20 Oct 2017 18:02:33 +
> From: "MacQueen, Don" <macque...@llnl.gov>
> To: David Winsemius <dwinsem...@comcast.net>, Rainer Krug
> <rainer_k...@icloud.com>
> Cc: John <miao...@gmail.com>, "r-sig-mac@r-project.org"
> <r-sig-mac@r-project.org>
> Subject: Re: [R-SIG-Mac] Macports installation problem
> Message-ID: <303cd3a3-230a-4d18-a190-e6c2d1160...@llnl.gov>
> Content-Type: text/plain; charset="utf-8"
> 
> The OP's question has inspired an interestingly large number of responses.
> 
> One thing I'm curious about, and I don't think I've seen in the discussion, 
> is why the OP needed to install Cairo graphics with respect to R (otherwise 
> the question was indeed off-topic for R-sig-Mac).
> 
> In summary (and I think this is reasonably consistent with other responses; 
> discussion to support my summary follows):
> 
> 1)  Use CRAN R, install dependencies needed for extended R capability on the 
> OS as needed, from whatever source you prefer, or whichever is easiest for R 
> to use
> 2)  If one chooses to install R using MacPorts or homebrew, be prepared to 
> exercise a greater depth of computer science smarts
> 3)  Feel free to install other useful stuff using MacPorts or homebrew, 
> whichever one prefers; there is unlikely to be any conflict with R
> 
> 
> In close to 20 years of using R on Mac, I have always been able to use 
> whatever capabilities R offers that I wanted to use, using the R provided on 
> CRAN. Nothing has ever motivated me to install R using MacPorts or homebrew 
> in order to obtain some capability that I couldn't have using CRAN's binary 
> download for Mac. This includes things like access to remote Oracle 
> databases, using various spatial packages built around sp and rgdal, reading 
> and writing MS Office files (both Word and Excel), building simple tcl/tk 
> interfaces, writing my own packages that link to Fortran, and probably more 
> that I don't remember. I see no necessity to install R from MacPorts or 
> homebrew. Of course, if one wishes to for whatever reason, great! And I'm 
> glad that people have wanted to make R available from those package managers.
> 
> I do use MacPorts, however, to get useful software such as an X Windows aware 
> version of emacs, ghostscript, and ImageMagick. Indeed, I even have cairo 
> installed using MacPorts, albeit on a 10.11.6 system, not a 10.12.x system 
> like the OP. (It's probably there as a dependency for some other MacPorts 
> package.) From that point of view, the OP's command to install it using 
> MacPorts was correct. I'd need more information to make a guess at why it 
> didn't succeed.
> 
> Some R packages do, of course, depend on external libraries not provided with 
> R. One has to install these from somewhere.  For example, the

Re: [R-SIG-Mac] Macports installation problem

[David Winsemius]

> On Oct 19, 2017, at 11:33 PM, Rainer Krug <rainer_k...@icloud.com> wrote:
> 
> 
> 
>> On 19 Oct 2017, at 20:25, Robert Baer <rb...@atsu.edu> wrote:
>> 
>> 
>> -- snip --
>> 
>>>>> I think using MacPorts might actually be the "error" that needs 
>>>>> correction. I would suggest an alternate strategy. Go to 
>>>>> http://r.research.att.com/libs/ and get the appropriate version of cairo, 
>>>>> probably the most recent one.
>>>>> 
>>>>> http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
>>>>> 
>>>>> Scroll down to the bottom of that page and an appropriate modification of 
>>>>> the two lines for unpacking to the root.
>>>>> 
>>>>> curl -O 
>>>>> http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
>>>>> sudo tar fvxz gmp-4.2.4-darwin8-bin4.tar.gz -C /
>> Even though its not my question, I appreciate the specific recommendations 
>> on best practices for move ahead.
>> 
>>>>> 
>>>>> The Mac version of R does not do well with either MacPorts or homebrew 
>>>>> installation of required system packages because those package managers 
>>>>> put them in loaction that are not recognized by the static build that is 
>>>>> the default.
>>>> Using homebrew (and as far as I know Macports as well) works without major 
>>>> problems. The problem start when you mix standard installations / homebrew 
>>>> / Macports. This results in problems.
>>> The fact that the original poster had obviously not used MacPorts (and 
>>> perhaps did not even know what it was) suggests that the appropriate reply 
>>> should be to discourage him from using it and offer a strategy with greater 
>>> likelihood of success in combination with the more typical installation 
>>> method for the Mac R fork.
>> I  am brand new to this list, but have been using R since about 2000.  The 
>> reason I'm here is to translate Mac-speak like "homebrew" and "MacPorts" 
>> into grounded advice that lets me use R as effectively on my new Mac as my 
>> Windows and Linux machines. 
> 
> If you know your way around in Linux, I would suggest looking into homebrew - 
> it essentially brings the approach of apt (in the case of debian) to a Mac. 
> If not, you might be better off with the official R installers. But all work 
> equally after installed.

Dear Rainer;

I think it might be a bit more complicated than "just use the same installer 
all the time", but am not a user of either homebrew or MacPorts so am speaking 
only from reports I have read in this mailing list and SO. Bob Rudis whom I 
also respect in such matters has several times made the same suggestion. I 
think there may need to be supplemental instructions on setting system 
environment variables and also possibly further changes to Makevars files in 
some packages being obtained from CRAN or BioC. I have been encouraged by 
others to switch to homebrew, but have never found a sufficiently complete 
tutorial that appeared to cover these other issues. If you know of one, Rainer, 
I think you should share it.

Best;
David.
> 
> 
> Cheers,
> 
> Rainer
> 
> 
>> I appreciate John's predicament and this approach to answering his question 
>> is highly informative to me as I lurk and learn.   Thanks from this newbie 
>> Mac user.
>> 
>> -- 
>> 
>> 
>> --
>> Robert W. Baer, Ph.D.
>> Professor of Physiology
>> Kirksville College of Osteopathic Medicine
>> A T Still University of Health Sciences
>> 800 W. Jefferson St
>> Kirksville, MO 63501
>> 660-626-2321 Department
>> 660-626-2965 FAX
>> 
> 
> --
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
> UCT), Dipl. Phys. (Germany)
> 
> University of Zürich
> 
> Cell:   +41 (0)78 630 66 57
> email:  rai...@krugs.de
> Skype:  RMkrug
> 
> PGP: 0x0F52F982
> 
> 
> 

David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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Re: [R-SIG-Mac] Macports installation problem

[David Winsemius]

> On Oct 18, 2017, at 6:09 PM, John <miao...@gmail.com> wrote:
> 
> Thanks, David and Rainer. 
> 
> Where should I type them? On RStudio command line?  
> 
> curl -O http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
> sudo tar fvxz gmp-4.2.4-darwin8-bin4.tar.gz -C /

Those are Unix system functions, not R or RStudio functions. Do some reading 
regarding Unix bash and the MacOS Terminal.app

-- 
David.
> 
> 
> I got this after typing in RStudio command line
> > curl -O http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
> Error: unexpected symbol in "curl -O http"
> 
> 
> J
> 
> 2017-10-18 9:54 GMT-07:00 David Winsemius <dwinsem...@comcast.net>:
> 
> > On Oct 18, 2017, at 8:40 AM, Rainer Krug <rainer_k...@icloud.com> wrote:
> >
> >
> >
> >> On 18 Oct 2017, at 17:17, David Winsemius <dwinsem...@comcast.net> wrote:
> >>
> >>>
> >>> On Oct 17, 2017, at 11:58 PM, Rainer Krug <rainer_k...@icloud.com> wrote:
> >>>
> >>> This is related to Macports and not to R - please post your question on 
> >>> their mailing list. If it would be about errors installing R, that would 
> >>> be different.
> >>>
> >>
> >> I think using MacPorts might actually be the "error" that needs 
> >> correction. I would suggest an alternate strategy. Go to 
> >> http://r.research.att.com/libs/ and get the appropriate version of cairo, 
> >> probably the most recent one.
> >>
> >> http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
> >>
> >> Scroll down to the bottom of that page and an appropriate modification of 
> >> the two lines for unpacking to the root.
> >>
> >> curl -O http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
> >> sudo tar fvxz gmp-4.2.4-darwin8-bin4.tar.gz -C /
> >>
> >>
> >> The Mac version of R does not do well with either MacPorts or homebrew 
> >> installation of required system packages because those package managers 
> >> put them in loaction that are not recognized by the static build that is 
> >> the default.
> >
> > Using homebrew (and as far as I know Macports as well) works without major 
> > problems. The problem start when you mix standard installations / homebrew 
> > / Macports. This results in problems.
> 
> The fact that the original poster had obviously not used MacPorts (and 
> perhaps did not even know what it was) suggests that the appropriate reply 
> should be to discourage him from using it and offer a strategy with greater 
> likelihood of success in combination with the more typical installation 
> method for the Mac R fork.
> 
> >
> > So: each of the approaches has it’s own pros and cons - it is only that 
> > homebrew and Macports are not officially supported by the R team.
> 
> One of the cons is that both homebrew and MacPorts requires a greater 
> knowledge of the Unix under-pinnings of MacOS. If a poster is asking how to 
> install MacPorts, it suggests that he don't already have such skills and 
> perhaps doesn't even have the motivation to acquire them. (Your earlier 
> response suggested that posting in R-SIG-Mac was the wrong way to do acquire 
> such skills and I agree. Appears the poster has not yet developed the habit 
> of reading supporting online documentation. He certainly did not do so 
> regarding R-SIG-Mac. My opinion: A person who chooses not to read or heed 
> online documentation should be actively discouraged from using either 
> MacPorts of homebrew.)
> 
> Best;
> David.
> 
> 
> >
> > Cheers,
> >
> > Rainer
> >
> >
> >>
> >> --
> >> David.
> >>
> >>> Cheers,
> >>>
> >>> Rainer
> >>>
> >>>
> >>>> On 18 Oct 2017, at 02:36, John <miao...@gmail.com> wrote:
> >>>>
> >>>> Hi,
> >>>>
> >>>> I tried to install Cairo graphics
> >>>>
> >>>> https://www.cairographics.org/download/
> >>>>
> >>>> and I need to install Macports.
> >>>>
> >>>> I tried to install Macports on my Mac OS Sierra 10.12.6, and type "sudo
> >>>> port install cairo", but it did not respond. I haven't seen any file name
> >>>> or app called Macports, but one file called "port" which is located at
> >>>>
> >>>> loca/bin/port"
> &g

Re: [R-SIG-Mac] Macports installation problem

[David Winsemius]

> On Oct 17, 2017, at 11:58 PM, Rainer Krug <rainer_k...@icloud.com> wrote:
> 
> This is related to Macports and not to R - please post your question on their 
> mailing list. If it would be about errors installing R, that would be 
> different.
> 

I think using MacPorts might actually be the "error" that needs correction. I 
would suggest an alternate strategy. Go to http://r.research.att.com/libs/ and 
get the appropriate version of cairo, probably the most recent one. 

http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz

Scroll down to the bottom of that page and an appropriate modification of the 
two lines for unpacking to the root. 

curl -O http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
sudo tar fvxz gmp-4.2.4-darwin8-bin4.tar.gz -C /


The Mac version of R does not do well with either MacPorts or homebrew 
installation of required system packages because those package managers put 
them in loaction that are not recognized by the static build that is the 
default.

-- 
David.

> Cheers,
> 
> Rainer
> 
> 
>> On 18 Oct 2017, at 02:36, John <miao...@gmail.com> wrote:
>> 
>> Hi,
>> 
>>  I tried to install Cairo graphics
>> 
>> https://www.cairographics.org/download/
>> 
>>  and I need to install Macports.
>> 
>>  I tried to install Macports on my Mac OS Sierra 10.12.6, and type "sudo
>> port install cairo", but it did not respond. I haven't seen any file name
>> or app called Macports, but one file called "port" which is located at
>> 
>> loca/bin/port"
>> 
>>  How should I do it?
>> 
>>  Thanks,
>> 
>> John
>> ***
>> 
>> Last login: Sun Oct 15 02:52:49 on console
>> Johns-MacBook-Pro:~ john$ /opt/local/bin/port ; exit;
>> MacPorts 2.4.2
>> Entering shell mode... ("help" for help, "quit" to quit)
>> [Users/john] > sudo port install cairo
>> Error: Unrecognized action "port sudo"
>> 
>>  [[alternative HTML version deleted]]
>> 
>> ___
>> R-SIG-Mac mailing list
>> R-SIG-Mac@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> --
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
> UCT), Dipl. Phys. (Germany)
> 
> University of Zürich
> 
> Cell:   +41 (0)78 630 66 57
> email:  rai...@krugs.de
> Skype:  RMkrug
> 
> PGP: 0x0F52F982
> 
> 
> 
> 
>   [[alternative HTML version deleted]]
> 
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David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

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Re: [R-SIG-Mac] homebrew install High Sierra - tcl-tk support

[David Winsemius]

> On Oct 18, 2017, at 12:09 AM, Rainer Krug <rai...@krugs.de> wrote:
> 
> 
> 
>> On 17 Oct 2017, at 17:18, David Winsemius <dwinsem...@comcast.net> wrote:
>> 
>>> 
>>> On Oct 17, 2017, at 7:56 AM, David Winsemius <dwinsem...@comcast.net> wrote:
>>> 
>>>> 
>>>> On Oct 17, 2017, at 1:43 AM, Rainer Krug <rai...@krugs.de> wrote:
>>>> 
>>>> Hi
>>>> 
>>>> One question about home-brew installation:
>>>> 
>>>> After upgrading to High Sierra (and update to R 3.4.2), I don’t get tcl-tk 
>>>> support in R.
>>>> 
>>>> I get the following error:
>>>> 
>>>>> library(tcltk)
>>>>Error: package or namespace load failed for ‘tcltk’:
>>>> .onLoad failed in loadNamespace() for 'tcltk', details:
>>>>  call: fun(libname, pkgname)
>>>>  error: Tcl/Tk support is not available on this system
>>>>In addition: Warning message:
>>>>S3 methods ‘as.character.tclObj’, ‘as.character.tclVar’, 
>>>> ‘as.double.tclObj’, ‘as.integer.tclObj’, ‘as.logical.tclObj’, 
>>>> ‘as.raw.tclObj’, ‘print.tclObj’, ‘[[.tclArray’, ‘[[<-.tclArray’, 
>>>> ‘$.tclArray’, ‘$<-.tclArray’, ‘names.tclArray’, ‘names<-.tclArray’, 
>>>> ‘length.tclArray’, ‘length<-.tclArray’, ‘tclObj.tclVar’, 
>>>> ‘tclObj<-.tclVar’, ‘tclvalue.default’, ‘tclvalue.tclObj’, 
>>>> ‘tclvalue.tclVar’, ‘tclvalue<-.default’, ‘tclvalue<-.tclVar’, 
>>>> ‘close.tkProgressBar’ were declared in NAMESPACE but not found
>>>> 
>>>> 
>>>> Is this a problem on my side, or is there a problem with R & homebrew & 
>>>> High Sierra & tcl-tk?
>>> 
>>> Caveat. I know almost nothing about homebrew other than its function and 
>>> the fact that users of it often have problems with installing R properly. 
>>> The CRAN page for the Mac R 3.4.2 fork says:
>>> 
>>> ---begin---
>>> Contains R 3.4.2 framework, R.app GUI 1.70 in 64-bit for Intel Macs, Tcl/Tk 
>>> 8.6.6 X11 libraries and Texinfo 5.2. The latter two components are optional 
>>> and can be ommitted when choosing "custom install", they are only needed if 
>>> you want to use the tcltk R package or build package documentation from 
>>> sources.
>> 
>> I intended that the next sentence be here (and wan't intending two copies of 
>> those sentences):
>> 
>> Note: the use of X11 (including tcltk) requires XQuartz to be installed 
>> since it is no longer part of OS X. Always re-install XQuartz when upgrading 
>> your OS X to a new major version.
>> 
>>> -end
>>> 
>>> So it makes me wonder if you need to add the correct versions of the 
>>> underlying system packages in a manner that your homebrew installation can 
>>> find them. (the 3.3 fork uses a differnt version of Tcl/Tk.) 
> 
> Thanks David - but no luck. Still the same problems - even after installing 
> quartz again.


I was not sure whether the  list of items included: "Intel Macs, Tcl/Tk 8.6.6 
X11 libraries and Texinfo 5.2" was missing a comma between 8.6.6 and X11 
libraries or conversely  that TCL/Tk 8.6.6 was supposed to indicate a 
particular version of Quartz. Looking at the various webpages for those two 
packages, I don't see any change in XQuartz' version numbers whereas there has 
been quite a bit of updating of TCL/Tk.

-- 
David.
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Re: [R-SIG-Mac] homebrew install High Sierra - tcl-tk support

[David Winsemius]

> On Oct 17, 2017, at 1:43 AM, Rainer Krug <rai...@krugs.de> wrote:
> 
> Hi
> 
> One question about home-brew installation:
> 
> After upgrading to High Sierra (and update to R 3.4.2), I don’t get tcl-tk 
> support in R.
> 
> I get the following error:
> 
>   > library(tcltk)
>   Error: package or namespace load failed for ‘tcltk’:
>.onLoad failed in loadNamespace() for 'tcltk', details:
> call: fun(libname, pkgname)
> error: Tcl/Tk support is not available on this system
>   In addition: Warning message:
>   S3 methods ‘as.character.tclObj’, ‘as.character.tclVar’, 
> ‘as.double.tclObj’, ‘as.integer.tclObj’, ‘as.logical.tclObj’, 
> ‘as.raw.tclObj’, ‘print.tclObj’, ‘[[.tclArray’, ‘[[<-.tclArray’, 
> ‘$.tclArray’, ‘$<-.tclArray’, ‘names.tclArray’, ‘names<-.tclArray’, 
> ‘length.tclArray’, ‘length<-.tclArray’, ‘tclObj.tclVar’, ‘tclObj<-.tclVar’, 
> ‘tclvalue.default’, ‘tclvalue.tclObj’, ‘tclvalue.tclVar’, 
> ‘tclvalue<-.default’, ‘tclvalue<-.tclVar’, ‘close.tkProgressBar’ were 
> declared in NAMESPACE but not found
> 
> 
> Is this a problem on my side, or is there a problem with R & homebrew & High 
> Sierra & tcl-tk?

Caveat. I know almost nothing about homebrew other than its function and the 
fact that users of it often have problems with installing R properly. The CRAN 
page for the Mac R 3.4.2 fork says:

---begin---
Contains R 3.4.2 framework, R.app GUI 1.70 in 64-bit for Intel Macs, Tcl/Tk 
8.6.6 X11 libraries and Texinfo 5.2. The latter two components are optional and 
can be ommitted when choosing "custom install", they are only needed if you 
want to use the tcltk R package or build package documentation from sources.

Contains R 3.4.2 framework, R.app GUI 1.70 in 64-bit for Intel Macs, Tcl/Tk 
8.6.6 X11 libraries and Texinfo 5.2. The latter two components are optional and 
can be ommitted when choosing "custom install", they are only needed if you 
want to use the tcltk R package or build package documentation from sources.
-end

So it makes me wonder if you need to add the correct versions of the underlying 
system packages in a manner that your homebrew installation can find them. (the 
3.3 fork uses a differnt version of Tcl/Tk.) 

-- 
David.

> 
> Thanks,
> 
> Rainer
> 
> 
> --
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
> UCT), Dipl. Phys. (Germany)
> 
> University of Zürich
> 
> Cell:   +41 (0)78 630 66 57
> email:  rai...@krugs.de
> Skype:  RMkrug
> 
> PGP: 0x0F52F982
> 
> 
> 
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Re: [R-SIG-Mac] Quartz output font is disabled in R version 3.4.1 (2017-06-30)?

[David Winsemius]

As soon as you "click" the override box the greyed out numbers should become 
black and you will be able to change their values. 

Sent from my iPhone

> On Sep 7, 2017, at 9:07 AM, BATES Timothy  wrote:
> 
> Seems like in R.app that accompanies  R version 3.4.1 (2017-06-30), the 
> preference to set an output -font  for graphics is disabled?
> 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
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Re: [R-SIG-Mac] R.app help viewer blank

[David Winsemius]

> On Sep 19, 2017, at 10:23 AM, Ben Tupper <btup...@bigelow.org> wrote:
> 
> Hello,
> 
> I just updated to R 3.4.1 [R.app GUI 1.70 (7375) x86_64-apple-darwin15.6.0] 
> from http://mirror.its.dal.ca/cran/ but have encountered a puzzler.  When I 
> lunch the help viewer like this...
> 
> ?data.frame 
> 
> the viewer launches but the page content is blank.  I have also tried he 
> search box in the help viewer as well as the menu selection 'Help > R Help' 
> with the same result.  I have restarted both R.app and the computer without 
> joy. The startup message and output of sessionInfo() are pasted in below.
> 
> I can get help successfully from a R session in Terminal.app.  I poked around 
> in the list archives but don't see anything recent on this issue.  
> 
> What should I do to enable the help viewer?


What's in your startup files?

Have you deleted or moved aside any .Rprofile and .Rdata files?

I think you would also look at:

getOption("help_type")

Looking at other options settings I see a reference to startDynamicHelp so 
perhaps try:

tools:::startDynamicHelp(start = TRUE)

-- 
David.

> 
> Thanks!
> Ben
> 
> 
> R version 3.4.1 (2017-06-30) -- "Single Candle"
> Copyright (C) 2017 The R Foundation for Statistical Computing
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
>  Natural language support but running in an English locale
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
> 
> [R.app GUI 1.70 (7375) x86_64-apple-darwin15.6.0]
> 
>> ?data.frame
> starting httpd help server ... done
> 
>> sessionInfo()
> R version 3.4.1 (2017-06-30)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: OS X El Capitan 10.11.6
> 
> Matrix products: default
> BLAS: 
> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/3.4/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_3.4.1 tools_3.4.1 
> 
> 
> 
> 
> 
> Ben Tupper
> Bigelow Laboratory for Ocean Sciences
> 60 Bigelow Drive, P.O. Box 380
> East Boothbay, Maine 04544
> http://www.bigelow.org
> 
> Ecocast Reports: http://seascapemodeling.org/ecocast.html
> Tick Reports: https://report.bigelow.org/tick/
> Jellyfish Reports: https://jellyfish.bigelow.org/jellyfish/
> 
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Re: [R-SIG-Mac] segfault on R v. 3.4.1

[David Winsemius]

> On Sep 14, 2017, at 9:13 AM, James Plante <jimpla...@me.com> wrote:
> 
> If I knew what a segfault was, I might be able to be more helpful. 
> Do any of you folks know what might’ve happened? I’ve d/l’d and installed the 
> 3.4.1. Mac binary from CRAN three times, and each time I get the text below.

But ... did you also update your library packages?


> Any help will be appreciated; let me know if I can include anything else. A 
> sysinfo() is out of the question, since my owly option is how I want to quit 
> R. The only guess I have is that I don’t have enough memory installed. 

That's pretty unlikely.


> Main system info: 
> MacOS Sierra v. 10.12.8; 27” iMac, late 2013; 3.4GHz Core i%; 8GB 1600MHz DDR3
> Thanks in advance,
> Jim
> R version 3.4.1 (2017-06-30) -- "Single Candle"
> Copyright (C) 2017 The R Foundation for Statistical Computing
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>  Natural language support but running in an English locale
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
> *** caught segfault ***
> address 0x1310, cause 'memory not mapped'
> Traceback:
> 1: dyn.load(file, DLLpath = DLLpath, ...)
> 2: library.dynam(lib, package, package.lib)
> 3: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = 
> vI[[j]])
> 4: asNamespace(ns)
> 5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
> .libPaths()), versionCheck = vI[[j]]),
> i[[2L]], from = package)
> 6: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = 
> vI[[j]])
> 7: asNamespace(ns)
> 8: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
> i[[2L]], from = package)
> .libPaths()), versionCheck = vI[[j]]),
> 9: loadNamespace(package, lib.loc)
> 10: doTryCatch(return(expr), name, parentenv, handler)
> 11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 12: tryCatchList(expr, classes, parentenv, handlers)
> 13: tryCatch({attr(package, "LibPath") <- which.lib.loc
> <- attachNamespace(ns, pos = pos, deps)}, error = function(e) {
> paste(" in", deparse(cc)[1L])else ""msg <- gettextf("package or 
> namespace load failed for %s%s:\n
> %s", sQuote(package), P, conditionMessage(e))if (logical.return)
> msg), domain = NA)else stop(msg, call. = FALSE, domain = NA)})
> 14: library(package, lib.loc = lib.loc, character.only = TRUE, logical.return 
> = TRUE,
> warn.conflicts, quietly = quietly)
> 15: doTryCatch(return(expr), name, parentenv, handler)
> 16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 17: tryCatchList(expr, classes, parentenv, handlers)
> 18: tryCatch(library(package, lib.loc = lib.loc, character.only = TRUE, 
> logical.return = TRUE,
> warn.conflicts = warn.conflicts, quietly = quietly), error = function(e) 
> e)
> 19: require(pkg, quietly = TRUE, warn.conflicts = FALSE, character.only = 
> TRUE)
> 20: .First.sys()

The problem apparently starts with .First.sys(). The .First.sys() function is 
called after the function .First which may reside in one of the startup files. 
See:  ?Startup  ... in particular:

"Next, if a function .First is found on the search path, it is executed as 
.First(). Finally, function .First.sys() in the base package is run. This calls 
require to attach the default packages specified by options("defaultPackages"). 
If the methods package is included, this will have been attached earlier (by 
function .OptRequireMethods()) so that namespace initializations such as those 
from the user workspace will proceed correctly."

So you would need to examine your Renviron.site file and maybe .Rprofile files 
and see if one of them is attempting to load a package that has not been 
updated properly.

-- 
David.



> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> 2017-09-14 08:14:57.208 R[11081:2277811] IMKClient Stall detected, *please 
> Report* your user scenario
> attaching a spindump (or sysdiagnose) that captures the problem - 
> (imkxpc_attributesForCharacterIndex:reply:)
> block performed very slowly (1.16 secs).
> Selection:
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] Poor plotting performance on Mac OS X

[David Winsemius]

> On Jul 6, 2017, at 4:12 AM, Ashley Betts <ashley.be...@saltbushsoftware.com> 
> wrote:
> 
> Hi All,
>I'm quite new to R and recently started investigating the geospatial 
> plotting capabilities of R via ggplot2. I started by using some of the 
> publicly available datasets from the Australian Bureau of Statistics. 
> Plotting the Level 3 Statistical Area boundaries took over 2 hours on my 2012 
> Mac Book Pro. As there were over 3M rows in the fortify’ed data frame I 
> initially thought this was just how long it must take. I then ran the exact 
> same script on my work laptop which is similarly spec’ed and it ran in 
> approximately 30 seconds. This now has me extremely disappointed in the 
> performance on the Mac which is where I use R the most. I changed my BLAS 
> library to the Accelerate library in a whim that this might make a 
> difference. It did not. Whilst I primarily use RStudio I also ran the same 
> script in R.app and if there was any improvement it was not noticeable. I did 
> notice in the Windows run that it seemed to use multiple cores (which is what 
> made me investigate the BLAS change) whilst the Mac seems to stay bound to a 
> single core. My initial thoughts were that it must be something to do with 
> ggplot but after sampling the rsession process a number of times (see 
> attached Sample of rsession.txt) it appears to be spending most of it’s time 
> in CGContextDrawPath in Apples CoreGraphics so I assume it is a Graphics 
> related issue. I’m running R 3.4 on my Mac and 3.3.2 on the Windows machine. 
> I’ve attached the script, process sample text and a number of screen shots 
> that I hope will be helpful in analysing the issue. Could someone possibly 
> let me know if this is PEBKAC issue or an actual problem with R. If the later 
> how do I go about getting the issue resolved?
> 
> The SA3 boundary data is available here:
> 
> http://www.abs.gov.au/AUSSTATS/abs@.nsf/DetailsPage/1270.0.55.001July%202016?OpenDocument
> 
> as 'Statistical Area Level 3 (SA3) ASGS Ed 2016 Digital Boundaries in ESRI 
> Shapefile Format’

I tried opening that .R file (which I was surprised made it through the usual 
scrubbing process) and I see this at the top.
=copied=
library(rio)
library(ggplot2)
library(rgdal)
library(rgeos)
library(dplyr)

convert("../Data/ABS/14100DS0001_2017-03.xlsx", "absregdata.csv")
==end-copy===

After seeing that I went looking in the linked document which was really not a 
link to a document. I did find the referenced document on that page and 
downloaded the file:

http://www.abs.gov.au/AUSSTATS/subscriber.nsf/log?openagent&1270055001_sa3_2016_aust_shape.zip&1270.0.55.001%20Cubes&43942523105745CBCA257FED0013DB07&0%202016&12.07.2016

That's the shapefile that is referenced later in the code, but I see no way to 
find the CSV file that you are loading. So I see no method of reproducing your 
observations.

You are also several version behind the current dplyr release. I happen to have 
the same outdated versions of rgdal, rgeos, and sp packages but they, too, are 
slightly out-of-date.

So unable to attempt reproducing your difficulties. You should try at a minimum 
to supply data that will allow this. You should also try starting your Mac with 
a minimum of of other loaded applications on a clean session. memory 
fragmentation often prevents execution of large jobs in memory and long times 
are possible if you need to page out to disk and do not have a SSD device as 
your system disk.

(I'm able to read but not to understand the results of your sampling. It's 
possible that more savvy users of macs will be able to tell whether my 
hypothesis, that this is caused by paging-out to disk, is correct.

Hope this helps;
David.



> 
> Regards,
> 
> Ashley
> 


David Winsemius
Alameda, CA, USA

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-Gehm's Corollary to Clarke's Third Law

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Re: [R-SIG-Mac] rJava problem in Mac OS Sierra 10.12.5

[David Winsemius]

> On Jul 19, 2017, at 8:34 AM, Manuel Spínola <mspinol...@gmail.com> wrote:
> 
> Dear list members,
> 
> I have problem loading some packages because rJava cannot be loaded.  I
> have the latest version of java, R and rJava.
> 
>> library(glmulti)
> Unable to find any JVMs matching version "(null)".
> No Java runtime present, try --request to install.
> running command '/usr/libexec/java_home' had status 1Error: package ‘rJava’
> could not be loaded
> 
> What I need to do to load the packages that depend on rJava?

I don't think you have provided enough information to know what to advise, but 
you might try looking through the r-sig-mac archives using one of the search 
engines:

http://markmail.org/search/?q=+list%3Aorg.r-project.r-sig-mac+No+Java+runtime+present%2C+try+--request+to+install

... although I found no questions reporting that exact error message, or you 
can use the StackOverflow search facilities:

https://stackoverflow.com/search?q=%5Br%5D+osx+rjava+install

People generally do have a Java runtime engine installed somewhere. Here's what 
I see at a Terminal session:

dw-mac-pro:~ davidwinsemius$ which java
/usr/bin/java


dw-mac-pro:~ davidwinsemius$ java -version
java version "1.8.0_131"
Java(TM) SE Runtime Environment (build 1.8.0_131-b11)
Java HotSpot(TM) 64-Bit Server VM (build 25.131-b11, mixed mode)

rJava says it only requires a much older version:

SystemRequirements: Java JDK 1.2 or higher (for JRI/REngine JDK 1.4 or
higher), GNU make

I think some packages do require the more recent Java runtime package, though.

Most people are running Yosemite or higher so the SO answer to this question 
may be helpful:

http://stackoverflow.com/questions/30738974/rjava-load-error-in-rstudio-r-after-upgrading-to-osx-yosemite

> 
> -- 
> *Manuel Spínola, Ph.D.*
> Instituto Internacional en Conservación y Manejo de Vida Silvestre
> 

> 
>   [[alternative HTML version deleted]]

Your question will have a better chance of coming through correctly if you use 
palin text for R mailing list submissions.

> 
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Re: [R-SIG-Mac] R-3.4.0 installation problem?

[David Winsemius]

> On Jun 13, 2017, at 4:19 AM, Alfonso Saera Vila <alfonsosa...@gmail.com> 
> wrote:
> 
> Hi everybody,
> 
> I am working in a MacBook Pro (15 inches, mid 2010), OSX El Capitan 
> (10.11.6), 2.4 GHz Intel Core i5, 8 GB 1067 MHz DDR3
> 
> Today I tried to update from R-3.3 to R-3.4.0. I downloaded the R-3.4.0.pkg 
> from https://cran.r-project.org/ site. After downloading I checked the MD5 
> checksum for the R-3.4.0.pkg image and it was the same than in the r-project 
> website. I executed the file by double-clicking and everything appear to work 
> fine, at the end it said that everything was installed with no problem.
> 
> The problem I have is that the old R.app was removed from my application 
> folder but the new (R-3.4.0) does not appear in the application folder either.

R does not appear in the Applications folder. It is fairly deep in the 
Frameworks tree that in part of your system files. The R.app program is just a 
GUI to manage tasks in R in a more Apple-typical manner. It knows where to find 
the core R programs and lets you choose where to keep your package files. When 
I update R and R.app, I see no change in the appearance of R.app in the 
Application folder, but the new IDE code takes hold if there have been any 
changes, which may not have happened.. I can tell I have a new one when I open 
the R.app and see a new version number in the startup messages. e.g:

[R.app GUI 1.70 (7338) x86_64-apple-darwin15.6.0]

One still needs to copy over the packages and do the update.packages with 
check.built = TRUE maneuver.

> 
> I tried to download and install the GNU Fortran 6.1 and then reinstall R but 
> nothing changed.

That is only needed if you are going to be compiling packages from source. If 
you go to http://r.research.att.com/ you can see the current version numbers 
for the disk images of GUIs that would be mated to various versions of R. (I 
seem to be somewhat out of date. So if I were having problems, which I'm not, I 
should be able to separately install the GUI from the current disk image.)


>From what you have written I think you have a current version of the GUI and 
>from what I see at http://r.research.att.com/, it appears that the same GUI 
>version could be used for R 3.3.x, 3.4.x and 3.5.x, so maybe no change was 
>needed.

> 
> I tried to look for a solution in google and stackoverblow forum but did not 
> find any clue of what to do. I hope I am not missing any stupid detail or 
> making a rookie mistake. Sorry if this is not the way of posting this.
> 
> Thanks for your help,
> 
> Alfonso
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Re: [R-SIG-Mac] R GUI very slow under mac OS 10.12.5 (Sierra)

[David Winsemius]

> On May 27, 2017, at 3:44 AM, Martin Batholdy via R-SIG-Mac 
> <r-sig-mac@r-project.org> wrote:
> 
> Dear all,
> 
> I just switched to a new 2016 Macbook Pro and noticed that R is very slow 
> when used over the R app. Using R via the terminal is significantly faster.
> Especially, drawing figures in quartz is really slow

Not sure what "drawing a figure" actually means. Can you present code?

> and sometimes the following error message is printed – but this might be 
> unrelated to the speed issue:
> 
> IMKInputSession 
> presentFunctionRowItemTextInputViewWithEndpoint:completionHandler: : [self 
> textInputContext]=0x0 *NO* NSRemoteViewController to client, NSError=Error 
> Domain=NSCocoaErrorDomain Code=4099 "The connection from pid 0 was 
> invalidated from this process." UserInfo={NSDebugDescription=The connection 
> from pid 0 was invalidated from this process.}, 
> com.apple.inputmethod.EmojiFunctionRowItem

This error in Sierra hosted apps has also been reported on other app forums (as 
well as once before on this mailing list Mon, 19 Dec 2016 by 
a.becker...@sheffield.ac.uk but got no response):

https://discuss.atom.io/t/imkinputsession-error/36273

https://github.com/macvim-dev/macvim/issues/422

https://stackoverflow.com/questions/41249603/tkinter-error-in-terminal-possibly-from-my-key-bind


> 
> Is this a known issue related to Sierra and/or the new Macbook Pros? Are 
> there any workarounds or fixes?

I surely don't know about workarounds but this does appear to be specific to 
Sierra. My MacbookPro is too old to get an update to Sierra. I do wonder if you 
have an updated (or any) XQuartz and XCode? Generally a complete question will 
include your versions of all essential system and R packages. 

What does sessionInfo() return?

Try clicking on the system taskbar XQuartz icon and  using `XQuartz/About X11` 
and copying the version. I get:

XQuartz 2.7.11 (xorg-server 1.18.4)

My XCode version is: Version 8.2.1 (8C1002) but ISTR that Sierra needs a later 
version.

And you should also probably indicate whether you have used either MacPorts or 
homebrew.

The other system resource needed in the past was Tcl/Tk although I think that 
now should get installed and attached by default with any current version of R. 
The last link of the three above appeared related to the Tk interface which is 
used by R.app and the tcltk package is part of the base installation, so might 
be relevant, but this is written at the level of speculation. My other 
hypothesis is that two different installations of Tcl/Tk might give problems on 
one machine that were not encountered by others.

-- 
David.

> 
> 
> Thanks for any suggestions!
> 
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Re: [R-SIG-Mac] R 3.4.0 problem

[David Winsemius]

> On May 26, 2017, at 7:13 PM, Simon Urbanek <simon.urba...@r-project.org> 
> wrote:
> 
> 
>> On May 16, 2017, at 4:01 PM, David Winsemius <dwinsem...@comcast.net> wrote:
>> 
>> 
>>> On Apr 24, 2017, at 11:49 PM, catalin roibu <catalinro...@gmail.com> wrote:
>>> 
>>> Dear all,
>>> 
>>> I have a problem with the newest R version. I'm trying to install a
>>> specific package dplR who need the gpm package and I have this error on my
>>> macbook (OS Sierra):
>> 
>> Generally one reads the error messages. Often, and this is one of those 
>> cases, the first error message tells what the problem might be. You either 
>> do not have the system package GMP or it is installed in a location where 
>> the R package 'gmp' cannot find it.
>> 
>> I had difficulties attempting to test the advice I found by (re-)installing 
>> the GNU GMP package from CRAN/r.research.att.com:
>> 
>> http://r.research.att.com/libs/gmp-6.0.0-darwin.13-x86_64.tar.gz
>> 
>> I got:
>> ~ davidwinsemius$ sudo tar fvxz ~/gmp-6.0.0-darwin.13-x86_64.tar.gz -C /
>> x usr/: Can't set user=0/group=0 for usrCan't update time for usr
>> x usr/local/
>> x usr/local/include/
>> x usr/local/lib/
>> x usr/local/share/
>> x usr/local/share/info/
>> x usr/local/share/info/dir
>> x usr/local/share/info/gmp.info
>> x usr/local/share/info/gmp.info-1
>> x usr/local/share/info/gmp.info-2
>> x usr/local/lib/libgmp.a
>> x usr/local/lib/libgmp.la
>> x usr/local/include/gmp.h
>> tar: Error exit delayed from previous errors.
>> 
>> Search on the "Can't update time for usr"-error brought up a bunch of stuff 
>> about 'XSAN' that I didn't really understand fully but did not seem terribly 
>> relevant ...
>> 
> 
> FWIW that simply tells you that macOS is refusing even root to modify 
> permissions and time for /usr which is deliberate by Apple for security 
> reasons. Since El Capitan even root doesn't have privileges to modify /usr 
> and its subdirectories other than /usr/local. So, yes, that error is beign.

I did know that Apple had locked down /usr/ subdirectories. I'm not sure what 
your conclusion implies, however. I generally assume that an error message 
implies lack of success.  Was the effort at installation of gmp from 
gmp-6.0.0-darwin.13-x86_64.tar.gz actually completed? (Which means my 
subsequent installation using gmp-6.1.2.tar.bz2 was not necessary, but I 
guessing also not harmful?

Best;
David.

> 
> Cheers,
> Simon
> 
> 
>>  but the package 'gmp-6.1.2.tar.bz2' at gmplib.org expanded and compiled 
>> without difficulty usign the switches recommended at the bottom of:
>> 
>> http://r.research.att.com/libs/
>> 
>> davidwinsemius$ sudo tar fvxz 
>> /Users/davidwinsemius/Downloads/gmp-6.1.2.tar.bz2 -C /
>> 
>> (I'm not on Sierra, since Apple has classified my MacPro as "obsolete".)
>> 
>> -- 
>> 
>> David
>> [R.app GUI 1.70 (7338) x86_64-apple-darwin15.6.0]
>> 
>>> 
>> 
>> 
>>>> install.packages("dplR")
>>> also installing the dependency ‘gmp’
>>> 
>>> Packages which are only available in source form, and may
>>> need compilation of C/C++/Fortran: ‘gmp’ ‘dplR’
>>> Do you want to attempt to install these from sources?
>>> y/n: y
>>> installing the source packages ‘gmp’, ‘dplR’
>>> 
>>> trying URL 'https://cran.rstudio.com/src/contrib/gmp_0.5-13.1.tar.gz'
>>> Content type 'application/x-gzip' length 131321 bytes (128 KB)
>>> ==
>>> downloaded 128 KB
>>> 
>>> trying URL 'https://cran.rstudio.com/src/contrib/dplR_1.6.5.tar.gz'
>>> Content type 'application/x-gzip' length 1672999 bytes (1.6 MB)
>>> ==
>>> downloaded 1.6 MB
>>> 
>>> * installing *source* package ‘gmp’ ...
>>> ** package ‘gmp’ successfully unpacked and MD5 sums checked
>>> creating cache ./config.cache
>>> checking for __gmpz_ui_sub in -lgmp... no
>>> configure: error: GNU MP not found, or not 4.1.4 or up, see
>>> http://gmplib.org
>>> ERROR: configuration failed for package ‘gmp’
>>> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
>>> Resources/library/gmp’
>>> Warning in install.packages :
>>> installation of package ‘gmp’ had non-zero exit status
>>> ERROR: dependency ‘gmp’ is not available for package ‘dplR’
>>> * removing ‘/Libr

Re: [R-SIG-Mac] rJava stops loading since I upgraded R to 3.4.0

[David Winsemius]

> On May 23, 2017, at 5:29 PM, David Winsemius <dwinsem...@comcast.net> wrote:
> 
> 
>> On May 23, 2017, at 4:44 PM, Christofer Bogaso <bogaso.christo...@gmail.com> 
>> wrote:
>> 
>> Hi David,
>> 
>> The file 'rJava.so' exists in my machine :
>> 
>>> file.exists('/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so')
>> 
>> [1] TRUE
>> 
>> Also the Javac version that I have :
>> 
>>> system('javac -version')
>> 
>> javac 1.6.0_65
>> 
>> Looks like mine is older than you. Do I need to download the latest?
>> In that case, do you suggest any link? As far as I know, javac comes
>> with Mac installed.
> 
> Yes, it does and some people seem to get success with that. I found that 
> installing 1.8 (also confusingly known as "Java 8") resolved my difficulties 
> with loading rJava. I'm not an expert, just reporting my ezxperience
>> 
>> On Peter's suggestion I also did sudo R CMD javareconf. However still
>> rJava couldnt be loaded.
> 
> For my machine:
> 
>> Sys.getenv()  # returns (among many other values)
> 
> 
> DYLD_LIBRARY_PATH
> /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/

And I just notice another value in the returns from that command:

LD_LIBRARY_PATH   :@JAVA_LD@

-- 
David.
> 
> 
>> 
>> Any other idea? Thanks,
>> 
>> On Wed, May 24, 2017 at 4:28 AM, peter dalgaard <pda...@gmail.com> wrote:
>>> [Christofer seemed to have fallen off the cc: list, now included]
>>> 
>>>> On 24 May 2017, at 00:18 , David Winsemius <dwinsem...@comcast.net> wrote:
>>>> 
>>>> What version of the Java Runtime Environment is available? What do you get 
>>>> for:
>>>> 
>>>> system('javac -version')
>>>> #I get:
>>>> #javac 1.8.0_65
>>>> 
>>>> I think that version was working with rJava, but I followed the "critical" 
>>>> advice on the Java SDK webpage ...
>>>> 
>>>> ... and after updating I now  get
>>>> #javac 1.8.0_131
>>>> 
>>>> And rJava still loads without error. I'm not on Sierra, however.
>>>> 
>>> 
>>> I am, and rJava doesn't load here either. However after
>>> 
>>> sudo R CMD javareconf
>>> 
>>> it seems happy as a clam.
>>> 
>>> 
>>>> Good luck;
>>>> David,
>>> 
>>> --
>>> 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
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
> 
> David Winsemius
> Alameda, CA, USA
> 
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Re: [R-SIG-Mac] rJava stops loading since I upgraded R to 3.4.0

[David Winsemius]

> On May 23, 2017, at 4:44 PM, Christofer Bogaso <bogaso.christo...@gmail.com> 
> wrote:
> 
> Hi David,
> 
> The file 'rJava.so' exists in my machine :
> 
>> file.exists('/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so')
> 
> [1] TRUE
> 
> Also the Javac version that I have :
> 
>> system('javac -version')
> 
> javac 1.6.0_65
> 
> Looks like mine is older than you. Do I need to download the latest?
> In that case, do you suggest any link? As far as I know, javac comes
> with Mac installed.

Yes, it does and some people seem to get success with that. I found that 
installing 1.8 (also confusingly known as "Java 8") resolved my difficulties 
with loading rJava. I'm not an expert, just reporting my ezxperience
> 
> On Peter's suggestion I also did sudo R CMD javareconf. However still
> rJava couldnt be loaded.

For my machine:

>Sys.getenv()  # returns (among many other values)


DYLD_LIBRARY_PATH
/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/


> 
> Any other idea? Thanks,
> 
> On Wed, May 24, 2017 at 4:28 AM, peter dalgaard <pda...@gmail.com> wrote:
>> [Christofer seemed to have fallen off the cc: list, now included]
>> 
>>> On 24 May 2017, at 00:18 , David Winsemius <dwinsem...@comcast.net> wrote:
>>> 
>>> What version of the Java Runtime Environment is available? What do you get 
>>> for:
>>> 
>>> system('javac -version')
>>> #I get:
>>> #javac 1.8.0_65
>>> 
>>> I think that version was working with rJava, but I followed the "critical" 
>>> advice on the Java SDK webpage ...
>>> 
>>> ... and after updating I now  get
>>> #javac 1.8.0_131
>>> 
>>> And rJava still loads without error. I'm not on Sierra, however.
>>> 
>> 
>> I am, and rJava doesn't load here either. However after
>> 
>> sudo R CMD javareconf
>> 
>> it seems happy as a clam.
>> 
>> 
>>> Good luck;
>>> David,
>> 
>> --
>> 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
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 

David Winsemius
Alameda, CA, USA

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Re: [R-SIG-Mac] rJava stops loading since I upgraded R to 3.4.0

[David Winsemius]

> On May 23, 2017, at 3:18 PM, David Winsemius <dwinsem...@comcast.net> wrote:
> 
>> 
>> On May 23, 2017, at 1:05 PM, Duncan Murdoch <murdoch.dun...@gmail.com> wrote:
>> 
>> On 23/05/2017 2:48 PM, Christofer Bogaso wrote:
>>> Hi again,
>>> 
>>> After I upgraded R to 3.4.0, I could not load rJava package. Below is
>>> the error :
>>> 
>>>> library(rJava)
>>> 
>>> Error: package or namespace load failed for ‘rJava’:
>>> 
>>> .onLoad failed in loadNamespace() for 'rJava', details:
>>> 
>>> call: dyn.load(file, DLLpath = DLLpath, ...)
>>> 
>>> error: unable to load shared object
>>> '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so':
> 
> To Christofer;
> 
> Does 
> '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so'
>  exist?
> 
> (You may need to check libPaths() in your new installation. )

You might also want to report the value that Sys.getenv() returns for:

DYLD_LIBRARY_PATH  

For me it is now:

   /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/


> 
> 
>>> dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so,
>>> 6): Library not loaded: @rpath/libjvm.dylib
>>> 
> 
> What version of the Java Runtime Environment is available? What do you get 
> for:
> 
> system('javac -version')
> #I get:
> #javac 1.8.0_65
> 
> I think that version was working with rJava, but I followed the "critical" 
> advice on the Java SDK webpage ...
> 
> ... and after updating I now  get
> #javac 1.8.0_131
> 
> And rJava still loads without error. I'm not on Sierra, however.
> 
> Good luck;
> David,
> 
> 
> 
>>> Referenced from:
>>> /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so
>>> 
>>> Reason: image not found
>>> 
>>> I have installed latest version of Java.
>> 
>> Did you re-install rJava?  Generally speaking you need to re-install all 
>> packages when switching R versions (except if the only change is in the 
>> patch level z, where the version number is x.y.z, you can usually use the 
>> old version).
>> 
>> Duncan Murdoch
>> 
>>> 
>>> R version :
>>> 
>>> R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
>>> 
>>> Copyright (C) 2017 The R Foundation for Statistical Computing
>>> 
>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>> 
>>> iOS : Sierra
>>> 
>>> With previous version of R, rJava was working fine. Could you please
>>> help how to fix it.
>>> 
>>> Thanks for your time.
>>> 
>>> Regards,
>>> 
>>> ___
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>> 
>> ___
>> R-SIG-Mac mailing list
>> R-SIG-Mac@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> David Winsemius
> Alameda, CA, USA
> 
> ___
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Re: [R-SIG-Mac] rJava stops loading since I upgraded R to 3.4.0

[David Winsemius]

> On May 23, 2017, at 1:05 PM, Duncan Murdoch <murdoch.dun...@gmail.com> wrote:
> 
> On 23/05/2017 2:48 PM, Christofer Bogaso wrote:
>> Hi again,
>> 
>> After I upgraded R to 3.4.0, I could not load rJava package. Below is
>> the error :
>> 
>>> library(rJava)
>> 
>> Error: package or namespace load failed for ‘rJava’:
>> 
>> .onLoad failed in loadNamespace() for 'rJava', details:
>> 
>>  call: dyn.load(file, DLLpath = DLLpath, ...)
>> 
>>  error: unable to load shared object
>> '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so':

To Christofer;

Does 
'/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so'
 exist?

(You may need to check libPaths() in your new installation. )


>>  
>> dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so,
>> 6): Library not loaded: @rpath/libjvm.dylib
>> 

What version of the Java Runtime Environment is available? What do you get for:

system('javac -version')
#I get:
#javac 1.8.0_65

I think that version was working with rJava, but I followed the "critical" 
advice on the Java SDK webpage ...

... and after updating I now  get
#javac 1.8.0_131

And rJava still loads without error. I'm not on Sierra, however.

Good luck;
David,



>>  Referenced from:
>> /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/libs/rJava.so
>> 
>>  Reason: image not found
>> 
>> I have installed latest version of Java.
> 
> Did you re-install rJava?  Generally speaking you need to re-install all 
> packages when switching R versions (except if the only change is in the patch 
> level z, where the version number is x.y.z, you can usually use the old 
> version).
> 
> Duncan Murdoch
> 
>> 
>> R version :
>> 
>> R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
>> 
>> Copyright (C) 2017 The R Foundation for Statistical Computing
>> 
>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>> 
>> iOS : Sierra
>> 
>> With previous version of R, rJava was working fine. Could you please
>> help how to fix it.
>> 
>> Thanks for your time.
>> 
>> Regards,
>> 
>> ___
>> 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] Please help! Package Installer doesn't work.

[David Winsemius]

> On Apr 26, 2017, at 9:39 AM, Luisa Bahnemann <luisabahnem...@gmx.de> wrote:
> 
> Hello ,
> I’ve only installed R (R 3.4.0 GUI 1.70 El Capitan build (7338))
> a few days ago . Now every time I try to install a package I can’t even see 
> the list of packages and R completely freezes.
> Then it shows this :
> 
> Warnung: unable to access index for repository 
> https://mirrors.cicku.me/CRAN/bin/macosx/el-capitan/contrib/3.4:

In Chrome I get:
#-
This site can’t be reached

mirrors.cicku.me refused to connect.
#


See this list:
https://cran.r-project.org/mirrors.html

I think you need a different CRAN mirror?

-- 
David



>  kann URL 
> 'https://mirrors.cicku.me/CRAN/bin/macosx/el-capitan/contrib/3.4/PACKAGES' 
> nicht öffnen
> 
> Could you please help me?
> I already reinstalled but it didn’t help.
> 
> Thankyou !
> Luisa Bahnemann
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Re: [R-SIG-Mac] R 3.4.0 problem

[David Winsemius]

> On Apr 24, 2017, at 11:49 PM, catalin roibu <catalinro...@gmail.com> wrote:
> 
> Dear all,
> 
> I have a problem with the newest R version. I'm trying to install a
> specific package dplR who need the gpm package and I have this error on my
> macbook (OS Sierra):

Generally one reads the error messages. Often, and this is one of those cases, 
the first error message tells what the problem might be. You either do not have 
the system package GMP or it is installed in a location where the R package 
'gmp' cannot find it.

I had difficulties attempting to test the advice I found by (re-)installing the 
GNU GMP package from CRAN/r.research.att.com:

http://r.research.att.com/libs/gmp-6.0.0-darwin.13-x86_64.tar.gz

I got:
~ davidwinsemius$ sudo tar fvxz ~/gmp-6.0.0-darwin.13-x86_64.tar.gz -C /
x usr/: Can't set user=0/group=0 for usrCan't update time for usr
x usr/local/
x usr/local/include/
x usr/local/lib/
x usr/local/share/
x usr/local/share/info/
x usr/local/share/info/dir
x usr/local/share/info/gmp.info
x usr/local/share/info/gmp.info-1
x usr/local/share/info/gmp.info-2
x usr/local/lib/libgmp.a
x usr/local/lib/libgmp.la
x usr/local/include/gmp.h
tar: Error exit delayed from previous errors.

Search on the "Can't update time for usr"-error brought up a bunch of stuff 
about 'XSAN' that I didn't really understand fully but did not seem terribly 
relevant ...

  but the package 'gmp-6.1.2.tar.bz2' at gmplib.org expanded and compiled 
without difficulty usign the switches recommended at the bottom of:

http://r.research.att.com/libs/

davidwinsemius$ sudo tar fvxz /Users/davidwinsemius/Downloads/gmp-6.1.2.tar.bz2 
-C /

(I'm not on Sierra, since Apple has classified my MacPro as "obsolete".)

-- 

David
[R.app GUI 1.70 (7338) x86_64-apple-darwin15.6.0]

> 


>> install.packages("dplR")
> also installing the dependency ‘gmp’
> 
> Packages which are only available in source form, and may
>  need compilation of C/C++/Fortran: ‘gmp’ ‘dplR’
> Do you want to attempt to install these from sources?
> y/n: y
> installing the source packages ‘gmp’, ‘dplR’
> 
> trying URL 'https://cran.rstudio.com/src/contrib/gmp_0.5-13.1.tar.gz'
> Content type 'application/x-gzip' length 131321 bytes (128 KB)
> ==
> downloaded 128 KB
> 
> trying URL 'https://cran.rstudio.com/src/contrib/dplR_1.6.5.tar.gz'
> Content type 'application/x-gzip' length 1672999 bytes (1.6 MB)
> ==
> downloaded 1.6 MB
> 
> * installing *source* package ‘gmp’ ...
> ** package ‘gmp’ successfully unpacked and MD5 sums checked
> creating cache ./config.cache
> checking for __gmpz_ui_sub in -lgmp... no
> configure: error: GNU MP not found, or not 4.1.4 or up, see
> http://gmplib.org
> ERROR: configuration failed for package ‘gmp’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/gmp’
> Warning in install.packages :
>  installation of package ‘gmp’ had non-zero exit status
> ERROR: dependency ‘gmp’ is not available for package ‘dplR’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.4/
> Resources/library/dplR’
> Warning in install.packages :
>  installation of package ‘dplR’ had non-zero exit status
> 
> The downloaded source packages are in
> ‘/private/var/folders/c5/6g4vbk5x55586m8ky2v_6pbcgn/T/RtmprYzSE8/
> downloaded_packages’
> 
> 
> All the other packages work in good conditions.
> Please help me to solve this annoying situation.
> 
> Best regards!
> 
> CR
> 
> 
> -- 
> 
> -
> -
> Catalin-Constantin ROIBU
> ​
> Lecturer PhD, Forestry engineer
> Forestry Faculty of Suceava
> Str. Universitatii no. 13, Suceava, 720229, Romania
> office phone  +4 0230 52 29 78, ext. 531
> mobile phone+4 0745 53 18 01
> FAX:+4 0230 52 16 64
> silvic.usv.ro <http://www.usv.ro/>
> 
> 
> 
>  <https://mailtrack.io/> Sent with Mailtrack
> <https://mailtrack.io/install?source=signature=en=catalinro...@gmail.com=22>
> <#>
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] R commander fonts on R 3.4.0

[David Winsemius]

> On May 9, 2017, at 3:08 PM, Jose G Conde Santiago via R-SIG-Mac 
> <r-sig-mac@r-project.org> wrote:
> 
> Hello,
> 
> I recently upgraded to R 3.4.0, but now I get very poor fonts from Rcmdr 
> 2.3-2 as shown below:
> 
> 

I'm not an Rcmdr user but I tried bringing a current version up. (I included a 
request to install Rcmdr with all dependencies but X11 complained that aplpack 
was missing and that needed to be installed as well.)  Seems you don't like teh 
proportionally space serif font you are seeing which was different than what I 
saw. Think you might want to show what this returns for you

names(X11Fonts())
[1] "serif""sans" "mono" "Times""Helvetica"   
[6] "CyrTimes" "CyrHelvetica" "Arial""Mincho" 

> X11Fonts()$serif
[1] "-*-times-%s-%s-*-*-%d-*-*-*-*-*-*-*"

I'm running R 3.4.0, El Cap, XQuartz 2.7.11 (xorg-server 1.18.4)  and that 
won't change since my box is "end of life" per Apple's inflexible OS support.

I tried running your test code and it seemed to lock up my X11 session as well 
as my R console (Perhaps this is due to running Rcmder in the R.app GUI?) 

Best;
David.



> I reloaded the older version of R (3.3.3), ran Rcmdr and the problem 
> disappeared. I downloaded R 3.4.0 again and the problem with Rcmdr reappeared.

> 
> I read a previous post on the list regarding an issue with Rcmdr and followed 
> your suggestions to that posting:
> 
> 1. The following test went well with R 3.4.0:
> 
>> > library (tcltk)
>> > tk_messageBox(message="test")
>> [1] "ok"
>> > 
> 
> 2. Ran R 3.4.0 from the terminal, and then ran R Commander. The problem 
> persists.
> 
> I am running XQuartz 2.7.11. My machine is an iMac (27-inch, Late 2012); 
> Processor 3.4 GHz Intel Core i7, with 32 GB RAM. Graphics: NVIDIA GeForce GTX 
> 675MX 1024 MB. OS X Sierra 10.12.4.
> 
> I will appreciate any suggestions.
> 
> Thanks in advance.
> 
> José
> 
> José G. Conde, MD, MPH
> Professor, School of Medicine
> Director, CentIT2
> UPR Medical Sciences Campus 
> 
> Tel  (787) 763-9401 Fax (787) 758-5206
> 
> Email: jose.con...@upr.edu
> 
> URL: http://rcmi.rcm.upr.edu
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

David Winsemius
Alameda, CA, USA

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
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[R-SIG-Mac] [SOLVED] Re: missing module when compiling R pkg:rms

[David Winsemius]

No longer failing in efforts to compile rms 5.1-1 from source. Probably related 
to the change in Makvears that Berend suggested. Appears the CRAN machine is 
now  also distributing that versions in binary. 

Thanks, Berend.

David.


> On May 5, 2017, at 7:46 AM, Frank Harrell <f.harr...@vanderbilt.edu> wrote:
> 
> Please remove me from the emails and substitute Cole Beck
> Frank
> 
> 
> Frank E Harrell JrProfessor and Chairman  School of 
> Medicine
> 
> Department of Biostatistics   Vanderbilt University
> 
> On Fri, May 5, 2017 at 2:13 AM, Berend Hasselman <b...@xs4all.nl> wrote:
> 
> > On 5 May 2017, at 03:12, David Winsemius <dwinsem...@comcast.net> wrote:
> >
> > Failing to get current rms package to compile (and appears that the CRAN 
> > build machine fails as well). The penultimate version of rms succeeds.
> >
> > Both from console and cmd-line I get this response in R 3.4.0 (just 
> > installed today) running El Cap 10.11.6 with Xcode Version 8.2.1 (8C1002):
> >
> > trying URL 'https://cran.cnr.berkeley.edu/src/contrib/rms_5.1-1.tar.gz'
> > Content type 'application/x-gzip' length 521311 bytes (509 KB)
> > ==
> > downloaded 509 KB
> >
> > Loading required package: lattice
> > Loading required package: sos
> > Loading required package: brew
> > Loading required package: rms
> > Loading required package: Hmisc
> > Loading required package: survival
> > Loading required package: Formula
> > Loading required package: stats
> > Loading required package: ggplot2
> >
> > Attaching package: ‘Hmisc’
> >
> > The following objects are masked from ‘package:base’:
> >
> >   format.pval, round.POSIXt, trunc.POSIXt, units
> >
> > Loading required package: SparseM
> >
> > Attaching package: ‘SparseM’
> >
> > The following object is masked from ‘package:base’:
> >
> >   backsolve
> >
> > ##-- 2017-05-04 --##
> > Loading required package: graphics
> >
> > Attaching package: ‘graphics’
> >
> > The following object is masked from ‘package:SparseM’:
> >
> >   image
> >
> > * installing *source* package ‘rms’ ...
> > ** package ‘rms’ successfully unpacked and MD5 sums checked
> > ** libs
> > clang -I/Library/Frameworks/R.framework/Resources/include  
> > -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
> > gfortran   -fPIC  -g -O2  -c lrmfit.f -o lrmfit.o
> > gfortran   -fPIC  -g -O2  -c mlmats.f -o mlmats.o
> > gfortran   -fPIC  -g -O2  -c ormuv.f -o ormuv.o
> > gfortran   -fPIC  -g -O2  -c robcovf.f -o robcovf.o
> > clang -dynamiclib -Wl,-headerpad_max_install_names -undefined 
> > dynamic_lookup -single_module -multiply_defined suppress 
> > -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rms.so 
> > init.o lrmfit.o mlmats.o ormuv.o robcovf.o 
> > -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 
> > -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm 
> > -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework 
> > -Wl,CoreFoundation
> > installing to 
> > /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs
> > ** R
> > ** demo
> > ** inst
> > ** preparing package for lazy loading
> > ** help
> > *** installing help indices
> > ** building package indices
> > ** testing if installed package can be loaded
> > Loading required package: lattice
> > Loading required package: sos
> > Loading required package: brew
> > Loading required package: rms
> > Loading required package: Hmisc
> > Loading required package: survival
> > Loading required package: Formula
> > Loading required package: stats
> > Loading required package: ggplot2
> >
> > Attaching package: ‘Hmisc’
> >
> > The following objects are masked from ‘package:base’:
> >
> >   format.pval, round.POSIXt, trunc.POSIXt, units
> >
> > Loading required package: SparseM
> >
> > Attaching package: ‘SparseM’
> >
> > The following object is masked from ‘package:base’:
> >
> >   backsolve
> >
> > Error: package or namespace load failed for ‘rms’ in dyn.load(file, DLLpath 
> > = DLLpath, ...):
> > unable to load shared object 
> > '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so':
> > dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so,
> >  6): Symbol not found: ___addtf3
>

Re: [R-SIG-Mac] missing module when compiling R pkg:rms or external package SYMPHONY (in support of Bioc pkg symphony)

[David Winsemius]

> On May 5, 2017, at 12:13 AM, Berend Hasselman <b...@xs4all.nl> wrote:
> 
> 
>> On 5 May 2017, at 03:12, David Winsemius <dwinsem...@comcast.net> wrote:
>> 
>> Failing to get current rms package to compile (and appears that the CRAN 
>> build machine fails as well). The penultimate version of rms succeeds.
>> 
>> Both from console and cmd-line I get this response in R 3.4.0 (just 
>> installed today) running El Cap 10.11.6 with Xcode Version 8.2.1 (8C1002):
>> 
>> trying URL 'https://cran.cnr.berkeley.edu/src/contrib/rms_5.1-1.tar.gz'
>> Content type 'application/x-gzip' length 521311 bytes (509 KB)
>> ==
>> downloaded 509 KB
>> 
>> Loading required package: lattice
>> Loading required package: sos
>> Loading required package: brew
>> Loading required package: rms
>> Loading required package: Hmisc
>> Loading required package: survival
>> Loading required package: Formula
>> Loading required package: stats
>> Loading required package: ggplot2
>> 
>> Attaching package: ‘Hmisc’
>> 
>> The following objects are masked from ‘package:base’:
>> 
>>  format.pval, round.POSIXt, trunc.POSIXt, units
>> 
>> Loading required package: SparseM
>> 
>> Attaching package: ‘SparseM’
>> 
>> The following object is masked from ‘package:base’:
>> 
>>  backsolve
>> 
>> ##-- 2017-05-04 --##
>> Loading required package: graphics
>> 
>> Attaching package: ‘graphics’
>> 
>> The following object is masked from ‘package:SparseM’:
>> 
>>  image
>> 
>> * installing *source* package ‘rms’ ...
>> ** package ‘rms’ successfully unpacked and MD5 sums checked
>> ** libs
>> clang -I/Library/Frameworks/R.framework/Resources/include  
>> -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
>> gfortran   -fPIC  -g -O2  -c lrmfit.f -o lrmfit.o
>> gfortran   -fPIC  -g -O2  -c mlmats.f -o mlmats.o
>> gfortran   -fPIC  -g -O2  -c ormuv.f -o ormuv.o
>> gfortran   -fPIC  -g -O2  -c robcovf.f -o robcovf.o
>> clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup 
>> -single_module -multiply_defined suppress 
>> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rms.so 
>> init.o lrmfit.o mlmats.o ormuv.o robcovf.o 
>> -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 
>> -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm 
>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework 
>> -Wl,CoreFoundation
>> installing to 
>> /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs
>> ** R
>> ** demo
>> ** inst
>> ** preparing package for lazy loading
>> ** help
>> *** installing help indices
>> ** building package indices
>> ** testing if installed package can be loaded
>> Loading required package: lattice
>> Loading required package: sos
>> Loading required package: brew
>> Loading required package: rms
>> Loading required package: Hmisc
>> Loading required package: survival
>> Loading required package: Formula
>> Loading required package: stats
>> Loading required package: ggplot2
>> 
>> Attaching package: ‘Hmisc’
>> 
>> The following objects are masked from ‘package:base’:
>> 
>>  format.pval, round.POSIXt, trunc.POSIXt, units
>> 
>> Loading required package: SparseM
>> 
>> Attaching package: ‘SparseM’
>> 
>> The following object is masked from ‘package:base’:
>> 
>>  backsolve
>> 
>> Error: package or namespace load failed for ‘rms’ in dyn.load(file, DLLpath 
>> = DLLpath, ...):
>> unable to load shared object 
>> '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so':
>> dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so,
>>  6): Symbol not found: ___addtf3
>> Referenced from: /usr/local/lib/libquadmath.0.dylib
>> Expected in: /usr/local/lib/libgcc_s.1.dylib
>> in /usr/local/lib/libquadmath.0.dylib
>> ##-- 2017-05-04 --##
>> Loading required package: graphics
>> 
>> Attaching package: ‘graphics’
>> 
>> The following object is masked from ‘package:SparseM’:
>> 
>>  image
>> 
>> Error: package or namespace load failed for ‘rms’ in dyn.load(file, DLLpath 
>> = DLLpath, ...):
>> unable to load shared object 
>> '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so':
>> dlopen(/Library/Frame

Re: [R-SIG-Mac] missing module when compiling R pkg:rms or external package SYMPHONY (in support of Bioc pkg symphony)

[David Winsemius]

> On May 4, 2017, at 6:12 PM, David Winsemius <dwinsem...@comcast.net> wrote:
> 
> Failing to get current rms package to compile (and appears that the CRAN 
> build machine fails as well). The penultimate version of rms succeeds.
> 
> Both from console and cmd-line I get this response in R 3.4.0 (just installed 
> today) running El Cap 10.11.6 with Xcode Version 8.2.1 (8C1002):

Also tried to see which gfortran was retruned along hte R search path:

> system("gfortran -v")
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin15/6.1.0/lto-wrapper
Target: x86_64-apple-darwin15
Configured with: ../gcc-6.1.0/configure --prefix=/usr/local/gfortran 
--with-gmp=/Users/fx/devel/gcc/deps-static/x86_64 
--enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin15
Thread model: posix
gcc version 6.1.0 (GCC) 


> 
> trying URL 'https://cran.cnr.berkeley.edu/src/contrib/rms_5.1-1.tar.gz'
> Content type 'application/x-gzip' length 521311 bytes (509 KB)
> ==
> downloaded 509 KB
> 
> Loading required package: lattice
> Loading required package: sos
> Loading required package: brew
> Loading required package: rms
> Loading required package: Hmisc
> Loading required package: survival
> Loading required package: Formula
> Loading required package: stats
> Loading required package: ggplot2
> 
> Attaching package: ‘Hmisc’
> 
> The following objects are masked from ‘package:base’:
> 
>   format.pval, round.POSIXt, trunc.POSIXt, units
> 
> Loading required package: SparseM
> 
> Attaching package: ‘SparseM’
> 
> The following object is masked from ‘package:base’:
> 
>   backsolve
> 
> ##-- 2017-05-04 --##
> Loading required package: graphics
> 
> Attaching package: ‘graphics’
> 
> The following object is masked from ‘package:SparseM’:
> 
>   image
> 
> * installing *source* package ‘rms’ ...
> ** package ‘rms’ successfully unpacked and MD5 sums checked
> ** libs
> clang -I/Library/Frameworks/R.framework/Resources/include  
> -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
> gfortran   -fPIC  -g -O2  -c lrmfit.f -o lrmfit.o
> gfortran   -fPIC  -g -O2  -c mlmats.f -o mlmats.o
> gfortran   -fPIC  -g -O2  -c ormuv.f -o ormuv.o
> gfortran   -fPIC  -g -O2  -c robcovf.f -o robcovf.o
> clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup 
> -single_module -multiply_defined suppress 
> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rms.so 
> init.o lrmfit.o mlmats.o ormuv.o robcovf.o 
> -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 
> -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm 
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework 
> -Wl,CoreFoundation
> installing to 
> /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs
> ** R
> ** demo
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> Loading required package: lattice
> Loading required package: sos
> Loading required package: brew
> Loading required package: rms
> Loading required package: Hmisc
> Loading required package: survival
> Loading required package: Formula
> Loading required package: stats
> Loading required package: ggplot2
> 
> Attaching package: ‘Hmisc’
> 
> The following objects are masked from ‘package:base’:
> 
>   format.pval, round.POSIXt, trunc.POSIXt, units
> 
> Loading required package: SparseM
> 
> Attaching package: ‘SparseM’
> 
> The following object is masked from ‘package:base’:
> 
>   backsolve
> 
> Error: package or namespace load failed for ‘rms’ in dyn.load(file, DLLpath = 
> DLLpath, ...):
> unable to load shared object 
> '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so':
> dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so,
>  6): Symbol not found: ___addtf3
> Referenced from: /usr/local/lib/libquadmath.0.dylib
> Expected in: /usr/local/lib/libgcc_s.1.dylib
> in /usr/local/lib/libquadmath.0.dylib
> ##-- 2017-05-04 --##
> Loading required package: graphics
> 
> Attaching package: ‘graphics’
> 
> The following object is masked from ‘package:SparseM’:
> 
>   image
> 
> Error: package or namespace load failed for ‘rms’ in dyn.load(file, DLLpath = 
> DLLpath, ...):
> unable to load shared object 
> '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so':
> dlopen(/Library/Frameworks/R.framework/Versions/3

[R-SIG-Mac] missing module when compiling R pkg:rms or external package SYMPHONY (in support of Bioc pkg symphony)

[David Winsemius]

Failing to get current rms package to compile (and appears that the CRAN build 
machine fails as well). The penultimate version of rms succeeds.

Both from console and cmd-line I get this response in R 3.4.0 (just installed 
today) running El Cap 10.11.6 with Xcode Version 8.2.1 (8C1002):

trying URL 'https://cran.cnr.berkeley.edu/src/contrib/rms_5.1-1.tar.gz'
Content type 'application/x-gzip' length 521311 bytes (509 KB)
==
downloaded 509 KB

Loading required package: lattice
Loading required package: sos
Loading required package: brew
Loading required package: rms
Loading required package: Hmisc
Loading required package: survival
Loading required package: Formula
Loading required package: stats
Loading required package: ggplot2

Attaching package: ‘Hmisc’

The following objects are masked from ‘package:base’:

   format.pval, round.POSIXt, trunc.POSIXt, units

Loading required package: SparseM

Attaching package: ‘SparseM’

The following object is masked from ‘package:base’:

   backsolve

##-- 2017-05-04 --##
Loading required package: graphics

Attaching package: ‘graphics’

The following object is masked from ‘package:SparseM’:

   image

* installing *source* package ‘rms’ ...
** package ‘rms’ successfully unpacked and MD5 sums checked
** libs
clang -I/Library/Frameworks/R.framework/Resources/include  
-I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
gfortran   -fPIC  -g -O2  -c lrmfit.f -o lrmfit.o
gfortran   -fPIC  -g -O2  -c mlmats.f -o mlmats.o
gfortran   -fPIC  -g -O2  -c ormuv.f -o ormuv.o
gfortran   -fPIC  -g -O2  -c robcovf.f -o robcovf.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup 
-single_module -multiply_defined suppress 
-L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rms.so 
init.o lrmfit.o mlmats.o ormuv.o robcovf.o 
-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 
-L/usr/local/gfortran/lib -lgfortran -lquadmath -lm 
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework 
-Wl,CoreFoundation
installing to 
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Loading required package: lattice
Loading required package: sos
Loading required package: brew
Loading required package: rms
Loading required package: Hmisc
Loading required package: survival
Loading required package: Formula
Loading required package: stats
Loading required package: ggplot2

Attaching package: ‘Hmisc’

The following objects are masked from ‘package:base’:

   format.pval, round.POSIXt, trunc.POSIXt, units

Loading required package: SparseM

Attaching package: ‘SparseM’

The following object is masked from ‘package:base’:

   backsolve

Error: package or namespace load failed for ‘rms’ in dyn.load(file, DLLpath = 
DLLpath, ...):
unable to load shared object 
'/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so':
 
dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so,
 6): Symbol not found: ___addtf3
 Referenced from: /usr/local/lib/libquadmath.0.dylib
 Expected in: /usr/local/lib/libgcc_s.1.dylib
in /usr/local/lib/libquadmath.0.dylib
##-- 2017-05-04 --##
Loading required package: graphics

Attaching package: ‘graphics’

The following object is masked from ‘package:SparseM’:

   image

Error: package or namespace load failed for ‘rms’ in dyn.load(file, DLLpath = 
DLLpath, ...):
unable to load shared object 
'/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so':
 
dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so,
 6): Symbol not found: ___addtf3
 Referenced from: /usr/local/lib/libquadmath.0.dylib
 Expected in: /usr/local/lib/libgcc_s.1.dylib
in /usr/local/lib/libquadmath.0.dylib
Error: loading failed
Execution halted

The downloaded source packages are in

‘/private/var/folders/yq/m3j1jqtj6hq6s5mq_v0jn3s8gn/T/Rtmpplg8Th/downloaded_packages’

(WARNING: partial output only, ask package author to use Rprintf instead!)
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms’
* restoring previous 
‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms’

I get the same result with this (minus the request "to use Rprinf instead!"

$ R CMD INSTALL /Users/davidwinsemius/Downloads/rms_5.1-1.tar.gz 

Reported to Frank but he has seen no problems in his Linux builds.

This page:

https://github.com/JuliaLang/julia/issues/636

...  has a posting that says:

"I found the solution: putting /usr/local/gfortran/lib at the beginning of 
DYLD_LIBRARY_PATH solved the problem. Previously I had .../gfortran/lib at the 
end of DYLD_LIBRARY_PATH."

What more do I need to supply?

-- 

David W

Re: [R-SIG-Mac] R-3.3.3.pkg not archived after R-3.4.0 release

[David Winsemius]

Sent from my iPhone

> On Apr 26, 2017, at 10:16 AM, Jim Hester  wrote:
> 
> Could R-3.3.3.pkg be moved into the `
> https://cloud.r-project.org/bin/macosx/old/` directory with the other past
> releases? We look for the `.pkg` file for past releases there in the travis
> script, and R-3.3.3 has not been copied there yet. (see also
> https://github.com/travis-ci/travis-ci/issues/7665)

If you need it in the meantime, you can get it here:

https://r.research.att.com/

David
> 
> Thanks,
> 
> Jim
> 
>[[alternative HTML version deleted]]
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

[[alternative HTML version deleted]]

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Re: [R-SIG-Mac] R-3.3.3.pkg not archived after R-3.4.0 release

[David Winsemius]

I don't think CRAN administers that repo.

> On Apr 26, 2017, at 10:16 AM, Jim Hester  wrote:
> 
> Could R-3.3.3.pkg be moved into the `
> https://cloud.r-project.org/bin/macosx/old/` directory with the other past
> releases? We look for the `.pkg` file for past releases there in the travis
> script, and R-3.3.3 has not been copied there yet. (see also
> https://github.com/travis-ci/travis-ci/issues/7665)
> 
> Thanks,
> 
> Jim
> 
>[[alternative HTML version deleted]]
> 

And rhelp is plain text.

David
> ___
> 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] R version 3.3.2 crashes on launching

[David Winsemius]

> On Feb 10, 2017, at 2:05 PM, Ossenbruggen, Paul <paul.ossenbrug...@unh.edu> 
> wrote:
> 
> Once R opens on my Mac, I have had no problems running it from that point on.
> 
> To resolve the opening issues, I reinstalled version 3.3.2 and XQuartz 
> version 2.7.11. No issues with these installations but R won’t open properly.
> 
> 
> Try 1. On opening it, I got the following message:
> 
> *** RController: caught ObjC exception while processing system events. Update 
> to the latest GUI version and consider reporting this properly (see FAQ) if 
> it persists and is not known.
> *** reason: -[_NSViewLayoutAux setRuleThickness:]: unrecognized selector sent 
> to instance 0x7f8a77744970
> 
> It worked regardless of the message.
> 
> 
> Try 2. I quit R and opened it again. This time I obtain R(not running) in 
> Force Quit
> 
> *** caught seqfault ***
> address 0xf110, cause `memory not mapped’
> 
> 
> Tries 3, 4 and 5. No messages but I obtain  R(not running) in Force Quit.
> 
> Terminal returns:
> 
> md5: R-3.3.2.pkg: No such file or directory
> 
> 
> Unfortunately, I am clueless on how to fix the problem.

So far you have not mentioned deleting the (hidden by default) files named 
.RData and .Rhistory and .Rapp.history

-- David.
> 
> Help will be greatly appreciated.
> 
> Thanks,
> 
> Paul
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] Unable to install quantstrat from sources on MAC

[David Winsemius]

meworks/R.framework/Versions/3.3/Resources/library/Per
> formanceAnalytics’
> Warning in install.packages :
> installation of package ‘PerformanceAnalytics’ had non-zero exit status
> ERROR: dependency ‘PerformanceAnalytics’ is not available for package
> ‘blotter’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/blo
> tter’
> Warning in install.packages :
> installation of package ‘blotter’ had non-zero exit status
> ERROR: dependency ‘blotter’ is not available for package ‘quantstrat’
> * removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/qua
> ntstrat’
> Warning in install.packages :
> installation of package ‘quantstrat’ had non-zero exit status
> 
> The downloaded source packages are in
>   
> ‘/private/var/folders/7l/dpy9h0ss2450qcp053x0_sk0gn/T/Rtmp7zLZ6J/download
> ed_packages’
> 
> Leo Shpiz
> 518-488-7326
> 
> 
> 
> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] R Console (R.app) crashes - on Mac OS - caught segfault * address 0x18, cause 'memory not mapped'

[David Winsemius]

> On Dec 30, 2016, at 8:44 AM, Christoph Napierala <napier...@gmx.net> wrote:
> 
> Dear All
> 
> macOS Sierra - V 10.12.2
> R 3.3.2 GUI 1.68 Mavericks build (7288)
> 
> I encountered an issue with the R console crashing after having saved the 
> image. Normally I work with R-Studio which still runs "perfectly".
> The following report was generated after having deleted R and R-Studio and 
> cleaned libraries. The following message was generated:
> 
>> Blockquote
> *** caught segfault ***
> address 0x18, cause 'memory not mapped'
> 
>   Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> 
> 2016-12-30 14:57:47.245 R[1475:47927] -[_CUIInternalLinkRendition 
> setRuleThickness:]: unrecognized selector sent to instance 0x7ffeb66745d0
> 
> 2016-12-30 14:57:47.247 R[1475:47927] *** RController: caught ObjC exception 
> while processing system events. Update to the latest GUI version and consider 
> reporting this properly (see FAQ) if it persists and is not known.

The latest GUI version at http://r.research.att.com/ is:

R-GUI-7299-3.3-mavericks-Debug.dmg


> 
> *** reason: -[_CUIInternalLinkRendition setRuleThickness:]: unrecognized 
> selector sent to instance 0x7ffeb66745d0
> 
> *** name: NSInvalidArgumentException, info: (null)
> 
> *** Version: R 3.3.2 (71607) R.app R 3.3.2 GUI 1.68 Mavericks build
> Consider saving your work soon in case this develops into a problem.

You should probably reinstall the whole bundle since your version of R is not 
uptodate either:

R-3.3-branch
3.3.2 Patched
(2016/12/28, r71859)

The installer bundles at either of these sites should be the same:

http://r.research.att.com/mavericks/R-3.3-branch/R-3.3-branch-mavericks.pkg
https://cloud.r-project.org/bin/macosx/R-3.3.2.pkg



> 
> And then I am offered to select one of the above options and the crash 
> reproduces.
> 
> Thanks for any support.
> 
> _______
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Re: [R-SIG-Mac] Download data from Internet contained in a Zip file

[David Winsemius]

> On Dec 26, 2016, at 3:19 AM, Christofer Bogaso <bogaso.christo...@gmail.com> 
> wrote:
> 
> Hi David et al,
> 
> Thanks for showing the pointers. With your approach, I see the
> "temp.zip" file in my working folder.
> 
> However still I could not extract the data within it. I tried using
> unzip() function, however not really going through :
> 
>> unzip("temp.zip")
> Warning message:
> In unzip("temp.zip") : error 1 in extracting from zip file

I didn't try to use R to unzip it. Just using my system facilities worked fine.

I'm not able to reproduce:

> ?unzip
> dat <- unzip("~/temp.zip")
> str(dat)
 chr "./NAV_File_23122016.out"
> dat_in <- read.table(dat)
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 1 did not have 17 elements
> dat_in <- read.csv(dat, header=FALSE)
> str(dat_in)
'data.frame':   75 obs. of  6 variables:
 $ V1: Factor w/ 1 level "12/23/2016": 1 1 1 1 1 1 1 1 1 1 ...
 $ V2: Factor w/ 7 levels "PFM001","PFM002",..: 1 1 1 1 1 1 1 1 1 1 ...
 $ V3: Factor w/ 7 levels "HDFC PENSION MANAGEMENT COMPANY LIMITED",..: 6 6 6 6 
6 6 6 6 6 6 ...
 $ V4: Factor w/ 75 levels "SM001001","SM001002",..: 5 7 8 11 12 13 1 2 3 4 ...
 $ V5: Factor w/ 75 levels "HDFC PENSION MANAGEMENT COMPANY LIMITED SCHEME A - 
TIER I",..: 62 59 63 37 56 57 54 55 60 58 ...
 $ V6: num  21.7 21.1 20.8 11.7 10.1 ...


-- 
David.
> 
> When I try to access the link
> "https://npscra.nsdl.co.in/download.php?path=download/=NAV_File_23122016.zip;
> manually, then download the zip file and then unzip it, I get a file
> called "NAV_File_23122016.out". Which next I open in excel and get all
> the data.
> 
> I was just trying to perform similar task, however through R, so that
> I can load data automatically directly from Web.
> 
> Any Idea please. I am using below version of R (I know this is quite
> old version, however I am not currently in a position to upgrade my
> Macbook)
> 
>> R.Version()
> $platform
> [1] "x86_64-apple-darwin10.8.0"
> 
> $arch
> [1] "x86_64"
> 
> $os
> [1] "darwin10.8.0"
> 
> $system
> [1] "x86_64, darwin10.8.0"
> 
> $status
> [1] ""
> 
> $major
> [1] "3"
> 
> $minor
> [1] "2.1"
> 
> $year
> [1] "2015"
> 
> $month
> [1] "06"
> 
> $day
> [1] "18"
> 
> $`svn rev`
> [1] "68531"
> 
> $language
> [1] "R"
> 
> $version.string
> [1] "R version 3.2.1 (2015-06-18)"
> 
> $nickname
> [1] "World-Famous Astronaut"
> 
> On Mon, Dec 26, 2016 at 7:18 AM, David Winsemius <dwinsem...@comcast.net> 
> wrote:
>> 
>>> On Dec 25, 2016, at 3:46 PM, Gábor Csárdi <csardi.ga...@gmail.com> wrote:
>>> 
>>> Your R build does not support HTTPS.
>>> 
>>> I suggest that you use the curl package if you can. HTTP support in
>>> base R is very limited currently.
>> 
>> I generally use the downloader package. It sets up the call to download.file 
>> so that it succeeds with https URLs.
>> 
>> 
>> install.packages("downloader", dependencies=TRUE)
>> trying URL 
>> 'http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.3/downloader_0.4.tgz'
>> Content type 'application/x-gzip' length 19459 bytes (19 KB)
>> ==
>> downloaded 19 KB
>> 
>> 
>> The downloaded binary packages are in
>>
>> /var/folders/68/vh2f8kzn09j8954r6q9100yhgn/T//Rtmpq8DVG4/downloaded_packages
>>> library(downloader)
>>> help(pac=downloader)
>> starting httpd help server ... done
>>> download("https://npscra.nsdl.co.in/download.php?path=download/=NAV_File_23122016.zip","temp.zip;)
>> 
>> # Requires both a source and destination file name.
>> 
>> trying URL 
>> 'https://npscra.nsdl.co.in/download.php?path=download/=NAV_File_23122016.zip'
>> Content type 'application/octet-stream' length 1228 bytes
>> ==
>> downloaded 1228 bytes
>> 
>> --
>> David.
>>> 
>>> Gabor
>>> 
>>> 
>>> 
>>> On Sun, Dec 25, 2016 at 10:37 PM, Christofer Bogaso
>>> <bogaso.christo...@gmail.com> wrote:
>>>> Hi again,
>>>> 
>>>> I posted this in general R thread, however it is suggested this group
>>>> since I am using MAC OS 10.7.5.
&g

Re: [R-SIG-Mac] Download data from Internet contained in a Zip file

[David Winsemius]

> On Dec 25, 2016, at 3:46 PM, Gábor Csárdi  wrote:
> 
> Your R build does not support HTTPS.
> 
> I suggest that you use the curl package if you can. HTTP support in
> base R is very limited currently.

I generally use the downloader package. It sets up the call to download.file so 
that it succeeds with https URLs.


 install.packages("downloader", dependencies=TRUE)
trying URL 
'http://cran.cnr.Berkeley.edu/bin/macosx/mavericks/contrib/3.3/downloader_0.4.tgz'
Content type 'application/x-gzip' length 19459 bytes (19 KB)
==
downloaded 19 KB


The downloaded binary packages are in

/var/folders/68/vh2f8kzn09j8954r6q9100yhgn/T//Rtmpq8DVG4/downloaded_packages
> library(downloader)
> help(pac=downloader)
starting httpd help server ... done
> download("https://npscra.nsdl.co.in/download.php?path=download/=NAV_File_23122016.zip","temp.zip;)

# Requires both a source and destination file name.

trying URL 
'https://npscra.nsdl.co.in/download.php?path=download/=NAV_File_23122016.zip'
Content type 'application/octet-stream' length 1228 bytes
==
downloaded 1228 bytes

-- 
David.
> 
> Gabor
> 
> 
> 
> On Sun, Dec 25, 2016 at 10:37 PM, Christofer Bogaso
>  wrote:
>> Hi again,
>> 
>> I posted this in general R thread, however it is suggested this group
>> since I am using MAC OS 10.7.5.
>> 
>> I was following the instruction available in
>> "http://stackoverflow.com/questions/3053833/using-r-to-download-zipped-data-file-extract-and-import-data;
>> to download data from Internet contained in a zip file from the
>> address :
>> 
>> https://npscra.nsdl.co.in/download.php?path=download/=NAV_File_23122016.zip
>> 
>> However when I tried to follow the instruction I am facing below error :
>> 
>>> temp <- tempfile()
>>> download.file("https://npscra.nsdl.co.in/download.php?path=download/=NAV_File_23122016.zip",temp)
>> Error in 
>> download.file("https://npscra.nsdl.co.in/download.php?path=download/=NAV_File_23122016.zip;,
>> :
>>  unsupported URL scheme
>> 
>> Can someone here please tell me what went wrong in above?
>> 
>> Highly appreciate your feedback.
>> 
>> Thanks for your time.
>> 
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
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Re: [R-SIG-Mac] Garch Model Library on Mac

[David Winsemius]

y/Frameworks/R.framework/Resources/modules//R_X11.so
>   Expected in: flat namespace
>  in /Library/Frameworks/R.framework/Resources/modules//R_X11.so
> ERROR: dependencies ‘DistributionUtils’, ‘GeneralizedHyperbolic’ are not 
> available for package ‘SkewHyperbolic’
> * removing ‘/Users/joshcchien/Library/R/3.3/library/SkewHyperbolic’
> Warning in install.packages :
>   installation of package ‘SkewHyperbolic’ had non-zero exit status
> Warning message:
> In doTryCatch(return(expr), name, parentenv, handler) :
>   unable to load shared object 
> '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
>   dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): 
> Symbol not found: _CGBitmapContextCreate
>   Referenced from: /Library/Frameworks/R.framework/Resources/modules//R_X11.so
>   Expected in: flat namespace
>  in /Library/Frameworks/R.framework/Resources/modules//R_X11.so
> ERROR: dependencies ‘Rsolnp’, ‘nloptr’, ‘ks’, ‘xts’, ‘zoo’, ‘chron’, 
> ‘SkewHyperbolic’, ‘expm’, ‘Rcpp’, ‘RcppArmadillo’ are not available for 
> package ‘rugarch’
> * removing ‘/Users/joshcchien/Library/R/3.3/library/rugarch’
> Warning in install.packages :
>   installation of package ‘rugarch’ had non-zero exit status
> 
> The downloaded source packages are in
> 
> ‘/private/var/folders/vs/tv8qhwdn4r58jtlc9yhmz35mgp/T/Rtmpw48bcl/downloaded_packages’
> 
> -- 
> Josh Chien
> Sent from my MacBook Pro
> Telegram @joshchien
> 

David Winsemius
Alameda, CA, USA

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Re: [R-SIG-Mac] Garch Model Library on Mac

[David Winsemius]

Library/Developer/CommandLineTools/usr/bin/xcrun
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> xcrun: error: invalid active developer path 
> (/Library/Developer/CommandLineTools), missing xcrun at: 
> /Library/Developer/CommandLineTools/usr/bin/xcrun
> 
> 
> -- 
> Josh Chien
> Sent from my Mac
> Telegram : @joshchien
> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] [Autosave]

[David Winsemius]

> On Nov 17, 2016, at 9:09 AM, Dr Didier G. Leibovici 
> <didier.leibov...@nottingham.ac.uk> wrote:
> 
> Hi, On MacOs X Sierra my R crashed, reopening it, it showed a file 
> myscript[Autosaved].R then trying to save this without the [Autosaved] 
> it crashed again  and now I can't recover my last version, i.e. I 
> can see the the myscript.R from 3 or 4 hours ago. Can I locate the 
> changes somewhere to recover the almost very last version of the file? 
> thanks, Didier

Don't you have TimeMachine working?

> 
> -- 
> Dr Didier G. Leibovici
>d-d'yeley-bow-v-c
> Senior Research Fellow
> Geocomputational Modelling & Geospatial Statistics
> Nottingham Geospatial Institute
> 
snipped
> 
>   [[alternative HTML version deleted]]
> 
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[R-SIG-Mac] gputools package installation on Mac perhaps fixed

[David Winsemius]

My old video card was dying and I got a donation of an older nVidia card 
(NVIDIA Quadro FX 5600 1536 MB) I tried installing gputools from source using 
current CRAN image. Had earlier installed the most recent CUDA compiler version 
8  (cuda_8.0.47_mac_network-dmg). The CRAN pages says no version is available. 
I'm currently working with R 3.3.1 patched on an El Cap version 10.11.6 
(15G1108) using an early 2008 MacPro.  Ran into compiler difficulties with the 
source image, but after corresponding with Josh Buckner and sharing the 
installation logs and errors he tweaked some of the configure file and  built a 
new version that does compile (with many warnings that he says are all safe to 
ignore). He suggests trying the github version 1.2 and posting any difficulties 
there:

install.packages("devtools")
library(devtools)
install_github("nullsatz/gputools")

He suggested announcing that we did this together, but I think all the 
intellectual credit goes to him and the other authors.
-- 

David Winsemius
Alameda, CA, USA

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Re: [R-SIG-Mac] How to put below code in Automator in iOS

[David Winsemius]

> On Oct 27, 2016, at 11:05 AM, Christofer Bogaso <bogaso.christo...@gmail.com> 
> wrote:
> 
> Hi,
> 
> The code is same as in that page. i.e.
> 
> require(tcltk)
> 
> tt <- tktoplevel()
> rb1 <- tkradiobutton(tt)
> rb2 <- tkradiobutton(tt)
> rbValue <- tclVar("oranges")
> tkconfigure(rb1,variable=rbValue,value="apples")
> tkconfigure(rb2,variable=rbValue,value="oranges")
> tkgrid(tklabel(tt,text="Which do you prefer?"))
> tkgrid(tklabel(tt,text="Apples "),rb1)
> tkgrid(tklabel(tt,text="Oranges "),rb2)
> 
> OnOK <- function()
> {
>rbVal <- as.character(tclvalue(rbValue))
>tkdestroy(tt)
>if (rbVal=="apples")
>tkmessageBox(message="Good choice!  An apple a day keeps the doctor away!")
>if (rbVal=="oranges")
>tkmessageBox(message="Good choice!  Oranges are full of Vitamin C!")
> }
> OK.but <- tkbutton(tt,text="OK",command=OnOK)
> tkgrid(OK.but)
> tkfocus(tt)

I'm predicting that you cannot get that file to do anything interesting with 
Rscript, so I don't understand why you think that you can use an Rscript-ing 
strategy within Automator.

-- 
David.
> 
> On Thu, Oct 27, 2016 at 11:10 PM, David Winsemius
> <dwinsem...@comcast.net> wrote:
>> 
>>> On Oct 27, 2016, at 10:32 AM, David Winsemius <dwinsem...@comcast.net> 
>>> wrote:
>>> 
>>> 
>>>> On Oct 27, 2016, at 10:16 AM, David Winsemius <dwinsem...@comcast.net> 
>>>> wrote:
>>>> 
>>>> 
>>>>> On Oct 27, 2016, at 10:07 AM, Christofer Bogaso 
>>>>> <bogaso.christo...@gmail.com> wrote:
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> Previously I posted this same thread in general R help, however folks
>>>>> there suggested to post in this specialized group for better answer.
>>>>> 
>>>>> I have a piece of code available here
>>>>> 
>>>>> http://mcu.edu.tw/~chenmh/teaching/project/r/reference/RTclTkExamples/radiobuttons.html
>>>>> 
>>>>> Now I put that code in a .R file and then created an .app file in Mac
>>>>> using Automator as explained below
>>>>> 
>>>>> https://www.r-bloggers.com/how-to-source-an-r-script-automatically-on-a-mac-using-automator-and-ical/
>>>>> 
>>>>> Surprisingly what I see is that, when I put that R code in a .app
>>>>> file, R fails to pop up the input window, which otherwise is fine when
>>>>> I just copy paste that code in R window.
>>>>> 
>>>>> Could you please help if I need to have anything extra so that my .app
>>>>> will be able to take the input.
>>>> 
>>>> You should post the code that is in your .R file.
>>> 
>>> I have further concerns that I should have mentioned because I suspect 
>>> you're trying to use functions that are not designed to be used inside 
>>> Rscript process. The Tcl/Tk functions are designed to use in interactive 
>>> sessions.
>> 
>> And some searching on this matter shows that there have been prior suggested 
>> approaches to starting interactive R processes from a system console session:
>> 
>> http://markmail.org/search/?q=list%3Aorg.r-project.r-help+rscript+interactive+tcl#query:list%3Aorg.r-project.r-help%20rscript%20interactive%20tcl+page:1+mid:uyykuacq77cuxoas+state:results
>> 
>> 
>>>> 
>>>> 
>>>>> 
>>>>> Thanks for your time.
>>>>> 
>>>>> ___
>>>>> R-SIG-Mac mailing list
>>>>> R-SIG-Mac@r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>> 
>>>> David Winsemius
>>>> Alameda, CA, USA
>>>> 
>>>> ___
>>>> R-SIG-Mac mailing list
>>>> R-SIG-Mac@r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>>> David Winsemius
>>> Alameda, CA, USA
>>> 
>>> ___
>>> R-SIG-Mac mailing list
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>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>> David Winsemius
>> Alameda, CA, USA
>> 

David Winsemius
Alameda, CA, USA

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Re: [R-SIG-Mac] How to put below code in Automator in iOS

[David Winsemius]

> On Oct 27, 2016, at 10:32 AM, David Winsemius <dwinsem...@comcast.net> wrote:
> 
> 
>> On Oct 27, 2016, at 10:16 AM, David Winsemius <dwinsem...@comcast.net> wrote:
>> 
>> 
>>> On Oct 27, 2016, at 10:07 AM, Christofer Bogaso 
>>> <bogaso.christo...@gmail.com> wrote:
>>> 
>>> Hi,
>>> 
>>> Previously I posted this same thread in general R help, however folks
>>> there suggested to post in this specialized group for better answer.
>>> 
>>> I have a piece of code available here
>>> 
>>> http://mcu.edu.tw/~chenmh/teaching/project/r/reference/RTclTkExamples/radiobuttons.html
>>> 
>>> Now I put that code in a .R file and then created an .app file in Mac
>>> using Automator as explained below
>>> 
>>> https://www.r-bloggers.com/how-to-source-an-r-script-automatically-on-a-mac-using-automator-and-ical/
>>> 
>>> Surprisingly what I see is that, when I put that R code in a .app
>>> file, R fails to pop up the input window, which otherwise is fine when
>>> I just copy paste that code in R window.
>>> 
>>> Could you please help if I need to have anything extra so that my .app
>>> will be able to take the input.
>> 
>> You should post the code that is in your .R file.
> 
> I have further concerns that I should have mentioned because I suspect you're 
> trying to use functions that are not designed to be used inside Rscript 
> process. The Tcl/Tk functions are designed to use in interactive sessions.

And some searching on this matter shows that there have been prior suggested 
approaches to starting interactive R processes from a system console session:

http://markmail.org/search/?q=list%3Aorg.r-project.r-help+rscript+interactive+tcl#query:list%3Aorg.r-project.r-help%20rscript%20interactive%20tcl+page:1+mid:uyykuacq77cuxoas+state:results


>> 
>> 
>>> 
>>> Thanks for your time.
>>> 
>>> _______
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>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>> David Winsemius
>> Alameda, CA, USA
>> 
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> 
> David Winsemius
> Alameda, CA, USA
> 
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Re: [R-SIG-Mac] How to put below code in Automator in iOS

[David Winsemius]

> On Oct 27, 2016, at 10:16 AM, David Winsemius <dwinsem...@comcast.net> wrote:
> 
> 
>> On Oct 27, 2016, at 10:07 AM, Christofer Bogaso 
>> <bogaso.christo...@gmail.com> wrote:
>> 
>> Hi,
>> 
>> Previously I posted this same thread in general R help, however folks
>> there suggested to post in this specialized group for better answer.
>> 
>> I have a piece of code available here
>> 
>> http://mcu.edu.tw/~chenmh/teaching/project/r/reference/RTclTkExamples/radiobuttons.html
>> 
>> Now I put that code in a .R file and then created an .app file in Mac
>> using Automator as explained below
>> 
>> https://www.r-bloggers.com/how-to-source-an-r-script-automatically-on-a-mac-using-automator-and-ical/
>> 
>> Surprisingly what I see is that, when I put that R code in a .app
>> file, R fails to pop up the input window, which otherwise is fine when
>> I just copy paste that code in R window.
>> 
>> Could you please help if I need to have anything extra so that my .app
>> will be able to take the input.
> 
> You should post the code that is in your .R file.

I have further concerns that I should have mentioned because I suspect you're 
trying to use functions that are not designed to be used inside Rscript 
process. The Tcl/Tk functions are designed to use in interactive sessions.
> 
> 
>> 
>> Thanks for your time.
>> 
>> ___
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>> R-SIG-Mac@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> David Winsemius
> Alameda, CA, USA
> 
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Re: [R-SIG-Mac] How to put below code in Automator in iOS

[David Winsemius]

> On Oct 27, 2016, at 10:07 AM, Christofer Bogaso <bogaso.christo...@gmail.com> 
> wrote:
> 
> Hi,
> 
> Previously I posted this same thread in general R help, however folks
> there suggested to post in this specialized group for better answer.
> 
> I have a piece of code available here
> 
> http://mcu.edu.tw/~chenmh/teaching/project/r/reference/RTclTkExamples/radiobuttons.html
> 
> Now I put that code in a .R file and then created an .app file in Mac
> using Automator as explained below
> 
> https://www.r-bloggers.com/how-to-source-an-r-script-automatically-on-a-mac-using-automator-and-ical/
> 
> Surprisingly what I see is that, when I put that R code in a .app
> file, R fails to pop up the input window, which otherwise is fine when
> I just copy paste that code in R window.
> 
> Could you please help if I need to have anything extra so that my .app
> will be able to take the input.

You should post the code that is in your .R file.


> 
> Thanks for your time.
> 
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Re: [R-SIG-Mac] RcppArmadillo errors

[David Winsemius]

> On Sep 1, 2016, at 11:58 AM, David Winsemius <dwinsem...@comcast.net> wrote:
> 
> 
>> On Aug 27, 2016, at 5:35 AM, Oskar Knapik <okna...@gmail.com> wrote:
>> 
>> Dear all
>> 
>> I am having some problems with your package.
>> 
>> It looks that I can't load it on my Mac computer (OS X El Capitan 10.11.6)
>> 
>> I got the following errors:
>> Error in dyn.load(file, DLLpath = DLLpath, ...) : 
>> can't load shared object
>> '/Users/oknapik/Library/R/3.3/library/RcppArmadillo/libs/RcppArmadillo.so':
>> dlopen(/Users/oknapik/Library/R/3.3/library/RcppArmadillo/libs/RcppArmadillo.so,
>>  6): Library not loaded: 
>> /Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libRlapack.dylib
>> Referenced from: 
>> /Users/oknapik/Library/R/3.3/library/RcppArmadillo/libs/RcppArmadillo.so
>> Reason: image not found
>> 
>> The newest OS X doesn't support X11 (I am not sure if you use it)
> 
> XQuartz is the X11 for the Mac:
> 
> https://www.xquartz.org/
> 
> This error can be found on SO and I think the second answer (to just (re-?) 
> install XQuartz) is the correct one.
> 
> http://stackoverflow.com/questions/26489928/cant-load-x11-in-r-after-os-x-yosemite-upgrade
> 
> -- 
> David.
>> 
>> I am also trying to install the package on Microsoft R
>> https://mran.microsoft.com <https://mran.microsoft.com/>
>> 
>> 
>> Below the errors from the installation:
>> 
>> install.packages("RcppArmadillo", verbose=T)
>> Installing package into ‘/Users/oknapik/Library/R/3.3/library’
>> (as ‘lib’ is unspecified)
>> system (cmd0): /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL
>> trying URL 
>> 'https://mran.revolutionanalytics.com/snapshot/2016-07-01/src/contrib/RcppArmadillo_0.7.100.3.1.tar.gz
>>  
>> <https://mran.revolutionanalytics.com/snapshot/2016-07-01/src/contrib/RcppArmadillo_0.7.100.3.1.tar.gz>'
>> Content type 'application/octet-stream' length 1055712 bytes (1.0 MB)
>> ==
>> downloaded 1.0 MB
>> 
>> foundpkgs: RcppArmadillo, 
>> /var/folders/mr/_t437jvd5v5fty4z3pypn_ycgn/T//RtmpPj3WB7/downloaded_packages/RcppArmadillo_0.7.100.3.1.tar.gz
>> files: 
>> /var/folders/mr/_t437jvd5v5fty4z3pypn_ycgn/T//RtmpPj3WB7/downloaded_packages/RcppArmadillo_0.7.100.3.1.tar.gz
>> Warning
>> In command 'doTryCatch(return(expr), name, parentenv, handler)':
>> can't load the shared object  
>> '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':

snipped

>> ld: warning: directory not found for option 
>> '-L/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/lib'
>> ld: warning: directory not found for option 
>> '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64'
>> ld: warning: directory not found for option '-L/usr/local/lib/x86_64'
>> ld: warning: directory not found for option 
>> '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3'
>> ld: library not found for -lgfortran
>> clang: error: linker command failed with exit code 1 (use -v to see 
>> invocation)

Apologies for the noise. 

The XQuartz concern wasn't the actual error. I didn't read down far enough. 
Appears you do have an earlier version of RcppArmadillo although it's not clear 
which one it might be. I was able to install both a binary 
(RcppArmadillo_0.7.400.2.0.tgz) and from source: 
https://cran.cnr.berkeley.edu/src/contrib/RcppArmadillo_0.7.400.2.0.tar.gz  
without difficulty. (No warnings.)  That appears to be the current version that 
would install from CRAN and it's also the one I see at MRAN: 
https://mran.microsoft.com/src/contrib/RcppArmadillo_0.7.400.2.0.tar.gz

You are installing a somewhat older version. Using https://mran.microsoft.com 
made me wonder if you may have an earlier version of R distributed by 
Microsoft, although your directory naming suggests they have now "caught up". 
The "standard" version of Fortran for the Mac is at 
http://r.research.att.com/tools/   The MRAN distribution is not entirely 
standar. I have not heard of discrepancies with Fortran dependencies in the 
past.

-- David


>> make: *** [RcppArmadillo.so] Error 1
>> ERROR: compilation failed for package ‘RcppArmadillo’
>> * removing ‘/Users/oknapik/Library/R/3.3/library/RcppArmadillo’
>> * restoring previous ‘/Users/oknapik/Library/R/3.3/library/RcppArmadillo’
>> Warning in install.packages :
>> installation of package ‘RcppArmadillo’ had non-zero exit status
>> 
>> 
>> 
>> I would be very grateful for help.
>> 
>> Best,
>> Oskar
>>  [[alternative HTML version deleted]]
&

Re: [R-SIG-Mac] RcppArmadillo errors

[David Winsemius]

/X11/include 
> -framework CoreFoundation -framework CoreGraphics -framework CoreText  -c 
> RcppExports.cpp -o RcppExports.o
> clang: warning: -framework CoreFoundation: 'linker' input unused
> clang: warning: -framework CoreGraphics: 'linker' input unused
> clang: warning: -framework CoreText: 'linker' input unused
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
> -I/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/include 
> -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include 
> -I"/Users/oknapik/Library/R/3.3/library/Rcpp/include"  -I../inst/include 
> -fPIC  
> -I/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/include 
> -DU_STATIC_IMPLEMENTATIN -Wall -mtune=core2 -g -O2 -I/opt/X11/include 
> -framework CoreFoundation -framework CoreGraphics -framework CoreText  -c 
> fastLm.cpp -o fastLm.o
> clang: warning: -framework CoreFoundation: 'linker' input unused
> clang: warning: -framework CoreGraphics: 'linker' input unused
> clang: warning: -framework CoreText: 'linker' input unused
> clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined 
> dynamic_lookup -single_module -multiply_defined suppress 
> -L/Library/Frameworks/R.framework/Resources/lib 
> -L/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/lib -o 
> RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -framework Accelerate 
> -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 
> -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -L/usr/local/lib -lgfortran 
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework 
> -Wl,CoreFoundation
> ld: warning: directory not found for option 
> '-L/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/lib'
> ld: warning: directory not found for option 
> '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64'
> ld: warning: directory not found for option '-L/usr/local/lib/x86_64'
> ld: warning: directory not found for option 
> '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3'
> ld: library not found for -lgfortran
> clang: error: linker command failed with exit code 1 (use -v to see 
> invocation)
> make: *** [RcppArmadillo.so] Error 1
> ERROR: compilation failed for package ‘RcppArmadillo’
> * removing ‘/Users/oknapik/Library/R/3.3/library/RcppArmadillo’
> * restoring previous ‘/Users/oknapik/Library/R/3.3/library/RcppArmadillo’
> Warning in install.packages :
>  installation of package ‘RcppArmadillo’ had non-zero exit status
> 
> 
> 
> I would be very grateful for help.
> 
> Best,
> Oskar
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] download R 3.2.1 on mac OS

[David Winsemius]

> On Aug 25, 2016, at 8:03 PM, Valentina Blohm Crenovich <vbl...@fen.uchile.cl> 
> wrote:
> 
> thanks, it helps a lot but I get the following instead of downloading:
> 
> 100  9443  100  94430 0  26789  0 --:--:-- --:--:--
> --:--:-- 46517 0  0 --:--:-- --:--:-- --:--:-- 0
>> 

> , also I tried
> 
>> fileUrl<- 
>> "https://data.baltimorecity.gov/api/views/dz54-2aru/rows.csv?accessType=DOWNLOAD;
>> download.file(fileUrl, destfile="cameras.csv", method="curl")

That's not an error message.

It's actually telling you that you got 9443 bytes. If the first number were 0, 
then you would be concerned (and you would have seen some sort of error 
message).

-- 
David.

> 
> and the output is:
> 
> 100  9443  100  94430 0   7196  0  0:00:01  0:00:01
> --:--:-- 65576  0 --:--:--  0:00:01 --:--:-- 0
> Valentina Blohm
> 
> Estudiante de Economía
> Facultad de Economía y Negocios
> Universidad de Chile
> 
> 
> 2016-08-25 22:42 GMT-04:00 David Winsemius <dwinsem...@comcast.net>:
>> 
>>> On Aug 25, 2016, at 7:11 PM, Valentina Blohm Crenovich 
>>> <vbl...@fen.uchile.cl> wrote:
>>> 
>>> *Hello!*
>>> 
>>> *I have the following error system Mac OS 10.6.8 R 3.2.1 :*
>>> 
>>> 
>>> *>fileUrl<-
>>> "https:data.baltimorecity.gov/api/views/dz54-2aru/rows.csv?accessType=DOWNLOAD
>>> <http://data.baltimorecity.gov/api/views/dz54-2aru/rows.csv?accessType=DOWNLOAD>"*
>> 
>> I'm not sure this is really a mac question but since there is a mac issue 
>> with downloading that I have solved with package::download I offer this 
>> suggestion. Need to know your working or target directory name (or create it 
>> with path.expand) since download.file does not do path expansion.
>> 
>> 
>> Also note that your url is either malformed or at the very least confusing. 
>> Cannot tell if it is https: or http:. Should just be:
>> 
>> 
>> fileUrl <-
>> "http://data.baltimorecity.gov/api/views/dz54-2aru/rows.csv?accessType=DOWNLOAD;
>> 
>> # Then with downloader installed and assuming that a ./data/ subdirectory 
>> exists:
>> 
>> library(downloader)
>> download( fileUrl, destfile=path.expand("./data/cameras.csv")
>> 
>> Note that it would be more typical on a Mac to see "~/" than "./" or to see 
>> a setwd("./data") call.
>> 
>> --
>> David.
>> 
>>> 
>>> *> download.file(fileUrl, destfile="./data/cameras.csv",method="curl")*
>>> 
>>> *curl: (6) Warning message:*
>>> *In download.file(fileUrl, destfile = "./data/cameras.csv", method =
>>> "curl") :*
>>> *  download had nonzero exit status*
>>> *Couldn't resolve host 'https:data.baltimorecity.gov
>>> <http://data.baltimorecity.gov>'*
>>> 
>>> Thank you
>>> Tina
>>> 
>>> ___
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>> 
>> David Winsemius
>> Alameda, CA, USA
>> 

David Winsemius
Alameda, CA, USA

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Re: [R-SIG-Mac] download R 3.2.1 on mac OS

[David Winsemius]

> On Aug 25, 2016, at 7:11 PM, Valentina Blohm Crenovich <vbl...@fen.uchile.cl> 
> wrote:
> 
> *Hello!*
> 
> *I have the following error system Mac OS 10.6.8 R 3.2.1 :*
> 
> 
> *>fileUrl<-
> "https:data.baltimorecity.gov/api/views/dz54-2aru/rows.csv?accessType=DOWNLOAD
> <http://data.baltimorecity.gov/api/views/dz54-2aru/rows.csv?accessType=DOWNLOAD>"*

I'm not sure this is really a mac question but since there is a mac issue with 
downloading that I have solved with package::download I offer this suggestion. 
Need to know your working or target directory name (or create it with 
path.expand) since download.file does not do path expansion.


Also note that your url is either malformed or at the very least confusing. 
Cannot tell if it is https: or http:. Should just be:


fileUrl <-
"http://data.baltimorecity.gov/api/views/dz54-2aru/rows.csv?accessType=DOWNLOAD;

# Then with downloader installed and assuming that a ./data/ subdirectory 
exists:

library(downloader)
download( fileUrl, destfile=path.expand("./data/cameras.csv")

Note that it would be more typical on a Mac to see "~/" than "./" or to see a 
setwd("./data") call.

-- 
David.

> 
> *> download.file(fileUrl, destfile="./data/cameras.csv",method="curl")*
> 
> *curl: (6) Warning message:*
> *In download.file(fileUrl, destfile = "./data/cameras.csv", method =
> "curl") :*
> *  download had nonzero exit status*
> *Couldn't resolve host 'https:data.baltimorecity.gov
> <http://data.baltimorecity.gov>'*
> 
> Thank you
> Tina
> 
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Re: [R-SIG-Mac] Help! R Freezes When Clicking on the Icons

[David Winsemius]

> On Jul 5, 2016, at 6:25 AM, Scott Novogoratz <sanov...@gmail.com> wrote:
> 
> While it started as an occasional freeze, I now can no longer get the R.app 
> Source Script icon to perform.  Each time I click it, I get the spinning 
> pinwheel and need to Force Quit R.
> 
> Here’s my sessionInfo():
> > sessionInfo()
> R version 3.3.1 Patched (2016-06-28 r70858)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X El Capitan (10.11.5)
> 
> 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] zoo_1.7-13  xts_0.9-7   grid_3.3.1  IBrokers_0.9-12
> [5] lattice_0.20-33

The presence of `zoo`, `xts`, and `IBrokers` in that list of non-attached 
namespaces seems unexplained. It's surely not a part of the standard base 
installation. `lattice` and `grid` are also not loaded by default so this 
suggests you have not completely removed all traces from the prior 
installation. Check to see that there isn't an .Rprofile or .Rdata still in the 
startup directory. (And delete them if there.)


> 
> Here’s my About R info:
> 
> 
> With help from David Winsemius, here’s what I tried so far:
>   1. Deleting the .Rdata and the .Rapp.history files from my working 
> directory
>   2. Reinstalling R

I actually suggested reinstalling the R.app GUI using the binary installer at:
http://r.research.att.com/mavericks/R-3.3-branch/R-GUI-7238-3.3-mavericks-Release.dmg

I'm now wondering if it would be of value to instead install the Debug version:
http://r.research.att.com/mavericks/R-devel/R-GUI-7238-3.4-mavericks-Debug.dmg 
but that is a decision above my pay grade.

>   3. Setting my working directory on startup
> 
> Additionally, I have 3 Macs and all of them are having the same problem.
> 
> Does anyone have any ideas on fixing this problem?
> 
> Thank you for your suggestions.
> 
> Scott Novogoratz
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[R-SIG-Mac] [SOLVED]: Help! Freezes Consistently When Trying to Execute R Source Script

[David Winsemius]

I got a solved-message from Scott.


> On Jul 3, 2016, at 10:57 AM, David Winsemius <dwinsem...@comcast.net> wrote:
> 
> I’m not at the level where I could effectively debug this issue and normally 
> I wouldn’t jump in, but this is a long holiday weekend in the US and it 
> wouldn’t surprise me if Simon didn’t see this for a couple of days.  I would 
> first try deleting R.app from the Applications folder and re-installing it 
> with a clean copy:
> 
> http://r.research.att.com/mavericks/R-3.3-branch/R-GUI-7238-3.3-mavericks-Release.dmg
>  
> <http://r.research.att.com/mavericks/R-3.3-branch/R-GUI-7238-3.3-mavericks-Release.dmg>
> 
> I do see  “debug” versions but I have never seen it suggested that ordinary 
> users deploy those versions as a first step.
> 
> I would also delete the .Rdata and the .Rapp.history files from your working 
> directory. They have a record of getting corrupted an causing instabilities 
> of obscure causes. They are “hidden files” so you either need to “show them” 
> in the Finder or you need to sue Terminal.app to run a bash session and use 
> mv.

… as well as a suggestion from a different source that `sue`-ing the Terminal 
might not be appropriate.


> This is the first method:
> 
> Open Terminal found in Finder > Applications > Utilities
> In Terminal, paste the following:  defaults write com.apple.finder 
> AppleShowAllFiles YES

I did wonder about using YES rather than TRUE. That was copied from a google 
hit.  ISTR that in the past I used TRUE. Didn’t notice the difference until 
after posting. I later did a search but failed to find documentation that YES 
was a bash synonym of TRUE. I now pulled up the $man defaults page and it 
includes this line:

-bool[ean]  Allows the user to specify a boolean as the value for the
 given preference key.  Value must be TRUE, FALSE, YES, or NO.

So at least Finder.app won’t be sueing me.

— 
David


> Press return
> Hold the ‘Option/alt’ key, then right click on the Finder icon in the dock 
> and click Relaunch.
> Tor reverse that after deleting those files you would use the same steps with 
> NO substituted for YES. (My preference is for leaving the hidden files shown.)
> 
> Best;
> David Winsemius 
> 
> 
>> On Jul 3, 2016, at 9:41 AM, Scott Novogoratz <sanov...@gmail.com> wrote:
>> 
>> While it started as an occasional freeze, I now can no longer get the R.app 
>> Source Script icon to perform.  Each time I click it, I get the spinning 
>> pinwheel and need to Force Quit R.
>> 
>> Here’s my sessionInfo():
>>> sessionInfo()
>> R version 3.3.1 Patched (2016-06-28 r70858)
>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>> Running under: OS X El Capitan (10.11.5)
>> 
>> 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] zoo_1.7-13  xts_0.9-7   grid_3.3.1  IBrokers_0.9-12
>> [5] lattice_0.20-33
>> 
>> Here’s my About R info:
>> 
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> 
> 
>   [[alternative HTML version deleted]]
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Re: [R-SIG-Mac] Help! Freezes Consistently When Trying to Execute R Source Script

[David Winsemius]

I’m not at the level where I could effectively debug this issue and normally I 
wouldn’t jump in, but this is a long holiday weekend in the US and it wouldn’t 
surprise me if Simon didn’t see this for a couple of days.  I would first try 
deleting R.app from the Applications folder and re-installing it with a clean 
copy:

http://r.research.att.com/mavericks/R-3.3-branch/R-GUI-7238-3.3-mavericks-Release.dmg
 
<http://r.research.att.com/mavericks/R-3.3-branch/R-GUI-7238-3.3-mavericks-Release.dmg>

I do see  “debug” versions but I have never seen it suggested that ordinary 
users deploy those versions as a first step.

I would also delete the .Rdata and the .Rapp.history files from your working 
directory. They have a record of getting corrupted an causing instabilities of 
obscure causes. They are “hidden files” so you either need to “show them” in 
the Finder or you need to sue Terminal.app to run a bash session and use mv. 
This is the first method:

Open Terminal found in Finder > Applications > Utilities
In Terminal, paste the following:  defaults write com.apple.finder 
AppleShowAllFiles YES
Press return
Hold the ‘Option/alt’ key, then right click on the Finder icon in the dock and 
click Relaunch.
Tor reverse that after deleting those files you would use the same steps with 
NO substituted for YES. (My preference is for leaving the hidden files shown.)

Best;
David Winsemius 


> On Jul 3, 2016, at 9:41 AM, Scott Novogoratz <sanov...@gmail.com> wrote:
> 
> While it started as an occasional freeze, I now can no longer get the R.app 
> Source Script icon to perform.  Each time I click it, I get the spinning 
> pinwheel and need to Force Quit R.
> 
> Here’s my sessionInfo():
> > sessionInfo()
> R version 3.3.1 Patched (2016-06-28 r70858)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X El Capitan (10.11.5)
> 
> 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] zoo_1.7-13  xts_0.9-7   grid_3.3.1  IBrokers_0.9-12
> [5] lattice_0.20-33
> 
> Here’s my About R info:
> 
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Re: [R-SIG-Mac] R vs. Microsoft R-Open updates?

[David Winsemius]

m/WitthoftResume
>> 
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> 
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Re: [R-SIG-Mac] R vs. Microsoft R-Open updates?

[David Winsemius]

> On Jun 26, 2016, at 8:17 PM, David Winsemius <dwinsem...@comcast.net> wrote:
> 
> 
>> On Jun 26, 2016, at 5:40 PM, Carl Witthoft <c...@witthoft.com> wrote:
>> 
>> Hi.
>> I D/L'd the 3.3.1 version of R for MacOSX and ran the installer. After 
>> getting some "can't load" error messages, I discovered that the installer 
>> had updated the MicrosoftROpen.app, not the "vanilla"  R.app . Is this 
>> expected behavior, or am I making a hash of my apps and libraries by trying 
>> to keep both R and MRO available on my (Yosemite) machine?
> 
> The MRO website says it's not possible. I have managed to have an 
> R.app/CRAN_R version 3.3.x running alongside MRO version 3.2.x but I have 
> needed to use the R_Switch.app (spelling?) from the r.att.research.com website

... make that:

http://r.research.att.com/


> to go back an forth between them.
> 
>> 
>> -- 
>> Carl Witthoft
>> c...@witthoft.com
>> resume: https://app.box.com/WitthoftResume
>> 
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> 
> David Winsemius
> Alameda, CA, USA
> 
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Re: [R-SIG-Mac] Problem with RJDBC in OS X 10.11

[David Winsemius]

 
>>>> jdbm <- JDBC('oracle.jdbc.OracleDriver', 
>>>> '/opt/ora11g/instantclient_11_2/ojdbc6.jar', "`")
>>> JavaVM: requested Java version ((null)) not available. Using Java at "" 
>>> instead.
>>> JavaVM: Failed to load JVM: /bundle/Libraries/libserver.dylib
>>> JavaVM FATAL: Failed to load the jvm library.
>>> Error in .jinit(classPath) : JNI_GetCreatedJavaVMs returned -1
>>> 
>>>> sessionInfo()
>>> R version 3.3.0 (2016-05-03)
>>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>> Running under: OS X 10.11.4 (El Capitan)
>>> 
>>> locale:
>>> [1] C
>>> 
>>> attached base packages:
>>> [1] stats graphics  grDevices utils datasets  methods   base 
>>> 
>>> other attached packages:
>>> [1] RJDBC_0.2-5 rJava_0.9-8 DBI_0.4-1  
>>> 
>>> 
>>> 
>>> [macqueen1-ml:~]% sudo R CMD javareconf
>>> 
>>> Java interpreter : /usr/bin/java
>>> Java version : 1.7.0_101
>>> Java home path   : 
>>> /Library/Java/JavaVirtualMachines/jdk1.7.0_101.jdk/Contents/Home/jre
>>> Java compiler: /usr/bin/javac
>>> Java headers gen.: /usr/bin/javah
>>> Java archive tool: /usr/bin/jar
>>> Non-system Java on OS X
>>> 
>>> 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
>>> clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG 
>>> -I/Library/Java/JavaVirtualMachines/jdk1.7.0_101.jdk/Contents/Home/jre/../include
>>>  
>>> -I/Library/Java/JavaVirtualMachines/jdk1.7.0_101.jdk/Contents/Home/jre/../include/darwin
>>>  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include
>>> -fPIC  -Wall -mtune=core2 -g -O2  -c conftest.c -o conftest.o
>>> clang -dynamiclib -Wl,-headerpad_max_install_names -undefined 
>>> dynamic_lookup -single_module -multiply_defined suppress 
>>> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o 
>>> conftest.so conftest.o 
>>> -L/Library/Java/JavaVirtualMachines/jdk1.7.0_101.jdk/Contents/Home/jre/lib/server
>>>  -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework 
>>> -Wl,CoreFoundation
>>> 
>>> 
>>> JAVA_HOME: 
>>> /Library/Java/JavaVirtualMachines/jdk1.7.0_101.jdk/Contents/Home/jre
>>> 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 /Library/Frameworks/R.framework/Resources
>>> Done.
>>> 
>>> 
>>> Also:
>>> [macqueen1-ml:~]% java -version
>>> java version "1.7.0_101"
>>> Java(TM) SE Runtime Environment (build 1.7.0_101-b14)
>>> Java HotSpot(TM) 64-Bit Server VM (build 24.101-b14, mixed mode)
>>> 
>>> 
>>> 
>>> Don MacQueen
>>> Lawrence Livermore National Laboratory
>>> macque...@llnl.gov
>>> 925-423-1062
>>> 
>>> 
>>> 
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Re: [R-SIG-Mac] third party installer

[David Winsemius]

> On May 9, 2016, at 1:19 PM, David Winsemius <dwinsem...@comcast.net> wrote:
> 
> 
>> On May 9, 2016, at 1:04 PM, Simon Urbanek <simon.urba...@r-project.org> 
>> wrote:
>> 
>> 
>> On May 9, 2016, at 2:50 PM, Mick Jordan <mick.jor...@oracle.com> wrote:
>> 
>>> What third party installer is used for the standard Mac OS X build? Looking 
>>> at the following I can't figure out where lzma is coming from. I am using 
>>> MacPorts (on El Cap) which puts lzma in /opt/local/include.
>>> 
>> 
>> 
>> No 3rd party, only static libs used on CRAN, i.e., what is in
>> http://r.research.att.com/libs/
> 
> It wasn't obvious where lzma was being derived in any of those sources, so I 
> made my best efforts and decided it was probably from xz-5.2.1.tar.bz2
> 
> Was my searching correct?
> 

As a followup can anyone suggest how I should  address (or whether I should 
even worry about) the error reported when I follow the installation advice for 
that package on that page:

$ curl -O http://r.research.att.com/libs/xz-5.2.1-darwin.13-x86_64.tar.gz
  % Total% Received % Xferd  Average Speed   TimeTime Time  Current
 Dload  Upload   Total   SpentLeft  Speed
100  617k  100  617k0 0   352k  0  0:00:01  0:00:01 --:--:--  352k
david-winsemiuss-mac-pro:~ davidwinsemius$ sudo tar fvxz 
xz-5.2.1-darwin.13-x86_64.tar.gz -C /
Password:
x usr/: Can't set user=0/group=0 for usrCan't update time for usr
x usr/local/
x usr/local/bin/
x usr/local/include/
x usr/local/lib/
x usr/local/share/
x usr/local/share/doc/
x usr/local/share/man/
x usr/local/share/man/man1/
x usr/local/share/man/man1/lzcat.1
x usr/local/share/man/man1/lzcmp.1
x usr/local/share/man/man1/lzdiff.1
x usr/local/share/man/man1/lzegrep.1
x usr/local/share/man/man1/lzfgrep.1
x usr/local/share/man/man1/lzgrep.1
x usr/local/share/man/man1/lzless.1
x usr/local/share/man/man1/lzma.1
x usr/local/share/man/man1/lzmadec.1
x usr/local/share/man/man1/lzmainfo.1
x usr/local/share/man/man1/lzmore.1
x usr/local/share/man/man1/unlzma.1
x usr/local/share/man/man1/unxz.1
x usr/local/share/man/man1/xz.1
x usr/local/share/man/man1/xzcat.1
x usr/local/share/man/man1/xzcmp.1
x usr/local/share/man/man1/xzdec.1
x usr/local/share/man/man1/xzdiff.1
x usr/local/share/man/man1/xzegrep.1
x usr/local/share/man/man1/xzfgrep.1
x usr/local/share/man/man1/xzgrep.1
x usr/local/share/man/man1/xzless.1
x usr/local/share/man/man1/xzmore.1
x usr/local/share/doc/xz/
x usr/local/share/doc/xz/AUTHORS
x usr/local/share/doc/xz/COPYING
x usr/local/share/doc/xz/COPYING.GPLv2
x usr/local/share/doc/xz/examples/
x usr/local/share/doc/xz/examples_old/
x usr/local/share/doc/xz/faq.txt
x usr/local/share/doc/xz/history.txt
x usr/local/share/doc/xz/lzma-file-format.txt
x usr/local/share/doc/xz/NEWS
x usr/local/share/doc/xz/README
x usr/local/share/doc/xz/THANKS
x usr/local/share/doc/xz/TODO
x usr/local/share/doc/xz/xz-file-format.txt
x usr/local/share/doc/xz/examples_old/xz_pipe_comp.c
x usr/local/share/doc/xz/examples_old/xz_pipe_decomp.c
x usr/local/share/doc/xz/examples/00_README.txt
x usr/local/share/doc/xz/examples/01_compress_easy.c
x usr/local/share/doc/xz/examples/02_decompress.c
x usr/local/share/doc/xz/examples/03_compress_custom.c
x usr/local/share/doc/xz/examples/04_compress_easy_mt.c
x usr/local/share/doc/xz/examples/Makefile
x usr/local/lib/liblzma.a
x usr/local/lib/liblzma.la
x usr/local/lib/pkgconfig/
x usr/local/lib/pkgconfig/liblzma.pc
x usr/local/include/lzma/
x usr/local/include/lzma.h
x usr/local/include/lzma/base.h
x usr/local/include/lzma/bcj.h
x usr/local/include/lzma/block.h
x usr/local/include/lzma/check.h
x usr/local/include/lzma/container.h
x usr/local/include/lzma/delta.h
x usr/local/include/lzma/filter.h
x usr/local/include/lzma/hardware.h
x usr/local/include/lzma/index.h
x usr/local/include/lzma/index_hash.h
x usr/local/include/lzma/lzma12.h
x usr/local/include/lzma/stream_flags.h
x usr/local/include/lzma/version.h
x usr/local/include/lzma/vli.h
x usr/local/bin/lzcat
x usr/local/bin/lzcmp
x usr/local/bin/lzdiff
x usr/local/bin/lzegrep
x usr/local/bin/lzfgrep
x usr/local/bin/lzgrep
x usr/local/bin/lzless
x usr/local/bin/lzma
x usr/local/bin/lzmadec
x usr/local/bin/lzmainfo
x usr/local/bin/lzmore
x usr/local/bin/unlzma
x usr/local/bin/unxz
x usr/local/bin/xz
x usr/local/bin/xzcat
x usr/local/bin/xzcmp
x usr/local/bin/xzdec
x usr/local/bin/xzdiff
x usr/local/bin/xzegrep
x usr/local/bin/xzfgrep
x usr/local/bin/xzgrep
x usr/local/bin/xzless
x usr/local/bin/xzmore
tar: Error exit delayed from previous errors.

System Version: OS X 10.11.4 (15E65)
  Kernel Version:   Darwin 15.4.0

Model Name: Mac Pro
  Model Identifier: MacPro3,1
  Processor Name:   Quad-Core Intel Xeon
  Processor Speed:  2.8 GHz
  Number of Processors: 2
  Total Number of Cores:8
  L2 Cache (per Process

Re: [R-SIG-Mac] Success with gfortran 5.1 on El Cap and R 3.3.0; was ... Error in compiling package with Fortran 4.8.2 on El Cap

[David Winsemius]

> On Apr 21, 2016, at 11:23 AM, Berend Hasselman <b...@xs4all.nl> wrote:
> 
>> 
>> On 21 Apr 2016, at 19:15, David Winsemius <dwinsem...@comcast.net> wrote:
>> 
>> 18 months ago I volunteered to fix a very tiny error in the documentation in 
>> the abandoned package, muhaz, so I am now the maintainer. I'm trying to be a 
>> responsible maintainer and test my package with R 3.3.0 in advance of its 
>> release. (I hope the fact that I have not gotten any email notices from CRAN 
>> about failed installation attempts means that all is well with my package 
>> under the R 3.3.0 and CRAN's current build machine.) 
>> 
>> Since then I have migrated to El Capitan (which I believe is not yet the 
>> current build OS for OSX branches of R).  I was trying to be a responsible 
>> maintainer and test my package with R 3.3.0 in advance of its release.  I 
>> was getting an error when building from source that my googling efforts 
>> suggested is due to incompatibility between El Cap and earlier versions of 
>> Fortran. I do not usually get errors with source packages because I have 
>> attempted in my halting manner to keep an up-to-date toolchain: XCode, 
>> Command_Line_Tools_OS_X_10.11_for_Xcode_7.3 and up until now 
>> gfortran-4.8.2-darwin13 from the r.att.research.com site.
>> 
>> * installing to library 
>> ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
>> * installing *source* package ‘muhaz’ ...
>> ** package ‘muhaz’ successfully unpacked and MD5 sums checked
>> ** libs
>> gfortran-4.8   -fPIC  -g -O2  -c muhaz.f -o muhaz.o
>> gfortran-4.8: warning: couldn’t understand kern.osversion ‘15.4.0
>> f951: internal compiler error: Illegal instruction: 4
>> 
> 
> Are you compiling on a computer with an Intel Core 2 Duo?
> I had  that problem too.

This is on an early 2008 MacPro: Quad-Core Intel Xeon (and I was getting a 
different error relating to osversion.) This is the oldest MacPro that El 
Capitan supports and I'm wondering if the next OSX version will drop it from 
support.

 
> See here https://stat.ethz.ch/pipermail/r-sig-mac/2014-May/010894.html
> and Simon's reply.
> 
> I now have a computer with an i5 processor; the gfortran 4.8.2 from 
> r.att.research.com works without that message.

That was the gfortran version that was throwing the error.

> 
>> The GNU Fortran Project mailing list has several contributions from 
>> François-Xavier Coudert who suggests that El Cap users install Fortran from 
>> a disk image installer that he makes available:
>> 
>> http://coudert.name/software.html
>> 
>> gfortran 5.2 for Yosemite:  
>> http://coudert.name/software/gfortran-5.2-Yosemite.dmg  , which I downloaded.
>>  noting that the author says "works well with El Capitan"
>> 
>> I've also found several other versions of gfortran at:
>> 
>> http://hpc.sourceforge.net/index.php
>> 
>> ... where versions 5.1, 5.3,and 6.0 are listed as appropriate for El Capitan.
>> 
>> It wasn't clear to me whether I needed to have matching sets of gcc and 
>> gfortran if I used these, but it appeared to me from the material I read in 
>> the R Install/Admin Guide that I would not need to add that additional 
>> complexity. 
>> 
>> I wondered:
>> 1) If I install this version of Fortran, what are my odds of failing to fix 
>> my problem and also crippling my capacity for compiling packages from source 
>> that were compiled and tested on Fortran 4.8.2. (I've decided to take the 
>> risk.)
>> 
>> 2) If I succeed with this for compiling muhaz, then will I later need to 
>> revert and what will I need to do to revert if needed.
>> 
> 
> In this thread 
> https://stat.ethz.ch/pipermail/r-sig-mac/2015-October/011641.html
> Brian Ripley in reply to my query said that Coudert's gfortran could be used.

I see that now, but I instead read the Admin/Install document and thought it 
was specific enough to attempt a solution which fortunately succeeded. I didn't 
have a ~/.R/Makevars file and didn't know how it would work. I thought 
apparently incorrectly that such a file was designed only for environment 
variable settings. I got the impression that modifying Makeconf would be the 
preferred method. Appears I could have gone that route as well after reading 
Prof Ripley's posting.

I would not necessarily have found that thread because I was searching on the 
specific error message and the original poster upthread did not include any 
specifics. She apparently had enough knowledge to be satisfied with  "general" 
problems statements and the correspondingly general responses, while I'm 
somewhat more 

[R-SIG-Mac] Success with gfortran 5.1 on El Cap and R 3.3.0; was ... Error in compiling package with Fortran 4.8.2 on El Cap

[David Winsemius]

arwin14/5.2.0 
-L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
FCPICFLAGS = -fPIC
FPICFLAGS = -fPIC

Then:

$ R CMD INSTALL /Users/davidwinsemius/muhaz_1.2.6.tar.gz 

Followed by compiler messages and R message and finally ...
* DONE (muhaz)

OK. I guess reading the manual and googling really does "work". 

-- 

David Winsemius
Alameda, CA, USA

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Re: [R-SIG-Mac] [R] 'nlme' package not compiling

[David Winsemius]

> On Apr 18, 2016, at 12:48 AM, Angelo Varlotta <angelovarlo...@gmail.com> 
> wrote:
> 
> Hi,
> I'm trying to install from source code the 'nlme' package in 
> RStudio. When I try, I get the following error message:
> 
> ld: warning: directory not found for option 
> '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
> ld: library not found for -lgfortran
> clang: error: linker command failed with exit code 1 (use -v to 
> see invocation)
> make: *** [nlme.so] Error 1
> ERROR: compilation failed for package ‘nlme’
> * removing 
> ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/nlme’
> * restoring previous 
> ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/nlme’
> Warning in install.packages :
>   installation of package ‘nlme’ had non-zero exit status
> 
> I'm using gfortran 4.8 from Macports and running OS X 10.11.4 
> with RStudio Version 0.99.893. I've tried to use the FLIBS 
> command in R:
> 
> FLIBS="-L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin15/4.8.5/"
> 
> so that it knows where the Fortran libraries are at and compile 
> again, but it still searchesregardless for the directory:
> 
> /usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2.

This is the fortran against which the Mac R is compiled, provided as a disk 
image:

gfortran-4.2.3.dmg:
http://r.research.att.com/gfortran-4.2.3.dmg

If you had been reading the R-SIG-Mac forum (or searching the archives you 
should have seen repeated warnings against Macports versions.)

The proper site for Mac questions regarding package compilation.
R-SIG-Mac:
https://stat.ethz.ch/mailman/listinfo/r-sig-mac


I'm was using Version 0.99.491 but updated to the same version as you have. The 
install packages dialog doesn't offer compiling from source as an options so 
the first test was to see if the binary could be install easily on version 
3.3.0 of R it did.

I then tried compiling from source and do get the same error as did you. I'm  
not a very capable Unix programmer and am unable to tell why this is happening. 
Perhaps something RStudio is doing? So I tried in the R.app gui with : 

install.packages("~/Downloads/nlme_3.1-127.tar.gz", repo=NULL, type="source")

# result===
* installing *source* package ‘nlme’ ...
** package ‘nlme’ successfully unpacked and MD5 sums checked
** libs
gfortran-4.8   -fPIC  -g -O2  -c chol.f -o chol.o
make: gfortran-4.8: No such file or directory
make: *** [chol.o] Error 1
ERROR: compilation failed for package ‘nlme’
Warning message:
In install.packages("~/Downloads/nlme_3.1-127.tar.gz", repo = NULL,  :
  installation of package ‘/Users/davidwinsemius/Downloads/nlme_3.1-127.tar.gz’ 
had non-zero exit status
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/nlme’
* restoring previous 
‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/nlme’

Also tried from Terminal.app session with similar error report.

> which of course doesn't exist. Any suggestions?

A) Install from binary. That's certainly seems easiest.

Or B)
-- install gfortran 4.8 in the directory that your installation of R expects it 
to be found. 
Perhaps:

http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2

Or at the Unix command line:

curl -s http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2 | sudo 
tar fxj - -C /

(As was suggested by Simon Urbanek two years ago and  was reported successful 
by Jason Eyerly on R-SIG-Mac.)

But in any case this thread belongs on R-SIG-MAC so copying there, and if any 
response is needed then when responding you should remove r-help from future 
replies.

-- 

David Winsemius


> 
> Cheers,
> Angelo
> 
> 
> 
>   [[alternative HTML version deleted]]
> 
> __
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

David Winsemius
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[R-SIG-Mac] Experience with upgrade to 3.3.0 beta

[David Winsemius]

I upgraded to 3.3.0 beta from: R-3.3-branch-mavericks-signed.pkg (70Mb, 
installer incl. GUI)  at the suggestion of Gabor Grothendieck who wanted to 
know whether Ryacas would install from github in R 3.3.0. So I installed the 
binary that includes GUI: R.app (which now displays the modern R logo).  It 
installed without difficulty on El Cap running on an ancient machine (early 
2008 MacPro). I then decided to move all my package folders over to the new 
../library/ and used a Terminal command to do it:

 cp -r -n /Library/Frameworks/R.framework/Versions/3.2/Resources/library/  
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/

I then ran:

update.packages(check.built=TRUE, ask=FALSE)

I replied "y" to questions about building from source and got mostly success on 
a reasonably large number of packages with just a few problems:


The downloaded source packages are in

‘/private/var/folders/yq/m3j1jqtj6hq6s5mq_v0jn3s8gn/T/RtmpHlANa6/downloaded_packages’
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘rgdal’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘rgeos’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘Rglpk’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘RODBC’ had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘RPostgreSQL’ had non-zero exit status

I tried updating GDAL from

GDAL 1.11 Complete: 
http://www.kyngchaos.com/files/software/frameworks/GDAL_Complete-1.11.dmg

and then reinstalling rgdal without success

Efforts to install the other failures were ... also failures.


None of these packages are essential to my typical use of R, but I'm thinking 
others may encounter similar problems, so if there are is a better installation 
process, perhaps you could let the list know.


-- 


David Winsemius
Alameda, CA, USA

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[R-SIG-Mac] Testers wanted: Ryacas has a new module

[David Winsemius]

The Ryacas package was formerly a client-side interface to YACAS (Yet Another 
Computer Algebra System). I couldn't get either version 1.0.63 or version 1.4.2 
to accept Ryacas' client messages on the R 2.3.4/OSX10.11.3 platform, despite 
being able to run YACAS as a standalone package. I contacted Gabor Grothendieck 
who was in correspondence with Grzegorz Mazur who had recently bolted on a 
recent version of YACAS to the package itself, obviating any server-client 
fragility. It seems to "just work" on my system. The only requirements would be 
current versions of XCode, Rcpp, XML, and devtools:


if( require(devtools) ) {
devtools::install_github("ggrothendieck/ryacas") }

Gabor has suggested that interested useRs may want to take this racehorse out 
on the track for further testing.

-- 

David Winsemius
Alameda, CA, USA


> packageDescription("Ryacas")
Package: Ryacas
Version: 0.3-1
Date: 2016-09-07
Title: R Interface to the Yacas Computer Algebra System
Author: Rob Goedman <goed...@mac.com>, Gabor Grothendieck
 <ggrothendi...@gmail.com>, Søren Højsgaard <soren.hojsga...@agrsci.dk>,
 Ayal Pinkus <apin...@xs4all.nl>, Grzegorz Mazur <teore...@gmail.com>
Maintainer: G. Grothendieck <ggrothendi...@gmail.com>
Encoding: UTF-8
Description: An interface to the yacas computer algebra system.
Imports: Rcpp (>= 0.12.0), XML, stats
LinkingTo: Rcpp
Suggests: testthat (>= 0.9.0)
License: GPL-2
URL: https://github.com/ggrothendieck/ryacas
Built: R 3.2.4; x86_64-apple-darwin13.4.0; 2016-04-13 00:47:16 UTC; unix
RemoteType: github
RemoteHost: api.github.com
RemoteRepo: ryacas
RemoteUsername: ggrothendieck
RemoteRef: master
RemoteSha: 48f659d5935452f5d89e4bffc0090e3151e43f0b
GithubRepo: ryacas
GithubUsername: ggrothendieck
GithubRef: master
GithubSHA1: 48f659d5935452f5d89e4bffc0090e3151e43f0b

-- File: 
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Ryacas/Meta/package.rds
 

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Re: [R-SIG-Mac] Save History Not Implemented?

[David Winsemius]

On a machine running the binary install version of R on OSX, the Mac OSX FAQ 
regarding this issue is at: 

file:///Applications/R.app/Contents/Resources/RMacOSX-FAQ.html#History

The default location for history files accrued while in R.app is .Rapp.history 
stored in the Starup directory.

And you are told: "Note that the functions loadhistory(), savehistory() and 
hence history() are not currently supported in R.app."


> On Mar 21, 2016, at 6:00 AM, Joseph Kunkel <jkunk...@une.edu> wrote:
> 
> I report new clues to lock-up of Mac R-GUI:
> 
>  Model Name:MacBook Pro
>  Model Identifier:MacBookPro10,1
>  Processor Name:Intel Core i7
>  Processor Speed:2.7 GHz
>  Number of Processors:1
>  Total Number of Cores:4
>  L2 Cache (per Core):256 KB
>  L3 Cache:6 MB
>  Memory:16 GB
>  Boot ROM Version:MBP101.00EE.B0A
>  SMC Version (system):2.3f36
>  Serial Number (system):C02KP40GFFT1
>  Hardware UUID:1C991826-2C15-5AF1-8C81-1F69F51034A1
> 
> R for Mac OS X GUI 1.67-devel Mavericks build
> 
> R for Mac OS X GUI written by:
> Simon Urbanek
> Hans-Jörg Bibiko
> Stefano M. Iacus
> 
> I installed R in my MacBook Pro (Retina, 15-inch, Early 2013).  I have been 
> using R since mid 2000s and started using the OS X GUI fairly early in my R 
> experience and value its organization of my R use.
> 
> About a year ago I started having interuptions in my R-GUI use where it locks 
> up.  All of several past interactions on the R-SIG-MAC so far have not 
> eliminated this locking up.  In the latest go-around it was terminated with 
> the idea that it was related to my use of large data sets and long 
> calculations particularly ones that also used the rgl library.
> 
> As part of the drama of R Mac OS X GUI locking up, which has not been 
> resolved for me yet, I now discovered new clues in the past month during 
> which I have not used rgl.
> 
> 1) When I boot R-GUI anew  the File/Open Recent has no entries.
>… if I do a carriage-return at the R prompt the File/Open Recent list is 
> populated.
> 2) The history for the active workspace has not been working for me.  It only 
> loads the history that was collected in some earlier work directory. It does 
> not save the current history in either an older directory or the (currently 
> set in R/Preferences/General/Startup/Directory[x]Always_apply) current work 
> directory .
> 3) When I try to save the current history using the > savehistory(file = 
> ".Rhistory”) or simply  > savehistory() … I get the following message:
> 
> ##
> 
>> savehistory(file = ".Rhistory”)
> Error in .External2(C_savehistory, file) :
>  'savehistory' is not currently implemented
> 
> #
> 
> I have only made changes to R operation through R-GUI Preferences.  Is there 
> something going wrong with the history functions in the GUI?
> 
> Work is slowed by lack of a useful history and continued need to reboot R in 
> a complicated way each time the GUI locks up.
> 
> When I run R in a terminal at my home directory,  history works as advertised 
> after I have done some work and q() with a save … then reboot R in terminal 
> and use up-arrow to retrieve old R statements.
> 
> 4) I reiterate the tedious procedure for rebooting after a lock-up of GUI 
> typically with a few R-scripts open in editors:
> a) kill the R process ID
> b) reboot the R-GUI, which by default loads the previously open R-scripts.
> c) close those R-scripts and do not do any R-work.
> d) quit()
> e) reboot the R-GUI and close it immediately with another q() {otherwise go 
> back to step ‘a’.}
> f) reboot the R-GUI and resume R-work {with no history … as usual} e.g. load 
> a script into the editor, edit and run it.  But, avoid trying to load another 
> R-script into the ediitor after having run the one script.
> … The scripts used are what I would call regular scripts accessing 
> relatively small data sets and plotting results and _not_ using the difficult 
> rgl library.
> 
> I am not sure how many other users are experiencing the same symptoms.
> 
> Joe
> 
> -·.  .· ·.  .><º>·.  .· ·.  .><º>·.  .· ·.  .><º> .··.· >=-   
> =º}><
> Joseph G. Kunkel, Research Professor
> 112A Marine Science Center
> University of New England
> Biddeford ME 04005
> http://www.bio.umass.edu/biology/kunkel/
> 
> This e-mail may contain information that is privileged and confidential. If 
> you suspect that you were not the intended recipient, please delete it and 
> notify the sender as soon as possible.
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David Winsemius
Alameda, CA, USA

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Re: [R-SIG-Mac] Red message...

[David Winsemius]

> On Mar 14, 2016, at 6:20 AM, Simon Urbanek <simon.urba...@r-project.org> 
> wrote:
> 
> Yes, this is a known bug in Mavericks, a spurious error message form the 
> system. Most apps don't forward stderr to the user and just put it in the 
> logs, so you don't see it for other apps, but we forward stderr in case you 
> run something you care about.
> 
> If you want to disable stderr forwarding because it bothers you,you can do so 
> - see
> http://r.research.att.com/bin/macosx/RMacOSX-FAQ.html#I-see-spurious-error-messages-when-starting-R_0021
> 

There used to be an innocuous system warning message that appearing at startup 
of R.app with the phrase something along the lines of "links to system flippers 
not found". I found it amusing to be starting up a software package that 
thought it needed pinball facilities. 

Anyone know of an R package that displays a simulated Pinball or old-style 
Pachinko machine?

-- 
David.


> Just note that you then won't see stderr form commands you start via system().
> 
> Cheers,
> Simon
> 
> 
> On Mar 14, 2016, at 6:30 AM, Ivan Calandra <ivan.calan...@univ-reims.fr> 
> wrote:
> 
>> Dear Mac useRs,
>> 
>> Since this morning, I regularly get this message in the console:
>> "2016-03-14 11:25:58.004 R[656:707] Unknown class '_FITagEditorView', using 
>> 'NSView' instead. Encountered in Interface Builder file at path 
>> /System/Library/Frameworks/AppKit.framework/Resources/French.lproj/NSNavPanelContentView.nib."
>> 
>> I cannot give any trigger because it comes randomly. It seems that it does 
>> not prevent R from working, but I'm wondering whether this is a known issue.
>> Any idea what this could be? It seems that this might not be an R problem by 
>> itself but I don't really know what this "Framework" is about.
>> 
>> sessionInfo()
>> R version 3.2.3 (2015-12-10)
>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>> Running under: OS X 10.9.5 (Mavericks)
>> 
>> locale:
>> [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8
>> 
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base
>> 
>> Thanks in advance,
>> Ivan
>> 
>> -- 
>> Ivan Calandra, PhD
>> University of Reims Champagne-Ardenne
>> GEGENAA - EA 3795
>> CREA - 2 esplanade Roland Garros
>> 51100 Reims, France
>> +33(0)3 26 77 36 89
>> ivan.calan...@univ-reims.fr
>> --
>> https://www.researchgate.net/profile/Ivan_Calandra
>> https://publons.com/author/705639/
>> 
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> 
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Re: [R-SIG-Mac] Permission denied error while updating R packages

[David Winsemius]

> On Feb 23, 2016, at 11:11 AM, Iryna Nikolayeva <iryna.v.nikolay...@gmail.com> 
> wrote:
> 
> Dear R-Sog-Mac members, 
> 
> I have an issue while automatically updating packages in R. 
> For the packages installed in my second library, while automatically updating 
> I get the following "Permission denied” messages(details below). 
> I suppose I know where this problem comes from: 
> I had installed a few different versions of R. 
> And now I have 2 library paths: 
>> .libPaths() 
> [1] "/Users/iryna/Library/R/3.1/library"  
>  
> [2] 
> "/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library” 

This is just a guess, ... did you install that version of R through MacPorts? 
The most recent version of OSX has nailed down a lot of system folders to which 
write access used to be available.
> 
> And for some reason R just doesn’t have rights to update packages in my 
> second library. 
> Do you know why is that? How should I fix this issue? 
> 
> 
> 
> Here is the error message: 
> 
> * installing *source* package ‘mgcv’ ... 
> ** package ‘mgcv’ successfully unpacked and MD5 sums checked 
> mv: rename 
> /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv 
> to 
> /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/00LOCK-mgcv/mgcv:
>  Permission denied 
> Warning in file.copy(f, instdir, TRUE) : 
>  problem copying ./NAMESPACE to 
> /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv/NAMESPACE:
>  Permission denied 
> Warning in file(file, ifelse(append, "a", "w")) : 
>  cannot open file 
> '/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv/DESCRIPTION':
>  Permission denied 
> Error in file(file, ifelse(append, "a", "w")) : 
>  cannot open the connection 
> ERROR: installing package DESCRIPTION failed for package ‘mgcv’ 
> * removing 
> ‘/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv’
>  
> 
> 
> Here are some additional information on my settings: 
>> version 
> platform   x86_64-apple-darwin13.4.0   
> arch   x86_64  
> os darwin13.4.0
> system x86_64, darwin13.4.0
> status 
> major  3   
> minor  1.2 
> year   2014
> month  10  
> day31  
> svn rev66913   
> language   R   
> version.string R version 3.1.2 (2014-10-31)

You should use the binary installer package to update to the current version of 
R. Then your .libPaths() result should be:

[1] "/Library/Frameworks/R.framework/Versions/3.2/Resources/library"

You can then add  "/Users/iryna/Library/R/3.2/library" with:

 .libPaths(c("/Users/iryna/Library/R/3.2/library", .libPaths() ) ) 

, then copy old packages from your libraries, 
 and run (from the R console):  update.packages(checkBuilt=TRUE)


> 
> nickname   Pumpkin Helmet  
> 
> Thanks in advance for your help, 
> Iryna Nikolayeva 
> 

>   [[alternative HTML version deleted]]

Please post in plain text.

> 
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Re: [R-SIG-Mac] R gui or Rstudio quits

[David Winsemius]

> On Mar 5, 2016, at 7:33 AM, peter dalgaard <pda...@gmail.com> wrote:
> 
> Hmm, there was _something_ at _some_ point, on El Cap, I seem to remember. 
> 
> Have you tried the daily versions at http://r.research.att.com ?
> 
> -pd
> 
>> On 05 Mar 2016, at 15:22 , Paul Schlesinger <phschlesin...@gmail.com> wrote:
>> 
>> On a Macbookpro and MacAir 2012-13 vintage running Osx 10.11.3. R installed
>> by standard package options the first time R is started The application
>> quits and I can send information to Apple.  Now if I restart from this
>> message or just restart R appears to run fine. This could be related to os
>> update but it was first noted a month after the upgrade. I have reinstalled
>> R several times without changing this behavior.  Other non-apple software,
>> Emacs and latex are running on these machines without a similar problem. Is
>> this a know problem and is there a correction.
>> 

Have you made sure that there is no hidden corrupt .Rdata  or .Rapp.history 
file? One way to do this is running R from a Terminal session with:

R --vanilla

I'm not a regular RStudio user, so If R is stable in that situation then your 
first act should be deleting those (invisible-by-default) files. It's fairly 
easy to find advice about how to make invisible files visible on OSX using a 
Google search. I'm not a regular RStudio user, so I don't know if finding such 
files in that environment is any more difficult. I suspect there would be such 
a file for every project.

--

David Winsemius
Alameda, CA, USA

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Re: [R-SIG-Mac] failed compilation "ld: library not found for -lquadmath"

[David Winsemius]

 LOGNAME baptiste
>> MAKEmake
>> PAGER   /usr/bin/less
>> PATH
>> /usr/bin:/bin:/usr/sbin:/sbin:/usr/texbin:/usr/local/bin:/opt/X11/bin
>> PDFLATEX/usr/texbin/pdflatex
>> R_BROWSER   /usr/bin/open
>> R_BZIPCMD   /usr/bin/bzip2
>> R_DOC_DIR   /Library/Frameworks/R.framework/Resources/doc
>> R_GZIPCMD   /usr/bin/gzip
>> R_HOME  /Library/Frameworks/R.framework/Resources
>> R_INCLUDE_DIR
>> /Library/Frameworks/R.framework/Resources/include
>> R_LIBS_SITE
>> R_LIBS_USER ~/Library/R/3.2/library
>> R_PAPERSIZE a4
>> R_PDFVIEWER /usr/bin/open
>> R_PLATFORM  x86_64-apple-darwin13.4.0
>> R_PRINTCMD  lpr
>> R_QPDF
>> /Library/Frameworks/R.framework/Resources/bin/qpdf
>> R_RD4PDFtimes,inconsolata,hyper
>> R_SESSION_TMPDIR
>> /var/folders/nh/4719qghd3bz60tc_n2806284gn/T//RtmpNqgTMe
>> R_SHARE_DIR /Library/Frameworks/R.framework/Resources/share
>> R_SYSTEM_ABIosx,gcc,gxx,gfortran,?
>> R_TEXI2DVICMD   /usr/local/bin/texi2dvi
>> R_UNZIPCMD  /usr/bin/unzip
>> R_ZIPCMD/usr/bin/zip
>> RMARKDOWN_MATHJAX_PATH
>> /Applications/RStudio.app/Contents/Resources/resources/mathjax-23
>> RS_RPOSTBACK_PATH
>> /Applications/RStudio.app/Contents/MacOS/rpostback
>> RS_SHARED_SECRET8dfae406-353d-44e7-bf9a-12efa87271a8
>> RSTUDIO 1
>> RSTUDIO_PANDOC  /Applications/RStudio.app/Contents/MacOS/pandoc
>> RSTUDIO_SESSION_PORT33826
>> RSTUDIO_USER_IDENTITY   baptiste
>> SED /usr/bin/sed
>> SHELL   /bin/bash
>> SSH_AUTH_SOCK
>> /private/tmp/com.apple.launchd.v82zIG6NDp/Listeners
>> TAR /usr/bin/tar
>> TMPDIR
>> /var/folders/nh/4719qghd3bz60tc_n2806284gn/T/
>> USERbaptiste
>> XPC_FLAGS   0x0
>> XPC_SERVICE_NAME0
>> 
> 
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