Re: [R-SIG-Mac] rlang and the new R version 4.1.0

2021-05-25 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Okay was able to find the link - 
https://www.r-bloggers.com/2020/04/updating-to-4-0-0-on-macos/

Also would suggest installing RSwitch  (https://rud.is/rswitch/) so you can 
keep both versions and switch between the until you ar certain all the kinks 
are gone.

-Roy


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

Re: [R-SIG-Mac] rlang and the new R version 4.1.0

2021-05-25 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
When R4.0 came out,  someone on R-Bloggers post a very nice to automate 
updating your packages from R3.6.  I just used it to do my update from R4.0 to 
R4.1 - it works perfectly.  I would include the script here,  but since I don't 
have the exact reference I don't like posting someone else's script without 
appropriate credit.  Do a search and you should be able to find the entry.

-Roy

> On May 25, 2021, at 1:10 PM, Simon Urbanek  
> wrote:
> 
> 
> Hans,
> 
> you seem to be using old library from 4.0 (see the 4.0 in the path). Make 
> sure you remove old packages and use a clean library for 4.1 since you cannot 
> mix packages from R 4.0.x and R 4.1.0. I would best recommend removing (or 
> re-naming) ~/Library/R before installation to make sure you don't have 
> incompatible old packages. Also don't forget to re-start R.
> 
> (Marc, I can't parse your post, it makes no sense to me, there no R-devel 
> involved in any of this, so please post separately about whatever is on your 
> heart as that doesn't seem to be related).
> 
> Cheers,
> Simon
> 
> 
> 
>> On May 26, 2021, at 2:06 AM, Marc Schwartz  wrote:
>> 
>> Hi,
>> 
>> You might try a different CRAN mirror to see if perhaps the rlang binary 
>> that you are getting is corrupted.
>> 
>> Looking at CRAN for the package, the results for rlang on what is supposed 
>> to be R release on macOS:
>> 
>> https://cran.r-project.org/web/checks/check_results_rlang.html
>> 
>> shows a header indicating that R devel is being used, not R release:
>> 
>> https://www.r-project.org/nosvn/R.check/r-release-macos-x86_64/rlang-00check.html
>> 
>> So, I am not clear if there is a macOS binary build issue that may be 
>> resulting in a conflict of sorts.
>> 
>> A spot check of other CRAN packages (including my own) shows the same use of 
>> R devel for macOS, and not R release, so perhaps there is a wider issue 
>> going on with CRAN builds, unless I am missing something here.
>> 
>> Simon (cc'd now) may be able to address that issue.
>> 
>> Regards,
>> 
>> Marc Schwartz
>> 
>> 
>> Hans W wrote on 5/25/21 9:16 AM:
>>> I installed the new R version 4.1.0 on my (normal) Macbook, and
>>> everything seemed to work fine until one of the packages depended on
>>> the 'rlang' package and I got the following error:
 library(rlang)
>>>Error: package or namespace load failed for ‘rlang’ in
>>>dyn.load(file, DLLpath = DLLpath, ...): unable to load
>>>shared object '/Users/hwb/Library/R/4.0/library/rlang/libs/rlang.so':
>>>dlopen(/Users/hwb/Library/R/4.0/library/rlang/libs/rlang.so, 6):
>>>Library not loaded:
>>>/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib
>>>Referenced from: /Users/hwb/Library/R/4.0/library/rlang/libs/rlang.so
>>>Reason: image not found
>>> So I removed 'rlang' and reinstalled it. There was no error message,
>>> but when I tried to load it, the error message was:
>>>Error: package or namespace load failed for ‘rlang’ in
>>>get(Info[i, 1], envir = env): lazy-load database
>>>'/Users/hwb/Library/R/4.0/library/rlang/R/rlang.rdb' is corrupt
>>>In addition: Warning message:
>>>In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1
>>> One of my current applications relies on 'rvest' which depends on
>>> 'rlang'. For the moment I am using it from a Linux computer, but it's
>>> quite unfortunate that I cannot run it from macOS as well.
>>> I also uninstalled the new R version and reinstalled it, but nothing
>>> changed. Could you give me a hint on what to do (or what I did wrong)?
>>> ___
>>> 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

**
"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: https://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


Re: [R-SIG-Mac] [External] tcltk on M1 mac?

2021-05-25 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Thanks.  That is what I want to know.

-Roy

> On May 25, 2021, at 8:20 AM, Duncan Murdoch  wrote:
> 
> On 25/05/2021 10:44 a.m., Roy Mendelssohn - NOAA Federal via R-SIG-Mac wrote:
>> I seem to remember a discussion not too long ago that the very latest 
>> version fo XQuartz did not install all the libraries needed by R, and to 
>> install the previous on instead  (I hav XQuartz 2.7.11, the latest is 
>> 2.8.1).  Is this still the case?
> 
> You may be thinking of a different discussion, but when the 2.8.x betas 
> started coming out, they included incompatible versions of the libs needed by 
> R on Intel machines.  That's no longer true.
> 
> I don't have any experience with M1 machines, so this may not be relevant.
> 
> Duncan Murdoch

**
"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: https://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


Re: [R-SIG-Mac] [External] tcltk on M1 mac?

2021-05-25 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
I seem to remember a discussion not too long ago that the very latest version 
fo XQuartz did not install all the libraries needed by R, and to install the 
previous on instead  (I hav XQuartz 2.7.11, the latest is 2.8.1).  Is this 
still the case?

Thanks,

-Roy

> On May 24, 2021, at 10:36 PM, Simon Urbanek  
> wrote:
> 
> 
> Rich,
> you need to instal XQuartz (see instructions on the CRAN page).
> Cheers,
> Simon
> 
> 
> 
>> On 25/05/2021, at 4:02 PM, Richard M. Heiberger  wrote:
>> 
>> I am not seeing tcltk in either the released R
>> R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
>> Copyright (C) 2021 The R Foundation for Statistical Computing
>> Platform: aarch64-apple-darwin20 (64-bit)
>> 
>> 
>> or the nightly
>> R version 4.1.0 Patched (2021-05-23 r80364) -- "Camp Pontanezen"
>> Copyright (C) 2021 The R Foundation for Statistical Computing
>> Platform: aarch64-apple-darwin20 (64-bit)
>> 
>> that I just downloaded.
>> 
>> Here is the transcript
>> 
>> R version 4.1.0 Patched (2021-05-23 r80364) -- "Camp Pontanezen"
>> Copyright (C) 2021 The R Foundation for Statistical Computing
>> Platform: aarch64-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.
>> 
>>> setwd('/Users/rmh/Rwd/')
>>> library(tcltk)
>> xcrun: error: invalid active developer path 
>> (/Library/Developer/CommandLineTools), missing xcrun at: 
>> /Library/Developer/CommandLineTools/usr/bin/xcrun
>> Error: package or namespace load failed for ‘tcltk’:
>> .onLoad failed in loadNamespace() for 'tcltk', details:
>> call: dyn.load(file, DLLpath = DLLpath, ...)
>> error: unable to load shared object 
>> '/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/tcltk/libs/tcltk.so':
>> dlopen(/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/tcltk/libs/tcltk.so,
>>  10): Library not loaded: /opt/X11/lib/libX11.6.dylib
>> Referenced from: 
>> /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/tcltk/libs/tcltk.so
>> Reason: no suitable image found.  Did find:
>>  /opt/X11/lib/libX11.6.dylib: no matching architecture in universal 
>> wrapper
>>  /opt/X11/lib/libX11.6.dylib: no matching architecture in universal 
>> wrapper
>> In addition: Warning message:
>> In system2("/usr/bin/otool", c("-L", shQuote(DSO)), stdout = TRUE) :
>> running command ''/usr/bin/otool' -L 
>> '/Library/Frameworks/R.framework/Resources/library/tcltk/libs//tcltk.so'' 
>> had status 1
>>> 
>> 
>> 
>>> On May 14, 2021, at 19:57, Simon Urbanek  
>>> wrote:
>>> 
>>> 
>>> Vince,
>>> 
>>> please try the latest build, Tcl/Tk should be included now.
>>> 
>>> Thanks,
>>> Simon
>>> 
>>> 
>>> 
 On May 14, 2021, at 7:45 AM, Simon Urbanek  
 wrote:
 
 Vince,
 
 Thanks for the report, yes, that is a known problem, because the R 
 installer for arm64 doesn't include Tcl/Tk unlike the Intel version. It is 
 a long story, but I hope to update the installer soon.
 
 Thanks,
 Simon
 
 
> On May 14, 2021, at 02:47, Vincent Carey  
> wrote:
> 
> I can't seem to get tcltk running with R on M1 machine.  Homebrew tcltk
> seems to have wrong architecture; attempt to build from source does not
> help.  Any hints appreciated.
> 
> 
> R version 4.1.0 RC (2021-05-10 r80283) -- "Camp Pontanezen"
> 
> Copyright (C) 2021 The R Foundation for Statistical Computing
> 
> Platform: aarch64-apple-darwin20 (64-bit)
> 
> 
>> library(tcltk)
> 
> *Error: package or namespace load failed for 'tcltk':*
> 
> * .onLoad failed in loadNamespace() for 'tcltk', details:*
> 
> *  call: dyn.load(file, DLLpath = DLLpath, ...)*
> 
> *  error: unable to load shared object
> '/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/tcltk/libs/tcltk.so':*
> 
> *
> dlopen(/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/tcltk/libs/tcltk.so,
> 10): Library not loaded: 
> /Library/Frameworks/Tcl.framework/Versions/8.6/Tcl*
> 
> *  Referenced from:
> /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/tcltk/libs/tcltk.so*
> 
> *  Reason: image not found*
> 
> -- 
> The information in this e-mail is intended only for the ...{{dropped:18}}
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> 

Re: [R-SIG-Mac] R 4.1 for my Mac M1 crashing on installing packages

2021-05-22 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Hi Simon:

So perhaps the take-home message is that if you depend on that suite of 
packages,  perhaps the time is not ripe to update to R4.1?

Also wondering how this will affect CRAN checks for packages that have on of 
those packages as "Suggest" or "Depend"?

Thanks,
-Roy

> On May 22, 2021, at 2:57 PM, Simon Urbanek  
> wrote:
> 
> 
> Renato,
> 
> rgdal didn't pass checks in the big-sur build, that's why it was not 
> available. rgdal has a very long list of dependencies that are very fragile, 
> so it is quite hard to build yourself (you'd need to build and compile quite 
> a few libraries).
> For now I have temporarily disabled the checks for some of the spatial 
> libraries like sf and rdgal since they don't pass them, but it would be good 
> if the issues could be sorted out upstream.
> 
> Cheers,
> Simon
> 
> 
> 
>> On May 22, 2021, at 12:31 PM, Renato Morais  
>> wrote:
>> 
>> Hi Simon and all,
>> 
>> After reinstalling the official binary and reinstalling all packages, almost 
>> everything is working fine. The only exception is rgdal, which is not 
>> available as a binary and, when I try to compile it, I get the error below. 
>> I did extract gFortran from the link you provided and moved it to the folder 
>> /opt/R/arm64 as indicated on CRAN (print screen below).
>> 
>> Anything I'm clearly doing wrong? I appreciate the help.
>> 
>> Cheers and thanks again,
>> Renato
>> 
>>> install.packages('rgdal')
>> Package which is only available in source form, and may need compilation of 
>> C/C++/Fortran: ‘rgdal’
>> Do you want to attempt to install these from sources? (Yes/no/cancel) yes
>> installing the source package ‘rgdal’
>> 
>> trying URL 'https://cran.csiro.au/src/contrib/rgdal_1.5-23.tar.gz'
>> Content type 'application/x-gzip' length 4393536 bytes (4.2 MB)
>> ==
>> downloaded 4.2 MB
>> 
>> configure: R_HOME: /Library/Frameworks/R.framework/Resources
>> configure: CC: clang -arch arm64
>> configure: CXX: clang++ -arch arm64 -std=gnu++14
>> configure: CFLAGS: -falign-functions=64 -Wall -g -O2
>> configure: CPPFLAGS: -I/opt/R/arm64/include
>> configure: CXXFLAGS: -falign-functions=64 -Wall -g -O2
>> configure: LDFLAGS: -L/opt/R/arm64/lib
>> configure: LDFLAGS: -L/opt/R/arm64/lib
>> configure: CXX11 is: clang++ -arch arm64, CXX11STD is: -std=gnu++11
>> configure: CXX is: clang++ -arch arm64 -std=gnu++11
>> configure: C++11 support available
>> configure: rgdal: 1.5-23
>> checking for /usr/bin/svnversion... no
>> configure: svn revision: 1121
>> checking for gdal-config... no
>> no
>> 
>> The downloaded source packages are in
>>  
>> ‘/private/var/folders/g0/k2tmg4q931s1x3cy_vm_m4crgn/T/RtmpydK1sm/downloaded_packages’
>> Warning message:
>> In install.packages("rgdal") :
>>  installation of package ‘rgdal’ had non-zero exit status
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> On Thu, 20 May 2021 at 11:46, Simon Urbanek  
>> wrote:
>> I was able to replicate the problem - it is a bug in select.list() in the 
>> R.app GUI and it is present in both the Intel and the arm64 version of R 
>> 4.1.0 so it is not M1-specific.
>> 
>> The work-around is as Jeroen said to set
>> options(menu.graphics=FALSE)
>> 
>> Cheers,
>> Simon
>> 
>> 
>> 
>> 
>> 
>>> On 20/05/2021, at 12:28 PM, Renato Morais  
>>> wrote:
>>> 
>>> Hi Simon,
>>> 
>>> I'll attach the crash reports available, I hope that helps and sorry 
>>> there's probably repeated crash reports, as I repeatedly tried the same 
>>> things.
>>> 
>>> So, relative to the source packages there's actually nothing I can do for 
>>> now?
>>> 
>>> Thanks for the attention,
>>> Renato
>>> 
>>> On Thu, 20 May 2021 at 08:52, Simon Urbanek  
>>> wrote:
>>> Renato,
>>> 
>>> just open the Console application (under Utilities) - it has all logs from 
>>> your machine - there will be either an R crash log or some entries in the 
>>> system log.
>>> 
>>> As for packages, it will be solved once the R 4.1.0 binaries for arm64 are 
>>> released (as soon as all builds finish), but you will have to make sure you 
>>> re-install all packages to remove the pre-releases.
>>> 
>>> Thanks,
>>> Simon
>>> 
>>> 
>>> 
 On 20/05/2021, at 10:27 AM, Renato Morais  
 wrote:
 
 Hi Simon,
 
 I'm happy to, I'm just not sure how to check previous logs...
 
 On another note, and I'm sure this is a problem with the compiler, now 
 that my packages are installed, the ones I had to compile from the source 
 cannot be loaded.
 
 Error: package or namespace load failed for ‘nlme’ in dyn.load(file, 
 DLLpath = DLLpath, ...):
 unable to load shared object 
 '/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/nlme/libs/nlme.so':
  
 dlopen(/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/nlme/libs/nlme.so,
  6): Library not loaded: /opt/R/arm64/gfortran/lib/libgfortran.5.dylib
  Referenced from: 
 

Re: [R-SIG-Mac] sf installation problem under Mac OS 11 - Big Sur

2020-11-19 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Ditto on the thanks.  Will also remind people that there were warnings that 
folks might want to hold off on upgrading to Big Sur because there might be 
hiccups, and to wait till it looked like most things were resolved.  

I imagine this is a huge amount of work.  Graeful to all who are working on it.

-Roy


> On Nov 19, 2020, at 4:07 PM, Milani Chaloupka  wrote:
> 
> Thank you Simon.
> 
> That worked exactly as you said for macOS Big Sur with rgdal, sf etc.
> 
> Simple. Sensible. No fuss. No nonsense.
> 
> I can also verify that after reinstall that cmdstanr and the Stan ecosystem 
> work as well on Big Sur including using sf for maps results,
> 
> So grateful for the work you do here.
> 
> Milani
> 
> 
> 
> 
> 
> 
> 
> 
>> On 20 Nov 2020, at 6:06 am, Simon Urbanek  
>> wrote:
>> 
>> Just for posterity, please do NOT follow those instructions unless you 
>> really want to build packages from sources and maintain them. Building GDAL 
>> can be tricky since the feature set depends on the libraries you have 
>> available, so use at your own risk.
>> 
>> CRAN libraries have been updated to be compatible with Big Sur which removed 
>> some system libraries, so just re-install rgdal and sf from CRAN (thanks to 
>> Jeroen). To make sure you get the latest versions use
>> install.packages(c("rgdal","sf"),,"https://mac.R-project.org;)
>> 
>> Cheers,
>> Simon
>> 
> 
> ___
> 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: https://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


Re: [R-SIG-Mac] Apple Silicon aka M1 Macs

2020-11-17 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Thank to all who are working on this.  Looks like a lot of work.  Also looks 
like when and if R can run in native mode on the M1 it will be very fast.

-Roy


> On Nov 17, 2020, at 6:57 AM, Prof Brian Ripley  wrote:
> 
> Mine (a 8GB MBA) arrived today, so I have started doing some comparisons.
> 
> For the CRAN build of R 4.0.3, §2.8 of R-admin recommends checking the 
> installation with
> 
> pdf("tests.pdf") ## optional, but prevents flashing graphics windows
> Sys.setenv(LC_COLLATE = "C", LC_TIME = "C", LANGUAGE = "en")
> tools::testInstalledBasic("both")
> tools::testInstalledPackages(scope = "base")
> tools::testInstalledPackages(scope = "recommended")
> 
> That took 454s (using Rosetta) against 895s for my late-2016 MBP (2.9GHz i5): 
> happily nothing untoward was reported (some recommended packages give 
> differences from reference output on both systems).
> 
> You need to install XQuartz to provide the X11() devices and support for 
> package Tcl/Tk: everything I tried using that worked as expected.
> 
> Having done that post-installation check I would happily use the Intel R on 
> an M1 machine.
> 
> We plan to check many of the Intel-compiled packages under Rosetta.
> 
> There are many hours of work ahead to build/test a native toolchain: our goal 
> is to have a native distribution for R 4.1.0 ca April 2021.
> 
> -- 
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
> 
> ___
> 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: https://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


Re: [R-SIG-Mac] Rstan compilation hangs misterisouly

2020-11-08 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Hi:

While it is possible you will get the help you seek here,  I think you would 
likely to get more help,  and more knowledgeable help, on this more specialized 
issue,  at the Stan Forum.  https://discourse.mc-stan.org.  I remember seeing 
in the summaries I get some issues with different combinations of versions of 
R,  Stan and compilers.

HTH,

-Roy

> On Nov 8, 2020, at 12:16 PM, Goncalo Ferraz via R-SIG-Mac 
>  wrote:
> 
> Hi, 
> 
> I’ve been struggling with an rstan problem for weeks. I installed R stan 
> following instructions in 
> https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started#how-to-use-rstan 
> 
>  to the letter, but when I try to compile any model R leaves me hanging 
> indefinitely (I’ve waited up to 30 minutes with ridiculously short models). 
> When I press esc R says:
> 
> Warning messages:
> 1: In readLines(file, warn = TRUE) :
>  incomplete final line found on '/Users/gferraz/Documents/MAF/R/schools.stan'
> 2: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
>  system call failed: Result too large
> 3: In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
>  error in running command
> 
> And then, R won’t quit. I can only close it by force quitting the software 
> itself and some R process that is set in motion and appears in the Activity 
> Monitor.
> 
> I have tried everything that was suggested in the stan forum, including 
> deleting all the contents of /usr/local, removing xcode, R and re-installing 
> everything again.
> 
> The only thing that I can think of now is to do a clean install of Mac OS on 
> my machine and really start from scratch.
> 
> Anyone has a less radical recommendation?
> 
> Thank you,
> 
> Gonçalo
>   [[alternative HTML version deleted]]
> 
> ___
> 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: https://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


[R-SIG-Mac] Thanks

2020-11-03 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
https://developer.r-project.org/Blog/public/2020/11/02/will-r-work-on-apple-silicon/

It reads like a lot of work.  Thanks for the efforts!

-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: https://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


Re: [R-SIG-Mac] Installation Problems

2020-09-17 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Thanks.  They eventually showed up.  What was weird was if you asked to check 
for packages available to be updated,  they were listed,  but then failed on 
the update.   I know nothing about how this system works  but it appears the 
"list" of what is new is somehow separate from a file list on the server,  if 
that is making any sense.  And this was true using the R-GUI as well as 
RStudio,  and I think I tried 3 different repositories,  including R-Cloud.  So 
that got me worried there was something nutty on my end.

Anyway,  thanks for the work.  One package had some things I particularly 
wanted to check out.

-Roy


> On Sep 17, 2020, at 8:19 PM, Simon Urbanek  
> wrote:
> 
> Roy,
> 
> it looks like the sync from the Mac master to CRAN was incomplete for some 
> reason (CCing CRAN in case there was some error). I presume it will fix 
> itself on next sync, but you can use the Mac master in the meantime which 
> worked for me:
> 
> install.packages(c("rpf", "statespacer", "tmap", 
> "workflows"),,"https://mac.R-project.org;)
> 
> Cheers,
> Simon
> 
> 
> 
> 
>> On Sep 18, 2020, at 3:57 AM, Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
>>  wrote:
>> 
>> Though what is shown below is from the RStudio repository,  I have tried 
>> several others,  including R-cloud.  Is it just something on my end or are 
>> there problems.  CRAN shows the versions trying to be installed.
>> 
>> -Roy
>> 
>> install.packages(c("rpf", "statespacer", "tmap", "workflows"))
>> Installing packages into ‘/Users/rmendels/Library/R/4.0/library’
>> (as ‘lib’ is unspecified)
>> trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/rpf_1.0.5.tgz'
>> Warning in install.packages :
>> cannot open URL 
>> 'https://cran.rstudio.com/bin/macosx/contrib/4.0/rpf_1.0.5.tgz': HTTP status 
>> was '404 Not Found'
>> Error in download.file(url, destfile, method, mode = "wb", ...) : 
>> cannot open URL 
>> 'https://cran.rstudio.com/bin/macosx/contrib/4.0/rpf_1.0.5.tgz'
>> Warning in install.packages :
>> download of package ‘rpf’ failed
>> trying URL 
>> 'https://cran.rstudio.com/bin/macosx/contrib/4.0/statespacer_0.3.0.tgz'
>> Warning in install.packages :
>> cannot open URL 
>> 'https://cran.rstudio.com/bin/macosx/contrib/4.0/statespacer_0.3.0.tgz': 
>> HTTP status was '404 Not Found'
>> Error in download.file(url, destfile, method, mode = "wb", ...) : 
>> cannot open URL 
>> 'https://cran.rstudio.com/bin/macosx/contrib/4.0/statespacer_0.3.0.tgz'
>> Warning in install.packages :
>> download of package ‘statespacer’ failed
>> trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/tmap_3.2.tgz'
>> Warning in install.packages :
>> cannot open URL 
>> 'https://cran.rstudio.com/bin/macosx/contrib/4.0/tmap_3.2.tgz': HTTP status 
>> was '404 Not Found'
>> Error in download.file(url, destfile, method, mode = "wb", ...) : 
>> cannot open URL 
>> 'https://cran.rstudio.com/bin/macosx/contrib/4.0/tmap_3.2.tgz'
>> Warning in install.packages :
>> download of package ‘tmap’ failed
>> trying URL 
>> 'https://cran.rstudio.com/bin/macosx/contrib/4.0/workflows_0.2.0.tgz'
>> Warning in install.packages :
>> cannot open URL 
>> 'https://cran.rstudio.com/bin/macosx/contrib/4.0/workflows_0.2.0.tgz': HTTP 
>> status was '404 Not Found'
>> Error in download.file(url, destfile, method, mode = "wb", ...) : 
>> cannot open URL 
>> 'https://cran.rstudio.com/bin/macosx/contrib/4.0/workflows_0.2.0.tgz'
>> Warning in install.packages :
>> download of package ‘workflows’ failed
>> **
>> "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: https://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
>>

[R-SIG-Mac] Installation Problems

2020-09-17 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Though what is shown below is from the RStudio repository,  I have tried 
several others,  including R-cloud.  Is it just something on my end or are 
there problems.  CRAN shows the versions trying to be installed.

-Roy

install.packages(c("rpf", "statespacer", "tmap", "workflows"))
Installing packages into ‘/Users/rmendels/Library/R/4.0/library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/rpf_1.0.5.tgz'
Warning in install.packages :
  cannot open URL 
'https://cran.rstudio.com/bin/macosx/contrib/4.0/rpf_1.0.5.tgz': HTTP status 
was '404 Not Found'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 
'https://cran.rstudio.com/bin/macosx/contrib/4.0/rpf_1.0.5.tgz'
Warning in install.packages :
  download of package ‘rpf’ failed
trying URL 
'https://cran.rstudio.com/bin/macosx/contrib/4.0/statespacer_0.3.0.tgz'
Warning in install.packages :
  cannot open URL 
'https://cran.rstudio.com/bin/macosx/contrib/4.0/statespacer_0.3.0.tgz': HTTP 
status was '404 Not Found'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 
'https://cran.rstudio.com/bin/macosx/contrib/4.0/statespacer_0.3.0.tgz'
Warning in install.packages :
  download of package ‘statespacer’ failed
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/tmap_3.2.tgz'
Warning in install.packages :
  cannot open URL 
'https://cran.rstudio.com/bin/macosx/contrib/4.0/tmap_3.2.tgz': HTTP status was 
'404 Not Found'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/tmap_3.2.tgz'
Warning in install.packages :
  download of package ‘tmap’ failed
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/workflows_0.2.0.tgz'
Warning in install.packages :
  cannot open URL 
'https://cran.rstudio.com/bin/macosx/contrib/4.0/workflows_0.2.0.tgz': HTTP 
status was '404 Not Found'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 
'https://cran.rstudio.com/bin/macosx/contrib/4.0/workflows_0.2.0.tgz'
Warning in install.packages :
  download of package ‘workflows’ failed
**
"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: https://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


Re: [R-SIG-Mac] Packages with updated spatial libraries.

2020-06-22 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
I ran package update this morning, so in CRAN terms I should be up to date.  
Based on this email:

https://stat.ethz.ch/pipermail/r-sig-mac/2020-June/013599.html

I installed  lwgeom rgdal rgeos sf from that repository.  These are built with 
GEOS 3.8.1, GDAL 3.1.0, PROJ 6.3.2.   It installed 'sf' 0.9-4.  I assume these 
builds are what will eventually make their way onto CRAN, so that is what I 
want to test against. It may well be that a CRS is not improperly defined in 
the call given the recent changes,  That is what I am trying to find out,  so I 
can have code that will work.

When I can isolate things I will give more information.

-Roy



> On Jun 22, 2020, at 12:34 PM, Edzer Pebesma  
> wrote:
> 
> Dear Roy, thanks for the message. Is it possible that the sf version you
> use links to an older version of GDAL/PROJ than the new rgdal does? In
> other words: if you update sf from CRAN, does the error persist?
> 
> Many regards,
> 
> On 6/22/20 9:28 PM, Roy Mendelssohn - NOAA Federal wrote:
>> I installed the whole suite available through Prof. Ripley's efforts, and 
>> finally have gotten time to do extensive testing.  I just ran into a problem 
>> with code that worked previously. It doesn't break all the mapping code,  
>> only some. The error I get is given below.  And yes I realize that this by 
>> itself it isn't much help.  It is a function calling a function in another 
>> package that causes the problem.  I am going to have to get in with the 
>> debugger and see what is actually being passed, and I will post what is 
>> going on in more detail when I figure it out.  This is more just a heads-up 
>> that the new versions can indeed break things in existing code.  This is 
>> what I was hoping to find out,  because it is going to take some time to 
>> pinpoint where.
>> 
>> -Roy
>> 
>>> Error in st_crs.character(comment(x)) : invalid crs: GEOGCRS["unknown",
>>>DATUM["World Geodetic System 1984",
>>>ELLIPSOID["WGS 84",6378137,298.257223563,
>>>LENGTHUNIT["metre",1]],
>>>ID["EPSG",6326]],
>>>PRIMEM["Greenwich",0,
>>>ANGLEUNIT["degree",0.0174532925199433],
>>>ID["EPSG",8901]],
>>>CS[ellipsoidal,2],
>>>AXIS["longitude",east,
>>>ORDER[1],
>>>ANGLEUNIT["degree",0.0174532925199433,
>>>ID["EPSG",9122]]],
>>>AXIS["latitude",north,
>>>ORDER[2],
>>>ANGLEUNIT["degree",0.0174532925199433,
>>>ID["EPSG",9122
>>> In addition: Warning messages:
>>> 1: In rgdal::rawTransform(projfrom, projto, nrow(xy), xy[, 1], xy[,  :
>>>  Using PROJ not WKT2 strings
>>> 2: In rgdal::rawTransform(projection(obj), crs, nrow(xy), xy[, 1],  :
>>>  Using PROJ not WKT2 strings
>>> 3: In rgdal::rawTransform(projto_int, projfrom, nrow(xy), xy[, 1],  :
>>> 
>>> Error in st_crs.character(comment(x)) : invalid crs: GEOGCRS["unknown",
>>>DATUM["World Geodetic System 1984",
>>>ELLIPSOID["WGS 84",6378137,298.257223563,
>>>LENGTHUNIT["metre",1]],
>>>ID["EPSG",6326]],
>>>PRIMEM["Greenwich",0,
>>>ANGLEUNIT["degree",0.0174532925199433],
>>>ID["EPSG",8901]],
>>>CS[ellipsoidal,2],
>>>AXIS["longitude",east,
>>>ORDER[1],
>>>ANGLEUNIT["degree",0.0174532925199433,
>>>ID["EPSG",9122]]],
>>>AXIS["latitude",north,
>>>ORDER[2],
>>>ANGLEUNIT["degree",0.0174532925199433,
>>>ID["EPSG",9122  
>> 
>> -Roy
>> 
>> 
>>> 
>>> On Jun 12, 2020, at 7:20 AM, Roy Mendelssohn - NOAA Federal 
>>>  wrote:
>>> 
>>> I will do the install sometime over the weekend,  and test what I have  
>>> (mainly the packages I have that use these).  Today is kind of tis up  (I 
>>> mean I can do the install easily enough,  just no time to do any testing).
>>> 
>>> Thanks,
>>> 
>>> -Roy
>>> 
>>> 
 On Jun 12, 2020, at 7:17 AM, Roger Bivand  wrote:
 
 On Fri, 12 Jun 2020, rmendelss gmail wrote:
 
> Thank you for these efforts.  I imagine it will also make it easier to 
> eventually have these on CRAN.
> 
 
 Do you have the possibility to try out the affected packages in your 
 workflows to provide feedback? At the moment, user feedback can help guide 
 the deployment of CRAN macOS R-spatial binaries.
 
 Roger
 
> -Roy
> 
> 
>> On Jun 12, 2020, at 7:11 AM, Prof Brian Ripley  
>> wrote:
>> 
>> I have put binary packages on CRANextras for lwgeom rgdal rgeos sf built 
>> with GEOS 3.8.1, GDAL 3.1.0, PROJ 6.3.2.
>> 
>> Install with (e.g.)
>> 
>> options(repos="https://www.stats.ox.ac.uk/pub/RWin;)
>> install.packages('rgdal', type = 'binary')
>> 
>> (This needed a development version of the rgdal sources.)
>> 
>> This is just to allow early access: it is planned to use these versions 
>> of the libs on the CRAN builders soon (but they do need package 

Re: [R-SIG-Mac] Packages with updated spatial libraries.

2020-06-22 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
I installed the whole suite available through Prof. Ripley's efforts, and 
finally have gotten time to do extensive testing.  I just ran into a problem 
with code that worked previously. It doesn't break all the mapping code,  only 
some. The error I get is given below.  And yes I realize that this by itself it 
isn't much help.  It is a function calling a function in another package that 
causes the problem.  I am going to have to get in with the debugger and see 
what is actually being passed, and I will post what is going on in more detail 
when I figure it out.  This is more just a heads-up that the new versions can 
indeed break things in existing code.  This is what I was hoping to find out,  
because it is going to take some time to pinpoint where.

-Roy

> Error in st_crs.character(comment(x)) : invalid crs: GEOGCRS["unknown",
> DATUM["World Geodetic System 1984",
> ELLIPSOID["WGS 84",6378137,298.257223563,
> LENGTHUNIT["metre",1]],
> ID["EPSG",6326]],
> PRIMEM["Greenwich",0,
> ANGLEUNIT["degree",0.0174532925199433],
> ID["EPSG",8901]],
> CS[ellipsoidal,2],
> AXIS["longitude",east,
> ORDER[1],
> ANGLEUNIT["degree",0.0174532925199433,
> ID["EPSG",9122]]],
> AXIS["latitude",north,
> ORDER[2],
> ANGLEUNIT["degree",0.0174532925199433,
> ID["EPSG",9122
> In addition: Warning messages:
> 1: In rgdal::rawTransform(projfrom, projto, nrow(xy), xy[, 1], xy[,  :
>   Using PROJ not WKT2 strings
> 2: In rgdal::rawTransform(projection(obj), crs, nrow(xy), xy[, 1],  :
>   Using PROJ not WKT2 strings
> 3: In rgdal::rawTransform(projto_int, projfrom, nrow(xy), xy[, 1],  :
>  
>  Error in st_crs.character(comment(x)) : invalid crs: GEOGCRS["unknown",
> DATUM["World Geodetic System 1984",
> ELLIPSOID["WGS 84",6378137,298.257223563,
> LENGTHUNIT["metre",1]],
> ID["EPSG",6326]],
> PRIMEM["Greenwich",0,
> ANGLEUNIT["degree",0.0174532925199433],
> ID["EPSG",8901]],
> CS[ellipsoidal,2],
> AXIS["longitude",east,
> ORDER[1],
> ANGLEUNIT["degree",0.0174532925199433,
> ID["EPSG",9122]]],
> AXIS["latitude",north,
> ORDER[2],
> ANGLEUNIT["degree",0.0174532925199433,
> ID["EPSG",9122  

-Roy


> 
> On Jun 12, 2020, at 7:20 AM, Roy Mendelssohn - NOAA Federal 
>  wrote:
> 
> I will do the install sometime over the weekend,  and test what I have  
> (mainly the packages I have that use these).  Today is kind of tis up  (I 
> mean I can do the install easily enough,  just no time to do any testing).
> 
> Thanks,
> 
> -Roy
> 
> 
>> On Jun 12, 2020, at 7:17 AM, Roger Bivand  wrote:
>> 
>> On Fri, 12 Jun 2020, rmendelss gmail wrote:
>> 
>>> Thank you for these efforts.  I imagine it will also make it easier to 
>>> eventually have these on CRAN.
>>> 
>> 
>> Do you have the possibility to try out the affected packages in your 
>> workflows to provide feedback? At the moment, user feedback can help guide 
>> the deployment of CRAN macOS R-spatial binaries.
>> 
>> Roger
>> 
>>> -Roy
>>> 
>>> 
 On Jun 12, 2020, at 7:11 AM, Prof Brian Ripley  
 wrote:
 
 I have put binary packages on CRANextras for lwgeom rgdal rgeos sf built 
 with GEOS 3.8.1, GDAL 3.1.0, PROJ 6.3.2.
 
 Install with (e.g.)
 
 options(repos="https://www.stats.ox.ac.uk/pub/RWin;)
 install.packages('rgdal', type = 'binary')
 
 (This needed a development version of the rgdal sources.)
 
 This is just to allow early access: it is planned to use these versions of 
 the libs on the CRAN builders soon (but they do need package updates, e.g. 
 for rgdal and proj4).
 
 These are all using static libraries to make these self-contained.
 
 (In case anyone is wondering why not PROJ 7 -- that would need unreleased 
 changes to the PROJ and GDAL sources and changes to many CRAN packages.)
 
 --
 Brian D. Ripley,  rip...@stats.ox.ac.uk
 Emeritus Professor of Applied Statistics, University of Oxford
 
 ___
 R-SIG-Mac mailing list
 R-SIG-Mac@r-project.org
 https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>>> 
>> 
>> -- 
>> 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
>> https://orcid.org/-0003-2392-6140
>> https://scholar.google.no/citations?user=AWeghB0J=en
> 
> **
> "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 

Re: [R-SIG-Mac] Packages with updated spatial libraries.

2020-06-12 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
I will do the install sometime over the weekend,  and test what I have  (mainly 
the packages I have that use these).  Today is kind of tis up  (I mean I can do 
the install easily enough,  just no time to do any testing).

Thanks,

-Roy


> On Jun 12, 2020, at 7:17 AM, Roger Bivand  wrote:
> 
> On Fri, 12 Jun 2020, rmendelss gmail wrote:
> 
>> Thank you for these efforts.  I imagine it will also make it easier to 
>> eventually have these on CRAN.
>> 
> 
> Do you have the possibility to try out the affected packages in your 
> workflows to provide feedback? At the moment, user feedback can help guide 
> the deployment of CRAN macOS R-spatial binaries.
> 
> Roger
> 
>> -Roy
>> 
>> 
>>> On Jun 12, 2020, at 7:11 AM, Prof Brian Ripley  
>>> wrote:
>>> 
>>> I have put binary packages on CRANextras for lwgeom rgdal rgeos sf built 
>>> with GEOS 3.8.1, GDAL 3.1.0, PROJ 6.3.2.
>>> 
>>> Install with (e.g.)
>>> 
>>> options(repos="https://www.stats.ox.ac.uk/pub/RWin;)
>>> install.packages('rgdal', type = 'binary')
>>> 
>>> (This needed a development version of the rgdal sources.)
>>> 
>>> This is just to allow early access: it is planned to use these versions of 
>>> the libs on the CRAN builders soon (but they do need package updates, e.g. 
>>> for rgdal and proj4).
>>> 
>>> These are all using static libraries to make these self-contained.
>>> 
>>> (In case anyone is wondering why not PROJ 7 -- that would need unreleased 
>>> changes to the PROJ and GDAL sources and changes to many CRAN packages.)
>>> 
>>> --
>>> Brian D. Ripley,  rip...@stats.ox.ac.uk
>>> Emeritus Professor of Applied Statistics, University of Oxford
>>> 
>>> ___
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>> 
> 
> -- 
> 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
> https://orcid.org/-0003-2392-6140
> https://scholar.google.no/citations?user=AWeghB0J=en

**
"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: https://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


Re: [R-SIG-Mac] R4.0.0 and Makevars

2020-05-26 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
That's muchly.  That was my memory.  I just wanted to reconfirm.  I do have the 
emails about OpenMP.  Right now I don't need that,  but I might down the line.  
I was just glad that I have been able to get the upgrade to go smoothly.  A 
fellow on R-bloggers posted a really nice script to upgrade.  What us nice is 
it re-installed not only packages from CRAN but from GIthub also.

-Roy


> On May 26, 2020, at 12:57 PM, Balamuta, James Joseph  
> wrote:
> 
> Roy,
> 
> For R 4.0.0, there is no need to keep Makevars or Renviron's PATH 
> configuration as everything should just "work." The R 4.0.0 binary will look 
> at the default installation location for OS-specific gfortran8.2 or 
> gfortran6.3 version.
> 
> Having said this, there is also the OpenMP opt-in possibility for developers 
> (avoid users) detailed here: 
> 
> http://mac.r-project.org/openmp/
> 
> Best,
> 
> JJB
> 
> On 5/26/20, 2:00 PM, "R-SIG-Mac on behalf of Roy Mendelssohn - NOAA Federal 
> via R-SIG-Mac"  r-sig-mac@r-project.org> wrote:
> 
>Hi All:
> 
>Awhile back Simon posted what if anything should be in your Makevars for 
> R4.0.0 if you needed to compile packages from source.  I thought I had saved 
> that email but i can't find it,  and I just looked at the archives and can't 
> find it either.  If anyone has that info I would appreciate it.  I know you 
> remove all the clang references that might have been there,  I have kept the 
> gfortran to gfortran8.2,  is there anything else.
> 
>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: https://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
> 
> ___
> 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: https://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


[R-SIG-Mac] R4.0.0 and Makevars

2020-05-26 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Hi All:

Awhile back Simon posted what if anything should be in your Makevars for R4.0.0 
if you needed to compile packages from source.  I thought I had saved that 
email but i can't find it,  and I just looked at the archives and can't find it 
either.  If anyone has that info I would appreciate it.  I know you remove all 
the clang references that might have been there,  I have kept the gfortran to 
gfortran8.2,  is there anything else.

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: https://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


Re: [R-SIG-Mac] R 3.6.2 installer / Catalina / Notarization

2019-12-13 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
$!$!$$$@!+!.  

So I went there,  still saw old version.  Cleared cache,  went again,  still 
saw old version.  Cleared cache again,  went there,  saw new version.  Grrr.  
The kind of small things that drive me nuts.

Thanks,

-Roy

> On Dec 13, 2019, at 9:55 AM, Bob Rudis  wrote:
> 
> It's definitely showing for me on https://cran.r-project.org/bin/macosx/
> 
>> On Dec 13, 2019, at 12:53, Roy Mendelssohn - NOAA Federal 
>>  wrote:
>> 
>> Yes but I don't see the installer on the CRAN site, I only see the installer 
>> for 3.6.1.  Am I missing something?  Not a complaint,  just don't see it?  I 
>> did clear my caches.
>> 
>> Thanks,
>> 
>> -Roy
>> 
>> 
>>> On Dec 13, 2019, at 9:51 AM, Bob Rudis  wrote:
>>> 
>>> 3.6.2 was released on the 12th and it's been on all the CRAN mirrors I, er, 
>>> "monitor", including the cran.r-project.org site 
>>> (https://cran.r-project.org/bin/macosx/R-3.6.2.pkg).
>>> 
 On Dec 13, 2019, at 12:49, rmendelss gmail  wrote:
 
 Is this on the CRAN page?  Am I missing something?
 
 Thanks,
 
 -Roy
 
 
> On Dec 13, 2019, at 9:39 AM, Simon Urbanek  
> wrote:
> 
> Bob,
> 
> thanks - oddly, it didn't show when I tested it on Catalina, there must 
> be a flag somewhere. As discussed before we cannot notarize any version 
> of R before 4.0.0 so Catalina users have to either stick to 3.5.1 (since 
> Apple has grand-fathered installers create before Catalina) or use the 
> Ctrl+click way to install R 3.6.2.
> 
> Cheers,
> Simon
> 
> 
>> On Dec 13, 2019, at 12:30 PM, Bob Rudis  wrote:
>> 
>> While easily remedied via right-click + open, out-of-the-box installer 
>> gives the Apple daft (and technically incorrect since Apple could most 
>> certainly check it for malicious software):
>> 
>> “R-3.6.2.pkg” can’t be opened because Apple cannot check it for 
>> malicious software.
>> 
>> message.
>> 
>> 
>> Here's what spctl returns:
>> 
>> $ spctl -a -vv -t install R-3.6.2.pkg
>> R-3.6.2.pkg: rejected
>> source=Unnotarized Developer ID
>> origin=Developer ID Installer: Simon Urbanek (VZLD955F6P)
>> 
>> 
>> NOTE: R & R.app work fine once installed.
>> 
>> Not sure if this is going to cause consternation in "corporate" 
>> environments.
>> 
>> -boB
>> ___
>> 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
 
>>> 
>> 
>> **
>> "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: https://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: https://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


Re: [R-SIG-Mac] R 3.6.2 installer / Catalina / Notarization

2019-12-13 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Yes but I don't see the installer on the CRAN site, I only see the installer 
for 3.6.1.  Am I missing something?  Not a complaint,  just don't see it?  I 
did clear my caches.

Thanks,

-Roy


> On Dec 13, 2019, at 9:51 AM, Bob Rudis  wrote:
> 
> 3.6.2 was released on the 12th and it's been on all the CRAN mirrors I, er, 
> "monitor", including the cran.r-project.org site 
> (https://cran.r-project.org/bin/macosx/R-3.6.2.pkg).
> 
>> On Dec 13, 2019, at 12:49, rmendelss gmail  wrote:
>> 
>> Is this on the CRAN page?  Am I missing something?
>> 
>> Thanks,
>> 
>> -Roy
>> 
>> 
>>> On Dec 13, 2019, at 9:39 AM, Simon Urbanek  
>>> wrote:
>>> 
>>> Bob,
>>> 
>>> thanks - oddly, it didn't show when I tested it on Catalina, there must be 
>>> a flag somewhere. As discussed before we cannot notarize any version of R 
>>> before 4.0.0 so Catalina users have to either stick to 3.5.1 (since Apple 
>>> has grand-fathered installers create before Catalina) or use the Ctrl+click 
>>> way to install R 3.6.2.
>>> 
>>> Cheers,
>>> Simon
>>> 
>>> 
 On Dec 13, 2019, at 12:30 PM, Bob Rudis  wrote:
 
 While easily remedied via right-click + open, out-of-the-box installer 
 gives the Apple daft (and technically incorrect since Apple could most 
 certainly check it for malicious software):
 
 “R-3.6.2.pkg” can’t be opened because Apple cannot check it for malicious 
 software.
 
 message.
 
 
 Here's what spctl returns:
 
 $ spctl -a -vv -t install R-3.6.2.pkg
 R-3.6.2.pkg: rejected
 source=Unnotarized Developer ID
 origin=Developer ID Installer: Simon Urbanek (VZLD955F6P)
 
 
 NOTE: R & R.app work fine once installed.
 
 Not sure if this is going to cause consternation in "corporate" 
 environments.
 
 -boB
 ___
 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
>> 
> 

**
"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: https://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


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

2019-08-20 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
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
>>> ___
>>> 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.
>> 
> 

**
"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


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

2019-08-20 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
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
> ___
> 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.

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac


Re: [R-SIG-Mac] Xcode 10.3 and header flles

2019-07-24 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
But is there a difference in where headers are being looked for when building R 
as compared to when a package is built from source.  As I said,  what was 
failing was try to do source installs of packages from CRAN.  

-Roy


> On Jul 24, 2019, at 8:09 AM, Simon Urbanek  
> wrote:
> 
> It's not what I'd expect because the system headers don't matter in the 
> current CRAN release as it's not relying on the system headers anymore. 
> That's why I'd need the actual full output - the command line and the error - 
> so I could tract why it's failing.
> 
> 
> 
>> On Jul 24, 2019, at 11:02 AM, Roy Mendelssohn - NOAA Federal 
>>  wrote:
>> 
>> HI Simon:
>> 
>> Perhaps if you can find someone who hasn't done the Xcode and Command Line 
>> Update,  have them list the directories that you are interested in, and then 
>> list the same after the update to see what it is doing.  Also is it possible 
>> you have something in your .Rpofile of the like that points to the location 
>> you want that I do not?  The errors you get on build are just what you 
>> expect - whatever *.h files it needed could not be found. 
>> 
>> HTH,
>> 
>> -Roy
>> 
>>> On Jul 24, 2019, at 7:57 AM, Simon Urbanek  
>>> wrote:
>>> 
>>> I want to avoid that "fix" because it is not guaranteed to work in the 
>>> future. Can someone who did NOT instal the system-level headers below 
>>> please report the actual issue? The whole point of using the SDK was to 
>>> make sure it's not necessary.
>>> 
>>> Thanks,
>>> Simon
>>> 
>>> 
>>> 
>>>> On Jul 24, 2019, at 10:54 AM, Bryan Hanson  wrote:
>>>> 
>>>> If it helps troubleshoot, I updated more or less on the same timeline as 
>>>> Roy did and had the same problems Roy had, and Roy’s most recent response 
>>>> below gives the same response on my Mac.  Roy’s fix * fixed things for me. 
>>>>  Bryan
>>>> 
>>>> * open  
>>>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>>>> 
>>>>> On Jul 24, 2019, at 10:46 AM, Roy Mendelssohn - NOAA Federal via 
>>>>> R-SIG-Mac  wrote:
>>>>> 
>>>>> Hi Simon:
>>>>> 
>>>>>> ls /Library/Developer/CommandLineTools/SDKs
>>>>>> MacOSX.sdk   MacOSX10.14.sdk
>>>>> 
>>>>> Also when  have done:
>>>>> 
>>>>>> sudo xcode-select --install
>>>>> 
>>>>> I often get a message to install through App store (the command line 
>>>>> tools).  I am not certain exactly what 
>>>>> macOS_SDK_headers_for_macOS_10.14.pkg installs nor where,  but I as I 
>>>>> said I went from being able to install packages from source to not being 
>>>>> able to because headers couldn't be found to be able to.  And I have a 
>>>>> feeling others will run into the same problem.
>>>>> 
>>>>> Thanks!
>>>>> 
>>>>> -Roy
>>>>> 
>>>>> 
>>>>>> On Jul 23, 2019, at 9:33 PM, Simon Urbanek  
>>>>>> wrote:
>>>>>> 
>>>>>> Roy,
>>>>>> 
>>>>>> thanks, I just wanted to clarify which headers have been deleted 
>>>>>> exactly. The system location (/usr/includes) is what Apple doesn't like, 
>>>>>> which is why we are now using the SDK. Can you check, please, whether 
>>>>>> you do have
>>>>>> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
>>>>>> I would hope that they don't touch that location. That said, if you have 
>>>>>> Xcode proper they may think that you no longer need command line tools 
>>>>>> or something like that -in principle that should be recoverable with
>>>>>> sudo xcode-select --install
>>>>>> hopefully.
>>>>>> 
>>>>>> Thanks,
>>>>>> Simon
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>>> On Jul 23, 2019, at 14:50, Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
>>>>>>>  wrote:
>>>>>>> 
>>>>>>> Hi Simon:
>>>>>>> 
>>>>>>> I am using CRAN release,  recommended CRAN compilers.  Yesterday 
>>>>>>> morning one updated package needed to be inst

Re: [R-SIG-Mac] Xcode 10.3 and header flles

2019-07-24 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Thanks Bryan.  Given my age,  I always have to wonder if I am hallucinating or 
did something careless.  I want to emphasize that I don't think it is an R 
issue,  it really does look like when installing the new Xcode,  the headers 
got wiped out. Since both a new Xcode and a new Command Line Tools were 
installed,  I don't know which did the damage.

-Roy


> On Jul 24, 2019, at 7:54 AM, Bryan Hanson  wrote:
> 
> If it helps troubleshoot, I updated more or less on the same timeline as Roy 
> did and had the same problems Roy had, and Roy’s most recent response below 
> gives the same response on my Mac.  Roy’s fix * fixed things for me.  Bryan
> 
> * open  
> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
> 
>> On Jul 24, 2019, at 10:46 AM, Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
>>  wrote:
>> 
>> Hi Simon:
>> 
>>> ls /Library/Developer/CommandLineTools/SDKs
>>> MacOSX.sdk  MacOSX10.14.sdk
>> 
>> Also when  have done:
>> 
>>> sudo xcode-select --install
>> 
>> I often get a message to install through App store (the command line tools). 
>>  I am not certain exactly what macOS_SDK_headers_for_macOS_10.14.pkg 
>> installs nor where,  but I as I said I went from being able to install 
>> packages from source to not being able to because headers couldn't be found 
>> to be able to.  And I have a feeling others will run into the same problem.
>> 
>> Thanks!
>> 
>> -Roy
>> 
>> 
>>> On Jul 23, 2019, at 9:33 PM, Simon Urbanek  
>>> wrote:
>>> 
>>> Roy,
>>> 
>>> thanks, I just wanted to clarify which headers have been deleted exactly. 
>>> The system location (/usr/includes) is what Apple doesn't like, which is 
>>> why we are now using the SDK. Can you check, please, whether you do have
>>> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
>>> I would hope that they don't touch that location. That said, if you have 
>>> Xcode proper they may think that you no longer need command line tools or 
>>> something like that -in principle that should be recoverable with
>>> sudo xcode-select --install
>>> hopefully.
>>> 
>>> Thanks,
>>> Simon
>>> 
>>> 
>>> 
>>>> On Jul 23, 2019, at 14:50, Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
>>>>  wrote:
>>>> 
>>>> Hi Simon:
>>>> 
>>>> I am using CRAN release,  recommended CRAN compilers.  Yesterday morning 
>>>> one updated package needed to be installed from source,  worked.  
>>>> Yesterday afternoon did the update of Xcode (and OSX).  This morning 
>>>> installing a package update from source failed,  couldn't find header 
>>>> files (gee I have seen this before).  Ran the command I put below,  
>>>> everybody was happy.  It does appear that the update literally deleted the 
>>>> headers.
>>>> 
>>>> HTH,
>>>> 
>>>> Roy
>>>> 
>>>> PS - not trying to build R from source,  just source updates of some 
>>>> packages
>>>> 
>>>>> On Jul 23, 2019, at 11:17 AM, Simon Urbanek  
>>>>> wrote:
>>>>> 
>>>>> Roy,
>>>>> 
>>>>> that shouldn't be necessary if you use the CRAN release since it 
>>>>> specifically points to the SDK. If you are compiling your own R you may 
>>>>> want to add
>>>>> CPPFLAGS='-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk 
>>>>> -I/usr/local/include'
>>>>> which is what the CRAN build uses. FWIW you can always check the current 
>>>>> flags at
>>>>> https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R-build/conf.el-capitan-x86_64
>>>>> 
>>>>> If the above doesn't address the issue you're seeing, please provide 
>>>>> details.
>>>>> 
>>>>> Thanks,
>>>>> Simon
>>>>> 
>>>>> 
>>>>>> On Jul 23, 2019, at 12:47 PM, Roy Mendelssohn - NOAA Federal via 
>>>>>> R-SIG-Mac  wrote:
>>>>>> 
>>>>>> If like me you updated to Xcode 10.3,  in Apple's infinite wisdom the 
>>>>>> install again wipes out the header files.  So if you did the update and 
>>>>>> install from source remember to re-install the headers:
>>>>>> 
>>>>>>> open  
>>>>>>&

Re: [R-SIG-Mac] Xcode 10.3 and header flles

2019-07-24 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
HI Simon:

Perhaps if you can find someone who hasn't done the Xcode and Command Line 
Update,  have them list the directories that you are interested in, and then 
list the same after the update to see what it is doing.  Also is it possible 
you have something in your .Rpofile of the like that points to the location you 
want that I do not?  The errors you get on build are just what you expect - 
whatever *.h files it needed could not be found. 

HTH,

-Roy

> On Jul 24, 2019, at 7:57 AM, Simon Urbanek  
> wrote:
> 
> I want to avoid that "fix" because it is not guaranteed to work in the 
> future. Can someone who did NOT instal the system-level headers below please 
> report the actual issue? The whole point of using the SDK was to make sure 
> it's not necessary.
> 
> Thanks,
> Simon
> 
> 
> 
>> On Jul 24, 2019, at 10:54 AM, Bryan Hanson  wrote:
>> 
>> If it helps troubleshoot, I updated more or less on the same timeline as Roy 
>> did and had the same problems Roy had, and Roy’s most recent response below 
>> gives the same response on my Mac.  Roy’s fix * fixed things for me.  Bryan
>> 
>> * open  
>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>> 
>>> On Jul 24, 2019, at 10:46 AM, Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
>>>  wrote:
>>> 
>>> Hi Simon:
>>> 
>>>> ls /Library/Developer/CommandLineTools/SDKs
>>>> MacOSX.sdk MacOSX10.14.sdk
>>> 
>>> Also when  have done:
>>> 
>>>> sudo xcode-select --install
>>> 
>>> I often get a message to install through App store (the command line 
>>> tools).  I am not certain exactly what 
>>> macOS_SDK_headers_for_macOS_10.14.pkg installs nor where,  but I as I said 
>>> I went from being able to install packages from source to not being able to 
>>> because headers couldn't be found to be able to.  And I have a feeling 
>>> others will run into the same problem.
>>> 
>>> Thanks!
>>> 
>>> -Roy
>>> 
>>> 
>>>> On Jul 23, 2019, at 9:33 PM, Simon Urbanek  
>>>> wrote:
>>>> 
>>>> Roy,
>>>> 
>>>> thanks, I just wanted to clarify which headers have been deleted exactly. 
>>>> The system location (/usr/includes) is what Apple doesn't like, which is 
>>>> why we are now using the SDK. Can you check, please, whether you do have
>>>> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
>>>> I would hope that they don't touch that location. That said, if you have 
>>>> Xcode proper they may think that you no longer need command line tools or 
>>>> something like that -in principle that should be recoverable with
>>>> sudo xcode-select --install
>>>> hopefully.
>>>> 
>>>> Thanks,
>>>> Simon
>>>> 
>>>> 
>>>> 
>>>>> On Jul 23, 2019, at 14:50, Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
>>>>>  wrote:
>>>>> 
>>>>> Hi Simon:
>>>>> 
>>>>> I am using CRAN release,  recommended CRAN compilers.  Yesterday morning 
>>>>> one updated package needed to be installed from source,  worked.  
>>>>> Yesterday afternoon did the update of Xcode (and OSX).  This morning 
>>>>> installing a package update from source failed,  couldn't find header 
>>>>> files (gee I have seen this before).  Ran the command I put below,  
>>>>> everybody was happy.  It does appear that the update literally deleted 
>>>>> the headers.
>>>>> 
>>>>> HTH,
>>>>> 
>>>>> Roy
>>>>> 
>>>>> PS - not trying to build R from source,  just source updates of some 
>>>>> packages
>>>>> 
>>>>>> On Jul 23, 2019, at 11:17 AM, Simon Urbanek 
>>>>>>  wrote:
>>>>>> 
>>>>>> Roy,
>>>>>> 
>>>>>> that shouldn't be necessary if you use the CRAN release since it 
>>>>>> specifically points to the SDK. If you are compiling your own R you may 
>>>>>> want to add
>>>>>> CPPFLAGS='-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk 
>>>>>> -I/usr/local/include'
>>>>>> which is what the CRAN build uses. FWIW you can always check the current 
>>>>>> flags at
>>>>>> https://svn.r-project.org/R-dev-web/trunk/QA

Re: [R-SIG-Mac] Xcode 10.3 and header flles

2019-07-24 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Hi Simon:

> ls /Library/Developer/CommandLineTools/SDKs
> MacOSX.sdkMacOSX10.14.sdk

Also when  have done:

> sudo xcode-select --install

I often get a message to install through App store (the command line tools).  I 
am not certain exactly what macOS_SDK_headers_for_macOS_10.14.pkg installs nor 
where,  but I as I said I went from being able to install packages from source 
to not being able to because headers couldn't be found to be able to.  And I 
have a feeling others will run into the same problem.

Thanks!

-Roy


> On Jul 23, 2019, at 9:33 PM, Simon Urbanek  
> wrote:
> 
> Roy,
> 
> thanks, I just wanted to clarify which headers have been deleted exactly. The 
> system location (/usr/includes) is what Apple doesn't like, which is why we 
> are now using the SDK. Can you check, please, whether you do have
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> I would hope that they don't touch that location. That said, if you have 
> Xcode proper they may think that you no longer need command line tools or 
> something like that -in principle that should be recoverable with
> sudo xcode-select --install
> hopefully.
> 
> Thanks,
> Simon
> 
> 
> 
>> On Jul 23, 2019, at 14:50, Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
>>  wrote:
>> 
>> Hi Simon:
>> 
>> I am using CRAN release,  recommended CRAN compilers.  Yesterday morning one 
>> updated package needed to be installed from source,  worked.  Yesterday 
>> afternoon did the update of Xcode (and OSX).  This morning installing a 
>> package update from source failed,  couldn't find header files (gee I have 
>> seen this before).  Ran the command I put below,  everybody was happy.  It 
>> does appear that the update literally deleted the headers.
>> 
>> HTH,
>> 
>> Roy
>> 
>> PS - not trying to build R from source,  just source updates of some packages
>> 
>>> On Jul 23, 2019, at 11:17 AM, Simon Urbanek  
>>> wrote:
>>> 
>>> Roy,
>>> 
>>> that shouldn't be necessary if you use the CRAN release since it 
>>> specifically points to the SDK. If you are compiling your own R you may 
>>> want to add
>>> CPPFLAGS='-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk 
>>> -I/usr/local/include'
>>> which is what the CRAN build uses. FWIW you can always check the current 
>>> flags at
>>> https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R-build/conf.el-capitan-x86_64
>>> 
>>> If the above doesn't address the issue you're seeing, please provide 
>>> details.
>>> 
>>> Thanks,
>>> Simon
>>> 
>>> 
>>>> On Jul 23, 2019, at 12:47 PM, Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
>>>>  wrote:
>>>> 
>>>> If like me you updated to Xcode 10.3,  in Apple's infinite wisdom the 
>>>> install again wipes out the header files.  So if you did the update and 
>>>> install from source remember to re-install the headers:
>>>> 
>>>>> open  
>>>>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>>>> 
>>>> -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 Opera

Re: [R-SIG-Mac] Xcode 10.3 and header flles

2019-07-23 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Hi Simon:

 I am using CRAN release,  recommended CRAN compilers.  Yesterday morning one 
updated package needed to be installed from source,  worked.  Yesterday 
afternoon did the update of Xcode (and OSX).  This morning installing a package 
update from source failed,  couldn't find header files (gee I have seen this 
before).  Ran the command I put below,  everybody was happy.  It does appear 
that the update literally deleted the headers.

HTH,

Roy

PS - not trying to build R from source,  just source updates of some packages

> On Jul 23, 2019, at 11:17 AM, Simon Urbanek  
> wrote:
> 
> Roy,
> 
> that shouldn't be necessary if you use the CRAN release since it specifically 
> points to the SDK. If you are compiling your own R you may want to add
> CPPFLAGS='-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk 
> -I/usr/local/include'
> which is what the CRAN build uses. FWIW you can always check the current 
> flags at
> https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R-build/conf.el-capitan-x86_64
> 
> If the above doesn't address the issue you're seeing, please provide details.
> 
> Thanks,
> Simon
> 
> 
>> On Jul 23, 2019, at 12:47 PM, Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
>>  wrote:
>> 
>> If like me you updated to Xcode 10.3,  in Apple's infinite wisdom the 
>> install again wipes out the header files.  So if you did the update and 
>> install from source remember to re-install the headers:
>> 
>>> open  
>>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>> 
>> -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.

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac


[R-SIG-Mac] Xcode 10.3 and header flles

2019-07-23 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
If like me you updated to Xcode 10.3,  in Apple's infinite wisdom the install 
again wipes out the header files.  So if you did the update and install from 
source remember to re-install the headers:

> open  
> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

-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


Re: [R-SIG-Mac] clang: error: unsupported option '-fopenmp'

2019-05-06 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Um you didn't mention what version of the compiler and where you downloaded it 
from.  The last couple of versions available through the tools links have 
supported OpenMP.  I have compiled that package,  but I am using R 3.5.3 and 
clang 6,  I believe R 3.6.0 uses clang 7, but that also supports openmp

HTH,

-Roy

> On May 6, 2019, at 4:16 PM, Spencer Graves  
> wrote:
> 
> Hello, All:
> 
> 
>   I'm getting "clang: error: unsupported option '-fopenmp'" when trying 
> to build "https://github.com/helske/bssm; under macOS 10.14.14 with R 3.6.0;  
> see below.
> 
> 
>   What do you suggest?
> 
> 
>   Thanks,
>   Spencer Graves
> 
> 
> p.s.  Helske told me he thought my compiler was out of date. However, I've so 
> far been unable to find instructions that are sufficiently current to 
> convince me I might not do more harm than good following them.
> 
> 
>> R CMD build bssm
> * checking for file ‘bssm/DESCRIPTION’ ... OK
> * preparing ‘bssm’:
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * installing the package to build vignettes
>   ---
> * installing *source* package ‘bssm’ ...
> ** using staged installation
> ** libs
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" 
> -DNDEBUG 
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" 
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include"
>  
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include"
>  
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ramcmc/include"
>  
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sitmo/include"
>  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk 
> -I/usr/local/include -fopenmp -fPIC  -Wall -g -O2  -c R_approx.cpp -o 
> R_approx.o
> clang: error: unsupported option '-fopenmp'
> make: *** [R_approx.o] Error 1
> ERROR: compilation failed for package ‘bssm’
> * removing 
> ‘/private/var/folders/mh/mrm_14nx19g13lsnj9zmvwjrgn/T/RtmppA2gBg/Rinst24427c5cbfeb/bssm’
>   ---
> ERROR: package installation failed
> 
> ___
> 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.

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac


Re: [R-SIG-Mac] [External] Re: Xcode 10.2.1

2019-04-28 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
I just saw that the Mac version was now available.  given the numbering this 
would mean reinstalling packages correct?  If i use in mechanism in the R GUI 
to do so,  does it preserve location - that is the packages in the Framework 
directory are update  to that system location,  and the packages in my own 
library stay in my own library?

If not,  I should be able to write a script to do so, but if the GUI will 
already do it,  i would prefer to use that.  May wait a few days for packages 
to keep up.

thanks for all your work,

-roy


> On Apr 28, 2019, at 3:13 PM, Simon Urbanek  
> wrote:
> 
> Yes, I did, if you used R 3.6.0 there would be no issue (as long as you have 
> command line tools installed).
> 
> Cheers,
> Simon
> 
> 
>> On Apr 24, 2019, at 12:06, Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
>>  wrote:
>> 
>> Yes that is where I found the command.  I would add though that I had done 
>> that for Xcode 10.2.0, and appears that when you install the new versions 
>> that the installer actually deletes the headers at that location.  At least 
>> that is what happened to me when I updated to Xcode 10.2.1.  So people 
>> should be aware of this.  Each update may delete the headers.
>> 
>> In the previous thread,  Simon was looking into possibly changing where the 
>> R tools look for the headers, but that sort of thing is beyond my pay grade. 
>>  
>> 
>> -Roy
>> 
>>> On Apr 24, 2019, at 9:01 AM, Tierney, Luke  wrote:
>>> 
>>> Also documented in the 'R Installation and Administration' manual --
>>> always a good place to look.
>>> 
>>> Best,
>>> 
>>> luke
>>> 
>>> On Wed, 24 Apr 2019, Kasper Daniel Hansen wrote:
>>> 
>>>> Doh! Sorry to have missed that email thread.
>>>> 
>>>> This advice solved the issue for me.
>>>> 
>>>> On Wed, Apr 24, 2019 at 11:41 AM Roy Mendelssohn - NOAA Federal <
>>>> roy.mendelss...@noaa.gov> wrote:
>>>> 
>>>>> Hi Kaspar:
>>>>> 
>>>>> There is an issue of where Xcode puts headers.  I have posted on this
>>>>> previously.  I did the same update as you,  and not only doesn't Xcode put
>>>>> the headers where R expects,  it appears to delete the existing headers.
>>>>> 
>>>>> Anyhow,  try running the following and see if your problems go away:
>>>>> 
>>>>>> sudo installer -pkg \
>>>>>> 
>>>>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>>>>> \
>>>>>> -target /
>>>>> 
>>>>> -Roy
>>>>> 
>>>>>> On Apr 24, 2019, at 8:36 AM, Kasper Daniel Hansen <
>>>>> kasperdanielhan...@gmail.com> wrote:
>>>>>> 
>>>>>> I am on Mojave. I recently updated to Xcode 10.2.1 and I did the
>>>>> associated
>>>>>> update of the command line tools. Following this, I reinstalled clang6
>>>>> and
>>>>>> gfortran 6 from CRAN.
>>>>>> 
>>>>>> When I use the clang6 compiler from CRAN, it is unable to find stdio.h.
>>>>>> 
>>>>>> When I compare the include path from clang6 to the Apple suppled clang
>>>>> with
>>>>>> `$CC -E - -v` I get
>>>>>> 
>>>>>> with Apple clang
>>>>>> #include <...> search starts here:
>>>>>> /usr/local/include
>>>>>> 
>>>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/10.0.1/include
>>>>>> 
>>>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
>>>>>> 
>>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include
>>>>>> 
>>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks
>>>>>> (framework directory)
>>>>>> End of search list.
>>>>>> 
>>>>>> with clang6 from CRAN
>>>>>> #include <...> search starts here:
>>>>>> /usr/local/include
>>>>>> /usr/local/clang6/lib/clang/6.0.0/include
>>>>>> /System/Library/Frameworks (framework directory)
>>>>>> /Librar

Re: [R-SIG-Mac] [External] Re: Xcode 10.2.1

2019-04-24 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Yes that is where I found the command.  I would add though that I had done that 
for Xcode 10.2.0, and appears that when you install the new versions that the 
installer actually deletes the headers at that location.  At least that is what 
happened to me when I updated to Xcode 10.2.1.  So people should be aware of 
this.  Each update may delete the headers.

In the previous thread,  Simon was looking into possibly changing where the R 
tools look for the headers, but that sort of thing is beyond my pay grade.  

-Roy

> On Apr 24, 2019, at 9:01 AM, Tierney, Luke  wrote:
> 
> Also documented in the 'R Installation and Administration' manual --
> always a good place to look.
> 
> Best,
> 
> luke
> 
> On Wed, 24 Apr 2019, Kasper Daniel Hansen wrote:
> 
>> Doh! Sorry to have missed that email thread.
>> 
>> This advice solved the issue for me.
>> 
>> On Wed, Apr 24, 2019 at 11:41 AM Roy Mendelssohn - NOAA Federal <
>> roy.mendelss...@noaa.gov> wrote:
>> 
>>> Hi Kaspar:
>>> 
>>> There is an issue of where Xcode puts headers.  I have posted on this
>>> previously.  I did the same update as you,  and not only doesn't Xcode put
>>> the headers where R expects,  it appears to delete the existing headers.
>>> 
>>> Anyhow,  try running the following and see if your problems go away:
>>> 
 sudo installer -pkg \
 
>>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>>> \
 -target /
>>> 
>>> -Roy
>>> 
 On Apr 24, 2019, at 8:36 AM, Kasper Daniel Hansen <
>>> kasperdanielhan...@gmail.com> wrote:
 
 I am on Mojave. I recently updated to Xcode 10.2.1 and I did the
>>> associated
 update of the command line tools. Following this, I reinstalled clang6
>>> and
 gfortran 6 from CRAN.
 
 When I use the clang6 compiler from CRAN, it is unable to find stdio.h.
 
 When I compare the include path from clang6 to the Apple suppled clang
>>> with
 `$CC -E - -v` I get
 
 with Apple clang
 #include <...> search starts here:
 /usr/local/include
 
>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/10.0.1/include
 
>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
 
>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include
 
>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks
 (framework directory)
 End of search list.
 
 with clang6 from CRAN
 #include <...> search starts here:
 /usr/local/include
 /usr/local/clang6/lib/clang/6.0.0/include
 /System/Library/Frameworks (framework directory)
 /Library/Frameworks (framework directory)
 End of search list.
 
 Did Apple move the headers around? Or have I somehow hosed my system?
 
 Best,
 Kasper
 
  [[alternative HTML version deleted]]
 
 ___
 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.
>>> 
>>> 
>> 
>>  [[alternative HTML version deleted]]
>> 
>> ___
>> R-SIG-Mac mailing list
>> R-SIG-Mac@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
> 
> -- 
> Luke Tierney
> Ralph E. Wareham Professor of Mathematical Sciences
> University of Iowa  Phone: 319-335-3386
> Department of Statistics andFax:   319-335-3017
>Actuarial Science
> 241 Schaeffer Hall  email:   luke-tier...@uiowa.edu
> Iowa City, IA 52242 WWW:  http://www.stat.uiowa.edu

**
"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 

Re: [R-SIG-Mac] Xcode 10.2.1

2019-04-24 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Hi Kaspar:

There is an issue of where Xcode puts headers.  I have posted on this 
previously.  I did the same update as you,  and not only doesn't Xcode put the 
headers where R expects,  it appears to delete the existing headers.  

Anyhow,  try running the following and see if your problems go away:

> sudo installer -pkg \
> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>  \
> -target /

-Roy

> On Apr 24, 2019, at 8:36 AM, Kasper Daniel Hansen 
>  wrote:
> 
> I am on Mojave. I recently updated to Xcode 10.2.1 and I did the associated
> update of the command line tools. Following this, I reinstalled clang6 and
> gfortran 6 from CRAN.
> 
> When I use the clang6 compiler from CRAN, it is unable to find stdio.h.
> 
> When I compare the include path from clang6 to the Apple suppled clang with
> `$CC -E - -v` I get
> 
> with Apple clang
> #include <...> search starts here:
> /usr/local/include
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/10.0.1/include
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks
> (framework directory)
> End of search list.
> 
> with clang6 from CRAN
> #include <...> search starts here:
> /usr/local/include
> /usr/local/clang6/lib/clang/6.0.0/include
> /System/Library/Frameworks (framework directory)
> /Library/Frameworks (framework directory)
> End of search list.
> 
> Did Apple move the headers around? Or have I somehow hosed my system?
> 
> Best,
> Kasper
> 
>   [[alternative HTML version deleted]]
> 
> ___
> 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.

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac


Re: [R-SIG-Mac] Compiling packages from source under Mojave (10.14.x)

2019-04-04 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Yes I had a feeling that the Xcode update did it,  which is why I included that 
fact.  The upgrade must have also zapped someone else,  because that note was 
in the R Admin and Install Doc.  I am not even quite certain all that command 
does,  just know the problem magically went away.

-Roy


> On Apr 4, 2019, at 1:58 PM, Simon Urbanek  wrote:
> 
> Roy,
> 
> great, thanks, I'll try to replicate that. I'm really surprised that an 
> upgrade would delete headers - that's very unfriendly to say the least ;). I 
> did upgrade Mojave but I did not upgrade Xcode (newer version tend to break 
> more and more things) so that's maybe why I didn't see it.
> 
> Thanks,
> Simon
> 
> 
> 
>> On Apr 4, 2019, at 4:19 PM, Roy Mendelssohn - NOAA Federal 
>>  wrote:
>> 
>> Hi Simon:
>> 
>> here goes.  I was running 10.13.xx,  xx being whatever was the most recent 
>> version.  I was compiling packages from source no problem.  Also,  the 
>> Upgrade Section of App Store was telling me there was an incompatible 
>> version of software available,  which was a new version of Xcode.
>> 
>> I upgraded to 10.14.4,  by the usual means,  did nothing special.
>> 
>> Upgrades in App Store said there was a new version of Xcode (among other 
>> things).  So installed that.
>> 
>> Ran Xcode,  so that it would install "Other Components" which it often does 
>> with a new version.
>> 
>> To be certain I had the Command lIne Tools,  in a terminal I ran:   sudo 
>> xcode-select --install
>> 
>> Next time I ran RStudio,  two package upgrades were from source  (I 
>> apologize I don't remember which packages).  Compilation failed with errors 
>> of couldn't find the appropriate header files.
>> 
>> Ran the command in my note.
>> 
>> Restarted RStudio,  asked it to check for package updates,  same packages 
>> appeared,  compilation went fine.
>> 
>> I am running Xcode 10.2
>> 
>> HTH,
>> 
>> -Roy
>> 
>> 
>>> On Apr 4, 2019, at 12:26 PM, Simon Urbanek  
>>> wrote:
>>> 
>>> Roy,
>>> 
>>> thanks, but can you give some details? I'm on a Mojave system and don't see 
>>> any issues - this will likely depend on your Xcode installation. Does it 
>>> mean some Xcode version is lacking headers? Which version, how did you 
>>> install it?
>>> 
>>> Thanks,
>>> Simon
>>> 
>>> 
>>>> On Mar 30, 2019, at 2:21 PM, Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
>>>>  wrote:
>>>> 
>>>> I recently updated to Mojave and all of a sudden I was getting header not 
>>>> found errors when trying to compile packages.  I was pretty certain my 
>>>> Makevars files was correct,  as I had been compiling before the upgrade 
>>>> successfully,  and the compilers hadn't changed.
>>>> 
>>>> The following is in some of the docs,  but just in case it helps,  cause 
>>>> it took me awhile to find it,  after installing the Command Line Tools for 
>>>> Xcode,  you should run:
>>>> 
>>>> sudo installer -pkg \
>>>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>>>>  \
>>>> -target /
>>>> 
>>>> and voila packages that had failed to compile just a few minutes ago 
>>>> compiled successfully.
>>>> 
>>>> Hope this helps someone.
>>>> 
>>>> -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-SI

Re: [R-SIG-Mac] Compiling packages from source under Mojave (10.14.x)

2019-04-04 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Hi Simon:

here goes.  I was running 10.13.xx,  xx being whatever was the most recent 
version.  I was compiling packages from source no problem.  Also,  the Upgrade 
Section of App Store was telling me there was an incompatible version of 
software available,  which was a new version of Xcode.

I upgraded to 10.14.4,  by the usual means,  did nothing special.

Upgrades in App Store said there was a new version of Xcode (among other 
things).  So installed that.

Ran Xcode,  so that it would install "Other Components" which it often does 
with a new version.

To be certain I had the Command lIne Tools,  in a terminal I ran:   sudo 
xcode-select --install

Next time I ran RStudio,  two package upgrades were from source  (I apologize I 
don't remember which packages).  Compilation failed with errors of couldn't 
find the appropriate header files.

Ran the command in my note.

Restarted RStudio,  asked it to check for package updates,  same packages 
appeared,  compilation went fine.

I am running Xcode 10.2

HTH,

-Roy


> On Apr 4, 2019, at 12:26 PM, Simon Urbanek  
> wrote:
> 
> Roy,
> 
> thanks, but can you give some details? I'm on a Mojave system and don't see 
> any issues - this will likely depend on your Xcode installation. Does it mean 
> some Xcode version is lacking headers? Which version, how did you install it?
> 
> Thanks,
> Simon
> 
> 
>> On Mar 30, 2019, at 2:21 PM, Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
>>  wrote:
>> 
>> I recently updated to Mojave and all of a sudden I was getting header not 
>> found errors when trying to compile packages.  I was pretty certain my 
>> Makevars files was correct,  as I had been compiling before the upgrade 
>> successfully,  and the compilers hadn't changed.
>> 
>> The following is in some of the docs,  but just in case it helps,  cause it 
>> took me awhile to find it,  after installing the Command Line Tools for 
>> Xcode,  you should run:
>> 
>> sudo installer -pkg \
>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>>  \
>> -target /
>> 
>> and voila packages that had failed to compile just a few minutes ago 
>> compiled successfully.
>> 
>> Hope this helps someone.
>> 
>> -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.

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac


[R-SIG-Mac] Compiling packages from source under Mojave (10.14.x)

2019-03-30 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
I recently updated to Mojave and all of a sudden I was getting header not found 
errors when trying to compile packages.  I was pretty certain my Makevars files 
was correct,  as I had been compiling before the upgrade successfully,  and the 
compilers hadn't changed.

The following is in some of the docs,  but just in case it helps,  cause it 
took me awhile to find it,  after installing the Command Line Tools for Xcode,  
you should run:

sudo installer -pkg \
/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
 \
 -target /

and voila packages that had failed to compile just a few minutes ago compiled 
successfully.

Hope this helps someone.

-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


Re: [R-SIG-Mac] libcurl

2019-02-27 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
BTW - I should add that my memory is that there is at least one package for 
having R interact with Python that does an Anaconda install without you really 
knowing it.  Personally  I consider that bad practice.  It may be more 
convenient but can lead to unexpected trouble down the line just because of 
issues like this.  I have also seen R and Julia packages install things under 
the covers using Homebrew. I also consider this bad practice, again because it 
can lead to conflicts that leave the user bewildered . (Homebrew installs is 
its own directory, but you must be careful about setting Paths, and path 
priority).   This was particularly true when building from source.

I have submitted to CRAN and while it can be an utter pain in the butt,  I also 
appreciate what CRAN does for users of the package - they can install with 
reasonable assurance that the needed pieces will work together and there won't 
be any hidden gotchas, and that is worth a lot to users, at least in my 
experience.  I recently spent a week in hell with conda-forge where different 
packages used the same library (by name) but the recipes installed different 
versions,  and they kept on crashing each other.

So the tl;dr version is you likely installed a package for interop between R 
and Python,  say from source or Github,  and undercover it installed Anaconda.  
And as people have mentioned,  Anaconda has its own R environment,  which may 
or may not interfere with the standard R install. I check my .profile or 
.bash_profile after installs just in case.  If there is a setting I will need 
to use some software,  I move that to a separate file to be sourced when 
needed.  Since I have started doing that,  a lot of conflicts have disappeared.

HTH,

-Roy



> On Feb 27, 2019, at 6:09 PM, Roy Mendelssohn - NOAA Federal 
>  wrote:
> 
> You are welcome  (my one good deed for the day - I guess I can go to bed 
> now!!!)  Anaconda is a great product, I use it  for my Python work,  they 
> actually ask you if you want them to modify the .profile, but people say yes 
> without realizing the implications.  First time I installed it, I said yes 
> but then looked at what was added to the file,  and realized that could cause 
> conflicts.  But since it is so easy to copy that part to another file and 
> then source it as needed,  you can keep things separate.  One of the main 
> things is anything in /usr/bin and /usr/local/bin that had similar things in 
> Anaconda were finding the Anaconda version.
> 
> -Roy
> 
>> On Feb 27, 2019, at 5:57 PM, robin hankin  wrote:
>> 
>> Roy, thanks for this!  Your insight explains a great deal of my
>> problems.  And indeed I see a whole bunch of PATH additions which were
>> created by anaconda (these are in  .bash_profile, certainly not put
>> there by me!).
>> 
>> Just to clarify, I'm not using anaconda by choice, it seems to have
>> been installed inadvertently.
>> 
>> stop press:  configure works!  Thanks!
>> 
>> 
>> Best wishes
>> 
>> Robin
>> 
>> 
>> 
>> hankin.ro...@gmail.com
>> 
>> 
>> 
>> hankin.ro...@gmail.com
>> 
>> 
>> 
>> 
>> On Thu, Feb 28, 2019 at 2:47 PM Roy Mendelssohn - NOAA Federal via
>> R-SIG-Mac  wrote:
>>> 
>>> Anaconda adds code to the end of your ,.profile that can really play havoc 
>>> with paths in other programs/settings - and off I remember correctly it 
>>> puts the changes at the front of your $PATH..  I moved that code in 
>>> .profile to a separate file.  When I want anaconda,  I just source the 
>>> file.  Makes problems such as that described  much less likely.  If you are 
>>> using iTerm2 or the like,  then you can easily have a tab with the Anaconda 
>>> paths and the rest of the tabs the more "usual" paths.
>>> 
>>> HTH,
>>> 
>>> -Roy
>>> 
>>> 
>>>> On Feb 27, 2019, at 5:32 PM, Simon Urbanek  
>>>> wrote:
>>>> 
>>>> That's anaconda - they don't include paths which is why it breaks 
>>>> everything until you insert a manual override via DYLD_LIBRARY_PATH. See 
>>>> Robin's e-mail he is NOT using the system curl, but rather a custom 
>>>> version from anaconda ("/Users/rhankin/anaconda3/lib").
>>>> 
>>>> Cheers,
>>>> Simon
>>>> 
>>>> 
>>>> 
>>>>> On Feb 25, 2019, at 04:28, peter dalgaard  wrote:
>>>>> 
>>>>> Hmm, how did "@rpath" get in there? I don't see it anywhere in my build 
>>>>> and source dirs. Looks like something that should have been substituted 
>>>>>

Re: [R-SIG-Mac] libcurl

2019-02-27 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
You are welcome  (my one good deed for the day - I guess I can go to bed 
now!!!)  Anaconda is a great product, I use it  for my Python work,  they 
actually ask you if you want them to modify the .profile, but people say yes 
without realizing the implications.  First time I installed it, I said yes but 
then looked at what was added to the file,  and realized that could cause 
conflicts.  But since it is so easy to copy that part to another file and then 
source it as needed,  you can keep things separate.  One of the main things is 
anything in /usr/bin and /usr/local/bin that had similar things in Anaconda 
were finding the Anaconda version.

-Roy

> On Feb 27, 2019, at 5:57 PM, robin hankin  wrote:
> 
> Roy, thanks for this!  Your insight explains a great deal of my
> problems.  And indeed I see a whole bunch of PATH additions which were
> created by anaconda (these are in  .bash_profile, certainly not put
> there by me!).
> 
> Just to clarify, I'm not using anaconda by choice, it seems to have
> been installed inadvertently.
> 
> stop press:  configure works!  Thanks!
> 
> 
> Best wishes
> 
> Robin
> 
> 
> 
> hankin.ro...@gmail.com
> 
> 
> 
> hankin.ro...@gmail.com
> 
> 
> 
> 
> On Thu, Feb 28, 2019 at 2:47 PM Roy Mendelssohn - NOAA Federal via
> R-SIG-Mac  wrote:
>> 
>> Anaconda adds code to the end of your ,.profile that can really play havoc 
>> with paths in other programs/settings - and off I remember correctly it puts 
>> the changes at the front of your $PATH..  I moved that code in .profile to a 
>> separate file.  When I want anaconda,  I just source the file.  Makes 
>> problems such as that described  much less likely.  If you are using iTerm2 
>> or the like,  then you can easily have a tab with the Anaconda paths and the 
>> rest of the tabs the more "usual" paths.
>> 
>> HTH,
>> 
>> -Roy
>> 
>> 
>>> On Feb 27, 2019, at 5:32 PM, Simon Urbanek  
>>> wrote:
>>> 
>>> That's anaconda - they don't include paths which is why it breaks 
>>> everything until you insert a manual override via DYLD_LIBRARY_PATH. See 
>>> Robin's e-mail he is NOT using the system curl, but rather a custom version 
>>> from anaconda ("/Users/rhankin/anaconda3/lib").
>>> 
>>> Cheers,
>>> Simon
>>> 
>>> 
>>> 
>>>> On Feb 25, 2019, at 04:28, peter dalgaard  wrote:
>>>> 
>>>> Hmm, how did "@rpath" get in there? I don't see it anywhere in my build 
>>>> and source dirs. Looks like something that should have been substituted 
>>>> (by perl?) with the appropriate path.
>>>> 
>>>> Is your library (...anaconda3/lib) correctly installed? I have, for the 
>>>> system libcurl:
>>>> 
>>>> pd$ ls -l /usr/lib/*curl*
>>>> lrwxr-xr-x  1 root  wheel  15 Nov 14 14:36 /usr/lib/libcurl.3.dylib -> 
>>>> libcurl.4.dylib
>>>> -rwxr-xr-x  1 root  wheel  854208 Nov 30 08:37 /usr/lib/libcurl.4.dylib
>>>> lrwxr-xr-x  1 root  wheel  15 Nov 14 14:36 /usr/lib/libcurl.dylib -> 
>>>> libcurl.4.dylib
>>>> 
>>>> -pd
>>>> 
>>>> 
>>>>> On 25 Feb 2019, at 01:28 , robin hankin  wrote:
>>>>> 
>>>>> thanks for this Peter, my config.log file looks like this:
>>>>> 
>>>>> configure:42615: result: yes
>>>>> configure:42629: checking if libcurl is version 7 and >= 7.22.0
>>>>> configure:42658: gcc -o conftest  -g -O2
>>>>> -I/Users/rhankin/anaconda3/include -I/usr/local/include
>>>>> -I/usr/local/include  -L/usr/local/lib conftest.c
>>>>> -L/Users/rhankin/anaconda3/lib -lcurl -lssh2 -lssh2 -lssl -lcrypto
>>>>> -lssl -lcrypto -lgssapi_krb5 -lresolv -lz -L/usr\
>>>>> /local/lib -lpcre2-8 -lpcre -llzma -lbz2 -lz -licucore -ldl -lm  -liconv 
>>>>> >&5
>>>>> configure:42658: $? = 0
>>>>> configure:42658: ./conftest
>>>>> dyld: Library not loaded: @rpath/libcurl.4.dylib
>>>>> Referenced from: /Users/rhankin/Downloads/R-devel/./conftest
>>>>> Reason: image not found
>>>>> ./configure: line 2254: 73408 Abort trap: 6   ./conftest$ac_exeext
>>>>> configure:42658: $? = 134
>>>>> configure: program exited with status 134
>>>>> configure: failed program was:
>>>>> | /* confdefs.h */
>>>>> | #define PACKAGE_NAME "R"
>>>>&g

Re: [R-SIG-Mac] libcurl

2019-02-27 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Anaconda adds code to the end of your ,.profile that can really play havoc with 
paths in other programs/settings - and off I remember correctly it puts the 
changes at the front of your $PATH..  I moved that code in .profile to a 
separate file.  When I want anaconda,  I just source the file.  Makes problems 
such as that described  much less likely.  If you are using iTerm2 or the like, 
 then you can easily have a tab with the Anaconda paths and the rest of the 
tabs the more "usual" paths.

HTH,

-Roy


> On Feb 27, 2019, at 5:32 PM, Simon Urbanek  
> wrote:
> 
> That's anaconda - they don't include paths which is why it breaks everything 
> until you insert a manual override via DYLD_LIBRARY_PATH. See Robin's e-mail 
> he is NOT using the system curl, but rather a custom version from anaconda 
> ("/Users/rhankin/anaconda3/lib").
> 
> Cheers,
> Simon
> 
> 
> 
>> On Feb 25, 2019, at 04:28, peter dalgaard  wrote:
>> 
>> Hmm, how did "@rpath" get in there? I don't see it anywhere in my build and 
>> source dirs. Looks like something that should have been substituted (by 
>> perl?) with the appropriate path.
>> 
>> Is your library (...anaconda3/lib) correctly installed? I have, for the 
>> system libcurl:
>> 
>> pd$ ls -l /usr/lib/*curl*
>> lrwxr-xr-x  1 root  wheel  15 Nov 14 14:36 /usr/lib/libcurl.3.dylib -> 
>> libcurl.4.dylib
>> -rwxr-xr-x  1 root  wheel  854208 Nov 30 08:37 /usr/lib/libcurl.4.dylib
>> lrwxr-xr-x  1 root  wheel  15 Nov 14 14:36 /usr/lib/libcurl.dylib -> 
>> libcurl.4.dylib
>> 
>> -pd
>> 
>> 
>>> On 25 Feb 2019, at 01:28 , robin hankin  wrote:
>>> 
>>> thanks for this Peter, my config.log file looks like this:
>>> 
>>> configure:42615: result: yes
>>> configure:42629: checking if libcurl is version 7 and >= 7.22.0
>>> configure:42658: gcc -o conftest  -g -O2
>>> -I/Users/rhankin/anaconda3/include -I/usr/local/include
>>> -I/usr/local/include  -L/usr/local/lib conftest.c
>>> -L/Users/rhankin/anaconda3/lib -lcurl -lssh2 -lssh2 -lssl -lcrypto
>>> -lssl -lcrypto -lgssapi_krb5 -lresolv -lz -L/usr\
>>> /local/lib -lpcre2-8 -lpcre -llzma -lbz2 -lz -licucore -ldl -lm  -liconv >&5
>>> configure:42658: $? = 0
>>> configure:42658: ./conftest
>>> dyld: Library not loaded: @rpath/libcurl.4.dylib
>>> Referenced from: /Users/rhankin/Downloads/R-devel/./conftest
>>> Reason: image not found
>>> ./configure: line 2254: 73408 Abort trap: 6   ./conftest$ac_exeext
>>> configure:42658: $? = 134
>>> configure: program exited with status 134
>>> configure: failed program was:
>>> | /* confdefs.h */
>>> | #define PACKAGE_NAME "R"
>>> | #define PACKAGE_TARNAME "R"
>>> 
>>> 
>>> 
>>> Best wishes
>>> 
>>> 
>>> Robin
>>> 
>>> 
>>> hankin.ro...@gmail.com
>>> 
>>> 
>>> 
>>> hankin.ro...@gmail.com
>>> 
>>> 
>>> 
>>> 
>>> On Mon, Feb 25, 2019 at 11:41 AM peter dalgaard  wrote:
 
 It doesn't usually happen on 10.13.6... Best guess is that somehow you are 
 picking up an older library (e.g. in /usr/local/lib) even if you are using 
 curl-config from a newer version.
 
 The detective work needed could take off from config.log, region around 
 this:
 
 configure:39937: checking if libcurl is version 7 and >= 7.22.0
 configure:39966: gcc -arch x86_64 -o conftest -g -O2   
 -I/usr/local/include  -L/usr/local/lib conftest.c -lcurl -lpcre -llzma 
 -lbz2 -lz -licucore -lm  -liconv >&5
 configure:39966: $? = 0
 configure:39966: ./conftest
 configure:39966: $? = 0
 configure:39976: result: yes
 
 That's for a succesful build, a failed one will usually give more info 
 including the failing program code.
 
 -pd
 
> On 24 Feb 2019, at 22:45 , robin hankin  wrote:
> 
> Hi,  macos 10.13.6, trying to compile 3.6.0, revision 76152.
> 
> ./configure
> [snip]
> 
> checking for curl-config... /Users/rhankin/anaconda3/bin/curl-config
> checking libcurl version ... 7.63.0
> checking curl/curl.h usability... yes
> checking curl/curl.h presence... yes
> checking for curl/curl.h... yes
> checking if libcurl is version 7 and >= 7.22.0... no
> configure: error: libcurl >= 7.22.0 library and headers are required
> with support for https
> 
> if we have libcurl 7.63, as it says in the output, why the error?  How
> to proceed?
> 
> hankin.ro...@gmail.com
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
 
 --
 Peter Dalgaard, Professor,
 Center for Statistics, Copenhagen Business School
 Solbjerg Plads 3, 2000 Frederiksberg, Denmark
 Phone: (+45)38153501
 Office: A 4.23
 Email: pd@cbs.dk  Priv: pda...@gmail.com
 
 
 
 
 
 
 
 
 
>> 
>> -- 
>> Peter Dalgaard, Professor,
>> Center for Statistics, Copenhagen Business School
>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> 

Re: [R-SIG-Mac] Issues with rj (requirement for StatET) since Mojave/3.5.1 update

2018-11-16 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac
Check that you have the latest version of the clang compiler from the r-mac 
site.  I believe the present version supports -fopenmp, previous version did 
not.  If not,  I can point you to a different link to download the compiler, 
but I think using the officially approved versions the cleanest solution.

HTH,

-Roy


> On Nov 16, 2018, at 11:10 AM, Jonathan Greenberg  wrote:
> 
> I'm hoping to get some insight into seeing if I can get "rj" working again in 
> Mojave/R 3.5.1 -- this is a requirements for the Eclipse interface to R 
> "Stat-ET") -- I'm seeing similar issues when trying to get rJava working also 
> from source, e.g.:
> 
> Rscript -e 'install.packages("rJava", repos="http://rforge.net;, 
> type="source")'
> 
> and
> 
> install.packages(c("rj", "rj.gd"), 
> repos="http://download.walware.de/rj-2.1",type="source;)
> 
> All issues lead to:
> 
> "clang: error: unsupported option '-fopenmp'"
> 
> I've installed clang6 and gfortran61 from CRAN, but that doesn't seem to 
> work.  I've tried tweaking the ~/.R/Makevars, e.g.:
> 
> FLIBS=-L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
> CC=/usr/local/clang6/bin/clang
> CXX=/usr/local/clang6/bin/clang++
> CXX1X=/usr/local/clang6/bin/clang++
> CXX98=/usr/local/clang6/bin/clang++
> CXX11=/usr/local/clang6/bin/clang++
> CXX14=/usr/local/clang6/bin/clang++
> CXX17=/usr/local/clang6/bin/clang++
> LDFLAGS=-L/usr/local/clang6/lib
> 
> Which only results in a different error:
> ld: warning: text-based stub file 
> /System/Library/Frameworks//JavaVM.framework/JavaVM.tbd and library file 
> /System/Library/Frameworks//JavaVM.framework/JavaVM are out of sync. Falling 
> back to library file for linking.
> ld: library not found for -lomp
> 
> Any ideas?
> --
> --
> Jonathan A. Greenberg, PhD
> Randall Endowed Professor and Associate Professor of Remote Sensing
> Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
> Natural Resources & Environmental Science
> University of Nevada, Reno
> 1664 N Virginia St MS/0186
> Reno, NV 89557
> Phone: 415-763-5476
> http://www.unr.edu/nres
> Gchat: jgrn...@gmail.com, Skype: jgrn3007
> 
>   [[alternative HTML version deleted]]
> 
> ___
> 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.

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac