subject:"\[R\-SIG\-Mac\] Problems compiling with R CMD build and devtools\:\:build\(\)"

Re: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

2023-05-17 Thread Prof Brian Ripley


On 17/05/2023 21:59, Simon Urbanek wrote:

Jarrett,

Duncan's suggestion was correct, but you are using older R, so I'd recommend 
simply upgrading R to the latest release.

If you want to use old R, you have to install the older Fortran binaries that 
match your R version, but that's not entirely trivial so it's easier to just 
upgrade R instead.


It is possible to use a binary R installation with a version of gfortran 
other than it was built with (I have occasionally needed to use a later 
gfortran).  This is discussed in the manual, at

https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#macOS-packages
and
https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Customizing-package-compilation

The crucial part is that FLIBS (in etc/Makeconf or overridden in a 
personal or site Makevars) has to match the compiler in use.


To reduce confusion I always specify the full path to gfortran in FC.



Cheers,
Simon



On 18/05/2023, at 6:43 AM, Jarrett Phillips  wrote:

Hi Duncan,

I did exactly that, but still got the error above when I try building in
both RStudio via devtools::build() and the Terminal via R CMD build.

To confirm that the right gfortran successfully installed in the correct
location, I did

jarrettphillips@Jarretts-MacBook-Pro ~ % /opt/gfortran/bin/gfortran

*aarch64-apple-darwin20.0-gfortran:* *fatal error: *no input files

compilation terminated.


Any other ideas?




On Wed, May 17, 2023 at 2:13 PM Duncan Murdoch 
wrote:


I think the simplest solution is to remove the gfortran you installed,
and then install it back using the installer on

   https://mac.r-project.org/tools/

Duncan Murdoch

On 17/05/2023 1:26 p.m., Jarrett Phillips wrote:

Hi Rodney,

When I paste the directories into the Terminal, I get

no such file or directory:



suggesting that they don't exist.


Seems like I need to create them (I'm a newbie)?


What should be my next steps?


Thanks!


Cheers,


Jarrett




On Wed, May 17, 2023 at 1:25 PM Jarrett Phillips <

phillipsjarre...@gmail.com>

wrote:


Hi Rodney,

When I paste the directories into the Terminal, I get

no such file or directory:



suggesting that they don't exist.


Seems like I need to create them (I'm a newbie)?


What should be my next steps?


Thanks!


Cheers,


Jarrett





On Wed, May 17, 2023 at 1:07 PM Sparapani, Rodney 
wrote:


Hi Jarrett:



Do the two directories exist that clang is warning you about?



'/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
'/opt/R/arm64/gfortran/lib'



--

Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His

Director, Wisconsin Chapter of the American Statistical Association

Institute for Health and Equity, Division of Biostatistics

Medical College of Wisconsin, Milwaukee Campus



*From: *R-SIG-Mac  on behalf of

Jarrett

Phillips 
*Date: *Wednesday, May 17, 2023 at 11:54 AM
*To: *r-sig-mac@r-project.org 
*Subject: *[R-SIG-Mac] Problems compiling with R CMD build and
devtools::build()

ATTENTION: This email originated from a sender outside of MCW. Use
caution when clicking on links or opening attachments.


Hi All,

I'm trying to generate a `tar.gz` file on a Mac for R package

submission

to
CRAN but am having issues.

I'm using `devtools`, specifically `build()` and `install()`.

My package relies on compiled code via `Rcpp/RcppArmadillo`.

 build("HACSim_OO")
 ── R CMD build
─
 ✔  checking for file ‘/Users/jarrettphillips/Desktop/HAC
simulation/HACSim_OO/DESCRIPTION’ ...
 ─  preparing ‘HACSim’:
 ✔  checking DESCRIPTION meta-information ...
 ─  cleaning src
 ─  installing the package to process help pages
  ---
 ─  installing *source* package ‘HACSim’ ...
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++11 -
I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG



-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'




-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include'

-I/opt/R/arm64/include-fPIC  -falign-functions=64 -Wall -g -O2

-Wall

-pedantic -fdiagnostics-color=always -c RcppExports.cpp -o

RcppExports.o

clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG



-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'




-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include'

-I/opt/R/arm64/include-fPIC  -falign-functions=64 -Wall -g -O2

-Wall

-pedantic -fdiagnostics-color=always -c accumulate.cpp -o accumulate.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib
-Wl,-headerpad_max_install_names -undefined dynamic_lookup

-single_module

-multiply_defined suppress

-L/Library/Frameworks/R.fra

Re: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

2023-05-17 Thread Jarrett Phillips

Thanks Simon,

Removing the old gfortran and updating R to the latest version (4.3.0)
fixed everything.

Now I'm able to build and install without issues.

I'll be sure to update R every time a new version is released.

Cheers,

Jarrett

On Wed, May 17, 2023 at 4:59 PM Simon Urbanek 
wrote:

> Jarrett,
>
> Duncan's suggestion was correct, but you are using older R, so I'd
> recommend simply upgrading R to the latest release.
>
> If you want to use old R, you have to install the older Fortran binaries
> that match your R version, but that's not entirely trivial so it's easier
> to just upgrade R instead.
>
> Cheers,
> Simon
>
>
> > On 18/05/2023, at 6:43 AM, Jarrett Phillips 
> wrote:
> >
> > Hi Duncan,
> >
> > I did exactly that, but still got the error above when I try building in
> > both RStudio via devtools::build() and the Terminal via R CMD build.
> >
> > To confirm that the right gfortran successfully installed in the correct
> > location, I did
> >
> > jarrettphillips@Jarretts-MacBook-Pro ~ % /opt/gfortran/bin/gfortran
> >
> > *aarch64-apple-darwin20.0-gfortran:* *fatal error: *no input files
> >
> > compilation terminated.
> >
> >
> > Any other ideas?
> >
> >
> >
> >
> > On Wed, May 17, 2023 at 2:13 PM Duncan Murdoch  >
> > wrote:
> >
> >> I think the simplest solution is to remove the gfortran you installed,
> >> and then install it back using the installer on
> >>
> >>   https://mac.r-project.org/tools/
> >>
> >> Duncan Murdoch
> >>
> >> On 17/05/2023 1:26 p.m., Jarrett Phillips wrote:
> >>> Hi Rodney,
> >>>
> >>> When I paste the directories into the Terminal, I get
> >>>
> >>> no such file or directory:
> >>>
> >>>
> >>>
> >>> suggesting that they don't exist.
> >>>
> >>>
> >>> Seems like I need to create them (I'm a newbie)?
> >>>
> >>>
> >>> What should be my next steps?
> >>>
> >>>
> >>> Thanks!
> >>>
> >>>
> >>> Cheers,
> >>>
> >>>
> >>> Jarrett
> >>>
> >>>
> >>>
> >>>
> >>> On Wed, May 17, 2023 at 1:25 PM Jarrett Phillips <
> >> phillipsjarre...@gmail.com>
> >>> wrote:
> >>>
> >>>> Hi Rodney,
> >>>>
> >>>> When I paste the directories into the Terminal, I get
> >>>>
> >>>> no such file or directory:
> >>>>
> >>>>
> >>>>
> >>>> suggesting that they don't exist.
> >>>>
> >>>>
> >>>> Seems like I need to create them (I'm a newbie)?
> >>>>
> >>>>
> >>>> What should be my next steps?
> >>>>
> >>>>
> >>>> Thanks!
> >>>>
> >>>>
> >>>> Cheers,
> >>>>
> >>>>
> >>>> Jarrett
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> On Wed, May 17, 2023 at 1:07 PM Sparapani, Rodney 
> >>>> wrote:
> >>>>
> >>>>> Hi Jarrett:
> >>>>>
> >>>>>
> >>>>>
> >>>>> Do the two directories exist that clang is warning you about?
> >>>>>
> >>>>>
> >>>>>
> >>>>> '/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
> >>>>> '/opt/R/arm64/gfortran/lib'
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>>
> >>>>> Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His
> >>>>>
> >>>>> Director, Wisconsin Chapter of the American Statistical Association
> >>>>>
> >>>>> Institute for Health and Equity, Division of Biostatistics
> >>>>>
> >>>>> Medical College of Wisconsin, Milwaukee Campus
> >>>>>
> >>>>>
> >>>>>
> >>>>> *From: *R-SIG-Mac  on behalf of
> >> Jarrett
> >>>>> Phillips 
> >>>>> *Date: *Wednesday, May 17, 2023 at 11:54 AM
> >>>>> *To: *r-sig-mac@r-project.org 
> >>>&g

Re: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

2023-05-17 Thread Simon Urbanek

Jarrett,

Duncan's suggestion was correct, but you are using older R, so I'd recommend 
simply upgrading R to the latest release.

If you want to use old R, you have to install the older Fortran binaries that 
match your R version, but that's not entirely trivial so it's easier to just 
upgrade R instead.

Cheers,
Simon


> On 18/05/2023, at 6:43 AM, Jarrett Phillips  
> wrote:
> 
> Hi Duncan,
> 
> I did exactly that, but still got the error above when I try building in
> both RStudio via devtools::build() and the Terminal via R CMD build.
> 
> To confirm that the right gfortran successfully installed in the correct
> location, I did
> 
> jarrettphillips@Jarretts-MacBook-Pro ~ % /opt/gfortran/bin/gfortran
> 
> *aarch64-apple-darwin20.0-gfortran:* *fatal error: *no input files
> 
> compilation terminated.
> 
> 
> Any other ideas?
> 
> 
> 
> 
> On Wed, May 17, 2023 at 2:13 PM Duncan Murdoch 
> wrote:
> 
>> I think the simplest solution is to remove the gfortran you installed,
>> and then install it back using the installer on
>> 
>>   https://mac.r-project.org/tools/
>> 
>> Duncan Murdoch
>> 
>> On 17/05/2023 1:26 p.m., Jarrett Phillips wrote:
>>> Hi Rodney,
>>> 
>>> When I paste the directories into the Terminal, I get
>>> 
>>> no such file or directory:
>>> 
>>> 
>>> 
>>> suggesting that they don't exist.
>>> 
>>> 
>>> Seems like I need to create them (I'm a newbie)?
>>> 
>>> 
>>> What should be my next steps?
>>> 
>>> 
>>> Thanks!
>>> 
>>> 
>>> Cheers,
>>> 
>>> 
>>> Jarrett
>>> 
>>> 
>>> 
>>> 
>>> On Wed, May 17, 2023 at 1:25 PM Jarrett Phillips <
>> phillipsjarre...@gmail.com>
>>> wrote:
>>> 
>>>> Hi Rodney,
>>>> 
>>>> When I paste the directories into the Terminal, I get
>>>> 
>>>> no such file or directory:
>>>> 
>>>> 
>>>> 
>>>> suggesting that they don't exist.
>>>> 
>>>> 
>>>> Seems like I need to create them (I'm a newbie)?
>>>> 
>>>> 
>>>> What should be my next steps?
>>>> 
>>>> 
>>>> Thanks!
>>>> 
>>>> 
>>>> Cheers,
>>>> 
>>>> 
>>>> Jarrett
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> On Wed, May 17, 2023 at 1:07 PM Sparapani, Rodney 
>>>> wrote:
>>>> 
>>>>> Hi Jarrett:
>>>>> 
>>>>> 
>>>>> 
>>>>> Do the two directories exist that clang is warning you about?
>>>>> 
>>>>> 
>>>>> 
>>>>> '/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
>>>>> '/opt/R/arm64/gfortran/lib'
>>>>> 
>>>>> 
>>>>> 
>>>>> --
>>>>> 
>>>>> Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His
>>>>> 
>>>>> Director, Wisconsin Chapter of the American Statistical Association
>>>>> 
>>>>> Institute for Health and Equity, Division of Biostatistics
>>>>> 
>>>>> Medical College of Wisconsin, Milwaukee Campus
>>>>> 
>>>>> 
>>>>> 
>>>>> *From: *R-SIG-Mac  on behalf of
>> Jarrett
>>>>> Phillips 
>>>>> *Date: *Wednesday, May 17, 2023 at 11:54 AM
>>>>> *To: *r-sig-mac@r-project.org 
>>>>> *Subject: *[R-SIG-Mac] Problems compiling with R CMD build and
>>>>> devtools::build()
>>>>> 
>>>>> ATTENTION: This email originated from a sender outside of MCW. Use
>>>>> caution when clicking on links or opening attachments.
>>>>> 
>>>>> 
>>>>> Hi All,
>>>>> 
>>>>> I'm trying to generate a `tar.gz` file on a Mac for R package
>> submission
>>>>> to
>>>>> CRAN but am having issues.
>>>>> 
>>>>> I'm using `devtools`, specifically `build()` and `install()`.
>>>>> 
>>>>> My package relies on compiled code via `Rcpp/RcppArmadillo`.
>>>>> 
>>>>> build("HACSim_OO")
>>>>> ── R CMD bu

Re: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

2023-05-17 Thread Duncan Murdoch

Sorry, I don't have an ARM64 Mac.  On my Intel Mac, gfortran is located 
somewhere else, not in the location you listed.  The output 
corresponding to the line that failed on your system looks like this on 
mine:


clang++ -arch x86_64 -std=gnu++11 -dynamiclib 
-Wl,-headerpad_max_install_names -undefined dynamic_lookup 
-single_module -multiply_defined suppress 
-L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o 
HACSim.so RcppExports.o accumulate.o 
-L/Library/Frameworks/R.framework/Resources/lib -lRlapack 
-L/Library/Frameworks/R.framework/Resources/lib -lRblas 
-L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 
-L/opt/gfortran/lib -lgfortran -lquadmath 
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework 
-Wl,CoreFoundation



Notice that mine has

 -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0
 -L/opt/gfortran/lib
 -lgfortran

where yours had

 -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1
 -L/opt/R/arm64/gfortran/lib
 -lgfortran

i.e. gfortran is in /opt/gfortran, not /opt/R/arm64/gfortran.  But I 
don't know if that difference is expected or not.


Duncan Murdoch

On 17/05/2023 2:43 p.m., Jarrett Phillips wrote:

Hi Duncan,

I did exactly that, but still got the error above when I try building in 
both RStudio via devtools::build() and the Terminal via R CMD build.


To confirm that the right gfortran successfully installed in the correct 
location, I did


jarrettphillips@Jarretts-MacBook-Pro ~ % /opt/gfortran/bin/gfortran

*aarch64-apple-darwin20.0-gfortran:* *fatal error: *no input files

compilation terminated.


Any other ideas?




On Wed, May 17, 2023 at 2:13 PM Duncan Murdoch <mailto:murdoch.dun...@gmail.com>> wrote:


I think the simplest solution is to remove the gfortran you installed,
and then install it back using the installer on

https://mac.r-project.org/tools/ <https://mac.r-project.org/tools/>

Duncan Murdoch

On 17/05/2023 1:26 p.m., Jarrett Phillips wrote:
 > Hi Rodney,
 >
 > When I paste the directories into the Terminal, I get
 >
 > no such file or directory:
 >
 >
 >
 > suggesting that they don't exist.
 >
 >
 > Seems like I need to create them (I'm a newbie)?
 >
 >
 > What should be my next steps?
 >
 >
 > Thanks!
 >
 >
 > Cheers,
 >
 >
 > Jarrett
 >
 >
 >
 >
 > On Wed, May 17, 2023 at 1:25 PM Jarrett Phillips
mailto:phillipsjarre...@gmail.com>>
 > wrote:
 >
 >> Hi Rodney,
 >>
 >> When I paste the directories into the Terminal, I get
 >>
 >> no such file or directory:
 >>
 >>
 >>
 >> suggesting that they don't exist.
 >>
 >>
 >> Seems like I need to create them (I'm a newbie)?
 >>
 >>
 >> What should be my next steps?
 >>
 >>
 >> Thanks!
 >>
 >>
 >> Cheers,
 >>
 >>
 >> Jarrett
 >>
 >>
 >>
 >>
 >>
 >> On Wed, May 17, 2023 at 1:07 PM Sparapani, Rodney
mailto:rspar...@mcw.edu>>
 >> wrote:
 >>
 >>> Hi Jarrett:
 >>>
 >>>
 >>>
 >>> Do the two directories exist that clang is warning you about?
 >>>
 >>>
 >>>
 >>> '/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
 >>> '/opt/R/arm64/gfortran/lib'
 >>>
 >>>
 >>>
 >>> --
 >>>
 >>> Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His
 >>>
 >>> Director, Wisconsin Chapter of the American Statistical Association
 >>>
     >>> Institute for Health and Equity, Division of Biostatistics
 >>>
 >>> Medical College of Wisconsin, Milwaukee Campus
 >>>
 >>>
 >>>
 >>> *From: *R-SIG-Mac mailto:r-sig-mac-boun...@r-project.org>> on behalf of Jarrett
 >>> Phillips mailto:phillipsjarre...@gmail.com>>
 >>> *Date: *Wednesday, May 17, 2023 at 11:54 AM
 >>> *To: *r-sig-mac@r-project.org <mailto:r-sig-mac@r-project.org>
mailto:r-sig-mac@r-project.org>>
 >>> *Subject: *[R-SIG-Mac] Problems compiling with R CMD build and
 >>> devtools::build()
 >>>
 >>> ATTENTION: This email originated from a sender outside of MCW. Use
 >>> caution when clicking on links or opening attachments.
 >>>

Re: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

2023-05-17 Thread Jarrett Phillips

Hi Duncan,

I did exactly that, but still got the error above when I try building in
both RStudio via devtools::build() and the Terminal via R CMD build.

To confirm that the right gfortran successfully installed in the correct
location, I did

jarrettphillips@Jarretts-MacBook-Pro ~ % /opt/gfortran/bin/gfortran

*aarch64-apple-darwin20.0-gfortran:* *fatal error: *no input files

compilation terminated.


Any other ideas?




On Wed, May 17, 2023 at 2:13 PM Duncan Murdoch 
wrote:

> I think the simplest solution is to remove the gfortran you installed,
> and then install it back using the installer on
>
>https://mac.r-project.org/tools/
>
> Duncan Murdoch
>
> On 17/05/2023 1:26 p.m., Jarrett Phillips wrote:
> > Hi Rodney,
> >
> > When I paste the directories into the Terminal, I get
> >
> > no such file or directory:
> >
> >
> >
> > suggesting that they don't exist.
> >
> >
> > Seems like I need to create them (I'm a newbie)?
> >
> >
> > What should be my next steps?
> >
> >
> > Thanks!
> >
> >
> > Cheers,
> >
> >
> > Jarrett
> >
> >
> >
> >
> > On Wed, May 17, 2023 at 1:25 PM Jarrett Phillips <
> phillipsjarre...@gmail.com>
> > wrote:
> >
> >> Hi Rodney,
> >>
> >> When I paste the directories into the Terminal, I get
> >>
> >> no such file or directory:
> >>
> >>
> >>
> >> suggesting that they don't exist.
> >>
> >>
> >> Seems like I need to create them (I'm a newbie)?
> >>
> >>
> >> What should be my next steps?
> >>
> >>
> >> Thanks!
> >>
> >>
> >> Cheers,
> >>
> >>
> >> Jarrett
> >>
> >>
> >>
> >>
> >>
> >> On Wed, May 17, 2023 at 1:07 PM Sparapani, Rodney 
> >> wrote:
> >>
> >>> Hi Jarrett:
> >>>
> >>>
> >>>
> >>> Do the two directories exist that clang is warning you about?
> >>>
> >>>
> >>>
> >>> '/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
> >>> '/opt/R/arm64/gfortran/lib'
> >>>
> >>>
> >>>
> >>> --
> >>>
> >>> Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His
> >>>
> >>> Director, Wisconsin Chapter of the American Statistical Association
> >>>
> >>> Institute for Health and Equity, Division of Biostatistics
> >>>
> >>> Medical College of Wisconsin, Milwaukee Campus
> >>>
> >>>
> >>>
> >>> *From: *R-SIG-Mac  on behalf of
> Jarrett
> >>> Phillips 
> >>> *Date: *Wednesday, May 17, 2023 at 11:54 AM
> >>> *To: *r-sig-mac@r-project.org 
> >>> *Subject: *[R-SIG-Mac] Problems compiling with R CMD build and
> >>> devtools::build()
> >>>
> >>> ATTENTION: This email originated from a sender outside of MCW. Use
> >>> caution when clicking on links or opening attachments.
> >>> 
> >>>
> >>> Hi All,
> >>>
> >>> I'm trying to generate a `tar.gz` file on a Mac for R package
> submission
> >>> to
> >>> CRAN but am having issues.
> >>>
> >>> I'm using `devtools`, specifically `build()` and `install()`.
> >>>
> >>> My package relies on compiled code via `Rcpp/RcppArmadillo`.
> >>>
> >>>  build("HACSim_OO")
> >>>  ── R CMD build
> >>> ─
> >>>  ✔  checking for file ‘/Users/jarrettphillips/Desktop/HAC
> >>> simulation/HACSim_OO/DESCRIPTION’ ...
> >>>  ─  preparing ‘HACSim’:
> >>>  ✔  checking DESCRIPTION meta-information ...
> >>>  ─  cleaning src
> >>>  ─  installing the package to process help pages
> >>>   ---
> >>>  ─  installing *source* package ‘HACSim’ ...
> >>> ** using staged installation
> >>> ** libs
> >>> clang++ -arch arm64 -std=gnu++11 -
> >>> I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
> >>>
> >>>
>  
> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/inc

Re: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

2023-05-17 Thread Duncan Murdoch

I think the simplest solution is to remove the gfortran you installed, 
and then install it back using the installer on


  https://mac.r-project.org/tools/

Duncan Murdoch

On 17/05/2023 1:26 p.m., Jarrett Phillips wrote:

Hi Rodney,

When I paste the directories into the Terminal, I get

no such file or directory:



suggesting that they don't exist.


Seems like I need to create them (I'm a newbie)?


What should be my next steps?


Thanks!


Cheers,


Jarrett




On Wed, May 17, 2023 at 1:25 PM Jarrett Phillips 
wrote:


Hi Rodney,

When I paste the directories into the Terminal, I get

no such file or directory:



suggesting that they don't exist.


Seems like I need to create them (I'm a newbie)?


What should be my next steps?


Thanks!


Cheers,


Jarrett





On Wed, May 17, 2023 at 1:07 PM Sparapani, Rodney 
wrote:


Hi Jarrett:



Do the two directories exist that clang is warning you about?



'/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
'/opt/R/arm64/gfortran/lib'



--

Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His

Director, Wisconsin Chapter of the American Statistical Association

Institute for Health and Equity, Division of Biostatistics

Medical College of Wisconsin, Milwaukee Campus



*From: *R-SIG-Mac  on behalf of Jarrett
Phillips 
*Date: *Wednesday, May 17, 2023 at 11:54 AM
*To: *r-sig-mac@r-project.org 
*Subject: *[R-SIG-Mac] Problems compiling with R CMD build and
devtools::build()

ATTENTION: This email originated from a sender outside of MCW. Use
caution when clicking on links or opening attachments.


Hi All,

I'm trying to generate a `tar.gz` file on a Mac for R package submission
to
CRAN but am having issues.

I'm using `devtools`, specifically `build()` and `install()`.

My package relies on compiled code via `Rcpp/RcppArmadillo`.

 build("HACSim_OO")
 ── R CMD build
─
 ✔  checking for file ‘/Users/jarrettphillips/Desktop/HAC
simulation/HACSim_OO/DESCRIPTION’ ...
 ─  preparing ‘HACSim’:
 ✔  checking DESCRIPTION meta-information ...
 ─  cleaning src
 ─  installing the package to process help pages
  ---
 ─  installing *source* package ‘HACSim’ ...
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++11 -
I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG

  
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'

-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include'
-I/opt/R/arm64/include-fPIC  -falign-functions=64 -Wall -g -O2  -Wall
-pedantic -fdiagnostics-color=always -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG

  
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'

-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include'
-I/opt/R/arm64/include-fPIC  -falign-functions=64 -Wall -g -O2  -Wall
-pedantic -fdiagnostics-color=always -c accumulate.cpp -o accumulate.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib
-Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module
-multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib
-L/opt/R/arm64/lib -o HACSim.so RcppExports.o accumulate.o
-L/Library/Frameworks/R.framework/Resources/lib -lRlapack
-L/Library/Frameworks/R.framework/Resources/lib -lRblas
-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1
-L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
ld: warning: directory not found for option
'-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
ld: warning: directory not found for option
'-L/opt/R/arm64/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see
invocation)
make: *** [HACSim.so] Error 1
ERROR: compilation failed for package ‘HACSim’
 ─  removing

‘/private/var/folders/r4/xm5blbcd2tn06tjv00lm1c78gn/T/RtmpN4uaYR/Rinstdf4219594de/HACSim’
  ---
 ERROR: package installation failed
 Error in `(function (command = NULL, args = character(),
error_on_status = TRUE, …`:
 ! System command 'R' failed
  ---
  Exit status: 1
  stdout & stderr: 
  ---
 Type .Last.error to see the more details.

`clang` is installed (since I am able to run the code within my package)
and I've verified by typing `gcc` in the Mac Terminal. I've also installed
`Homebrew` and `gfortran`, verifying via typing in the Terminal.

Any idea on what's going on and how to fix the is

Re: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

2023-05-17 Thread Jarrett Phillips

Hi Rodney,

When I paste the directories into the Terminal, I get

no such file or directory:



suggesting that they don't exist.


Seems like I need to create them (I'm a newbie)?


What should be my next steps?


Thanks!


Cheers,


Jarrett




On Wed, May 17, 2023 at 1:25 PM Jarrett Phillips 
wrote:

> Hi Rodney,
>
> When I paste the directories into the Terminal, I get
>
> no such file or directory:
>
>
>
> suggesting that they don't exist.
>
>
> Seems like I need to create them (I'm a newbie)?
>
>
> What should be my next steps?
>
>
> Thanks!
>
>
> Cheers,
>
>
> Jarrett
>
>
>
>
>
> On Wed, May 17, 2023 at 1:07 PM Sparapani, Rodney 
> wrote:
>
>> Hi Jarrett:
>>
>>
>>
>> Do the two directories exist that clang is warning you about?
>>
>>
>>
>> '/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
>> '/opt/R/arm64/gfortran/lib'
>>
>>
>>
>> --
>>
>> Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His
>>
>> Director, Wisconsin Chapter of the American Statistical Association
>>
>> Institute for Health and Equity, Division of Biostatistics
>>
>> Medical College of Wisconsin, Milwaukee Campus
>>
>>
>>
>> *From: *R-SIG-Mac  on behalf of Jarrett
>> Phillips 
>> *Date: *Wednesday, May 17, 2023 at 11:54 AM
>> *To: *r-sig-mac@r-project.org 
>> *Subject: *[R-SIG-Mac] Problems compiling with R CMD build and
>> devtools::build()
>>
>> ATTENTION: This email originated from a sender outside of MCW. Use
>> caution when clicking on links or opening attachments.
>> 
>>
>> Hi All,
>>
>> I'm trying to generate a `tar.gz` file on a Mac for R package submission
>> to
>> CRAN but am having issues.
>>
>> I'm using `devtools`, specifically `build()` and `install()`.
>>
>> My package relies on compiled code via `Rcpp/RcppArmadillo`.
>>
>> build("HACSim_OO")
>> ── R CMD build
>> ─
>> ✔  checking for file ‘/Users/jarrettphillips/Desktop/HAC
>> simulation/HACSim_OO/DESCRIPTION’ ...
>> ─  preparing ‘HACSim’:
>> ✔  checking DESCRIPTION meta-information ...
>> ─  cleaning src
>> ─  installing the package to process help pages
>>  ---
>> ─  installing *source* package ‘HACSim’ ...
>>** using staged installation
>>** libs
>>clang++ -arch arm64 -std=gnu++11 -
>> I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>>
>>  
>> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
>>
>> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include'
>> -I/opt/R/arm64/include-fPIC  -falign-functions=64 -Wall -g -O2  -Wall
>> -pedantic -fdiagnostics-color=always -c RcppExports.cpp -o RcppExports.o
>>clang++ -arch arm64 -std=gnu++11
>> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>>
>>  
>> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
>>
>> -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include'
>> -I/opt/R/arm64/include-fPIC  -falign-functions=64 -Wall -g -O2  -Wall
>> -pedantic -fdiagnostics-color=always -c accumulate.cpp -o accumulate.o
>>clang++ -arch arm64 -std=gnu++11 -dynamiclib
>> -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module
>> -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib
>> -L/opt/R/arm64/lib -o HACSim.so RcppExports.o accumulate.o
>> -L/Library/Frameworks/R.framework/Resources/lib -lRlapack
>> -L/Library/Frameworks/R.framework/Resources/lib -lRblas
>> -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1
>> -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath
>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>> -Wl,CoreFoundation
>>ld: warning: directory not found for option
>> '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
>>ld: warning: directory not found for option
>> '-L/opt/R/arm64/gfortran/lib'
>>ld: library not found for -lgfortran
>>clang: error: linker command failed with exit code 1 (use -v to see
>> invocation)
>>make: *** [HACSim.so] Error 1
>>ERROR: compil

Re: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

2023-05-17 Thread Sparapani, Rodney via R-SIG-Mac

Hi Jarrett:

Do the two directories exist that clang is warning you about?

'/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
'/opt/R/arm64/gfortran/lib'


--
Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His
Director, Wisconsin Chapter of the American Statistical Association
Institute for Health and Equity, Division of Biostatistics
Medical College of Wisconsin, Milwaukee Campus

From: R-SIG-Mac  on behalf of Jarrett Phillips 

Date: Wednesday, May 17, 2023 at 11:54 AM
To: r-sig-mac@r-project.org 
Subject: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()
ATTENTION: This email originated from a sender outside of MCW. Use caution when 
clicking on links or opening attachments.


Hi All,

I'm trying to generate a `tar.gz` file on a Mac for R package submission to
CRAN but am having issues.

I'm using `devtools`, specifically `build()` and `install()`.

My package relies on compiled code via `Rcpp/RcppArmadillo`.

build("HACSim_OO")
── R CMD build
─
✔  checking for file ‘/Users/jarrettphillips/Desktop/HAC
simulation/HACSim_OO/DESCRIPTION’ ...
─  preparing ‘HACSim’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  installing the package to process help pages
 ---
─  installing *source* package ‘HACSim’ ...
   ** using staged installation
   ** libs
   clang++ -arch arm64 -std=gnu++11 -
I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
 
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include'
-I/opt/R/arm64/include-fPIC  -falign-functions=64 -Wall -g -O2  -Wall
-pedantic -fdiagnostics-color=always -c RcppExports.cpp -o RcppExports.o
   clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
 
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include'
-I/opt/R/arm64/include-fPIC  -falign-functions=64 -Wall -g -O2  -Wall
-pedantic -fdiagnostics-color=always -c accumulate.cpp -o accumulate.o
   clang++ -arch arm64 -std=gnu++11 -dynamiclib
-Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module
-multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib
-L/opt/R/arm64/lib -o HACSim.so RcppExports.o accumulate.o
-L/Library/Frameworks/R.framework/Resources/lib -lRlapack
-L/Library/Frameworks/R.framework/Resources/lib -lRblas
-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1
-L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
   ld: warning: directory not found for option
'-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
   ld: warning: directory not found for option
'-L/opt/R/arm64/gfortran/lib'
   ld: library not found for -lgfortran
   clang: error: linker command failed with exit code 1 (use -v to see
invocation)
   make: *** [HACSim.so] Error 1
   ERROR: compilation failed for package ‘HACSim’
─  removing
‘/private/var/folders/r4/xm5blbcd2tn06tjv00lm1c78gn/T/RtmpN4uaYR/Rinstdf4219594de/HACSim’
 ---
ERROR: package installation failed
Error in `(function (command = NULL, args = character(),
error_on_status = TRUE, …`:
! System command 'R' failed
 ---
 Exit status: 1
 stdout & stderr: 
 ---
Type .Last.error to see the more details.

`clang` is installed (since I am able to run the code within my package)
and I've verified by typing `gcc` in the Mac Terminal. I've also installed
`Homebrew` and `gfortran`, verifying via typing in the Terminal.

Any idea on what's going on and how to fix the issue(s)?

Thanks!

Cheers,

Jarrett

P.S. - I've asked on the R package dev list and after trying a number of
solutions was suggested to try here as it seems to be a macOS issue.

[[alternative HTML version deleted]]

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[R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

2023-05-17 Thread Jarrett Phillips

Hi All,

I'm trying to generate a `tar.gz` file on a Mac for R package submission to
CRAN but am having issues.

I'm using `devtools`, specifically `build()` and `install()`.

My package relies on compiled code via `Rcpp/RcppArmadillo`.

build("HACSim_OO")
── R CMD build
─
✔  checking for file ‘/Users/jarrettphillips/Desktop/HAC
simulation/HACSim_OO/DESCRIPTION’ ...
─  preparing ‘HACSim’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  installing the package to process help pages
 ---
─  installing *source* package ‘HACSim’ ...
   ** using staged installation
   ** libs
   clang++ -arch arm64 -std=gnu++11 -
I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
 
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include'
-I/opt/R/arm64/include-fPIC  -falign-functions=64 -Wall -g -O2  -Wall
-pedantic -fdiagnostics-color=always -c RcppExports.cpp -o RcppExports.o
   clang++ -arch arm64 -std=gnu++11
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
 
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include'
-I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include'
-I/opt/R/arm64/include-fPIC  -falign-functions=64 -Wall -g -O2  -Wall
-pedantic -fdiagnostics-color=always -c accumulate.cpp -o accumulate.o
   clang++ -arch arm64 -std=gnu++11 -dynamiclib
-Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module
-multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib
-L/opt/R/arm64/lib -o HACSim.so RcppExports.o accumulate.o
-L/Library/Frameworks/R.framework/Resources/lib -lRlapack
-L/Library/Frameworks/R.framework/Resources/lib -lRblas
-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1
-L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
   ld: warning: directory not found for option
'-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1'
   ld: warning: directory not found for option
'-L/opt/R/arm64/gfortran/lib'
   ld: library not found for -lgfortran
   clang: error: linker command failed with exit code 1 (use -v to see
invocation)
   make: *** [HACSim.so] Error 1
   ERROR: compilation failed for package ‘HACSim’
─  removing
‘/private/var/folders/r4/xm5blbcd2tn06tjv00lm1c78gn/T/RtmpN4uaYR/Rinstdf4219594de/HACSim’
 ---
ERROR: package installation failed
Error in `(function (command = NULL, args = character(),
error_on_status = TRUE, …`:
! System command 'R' failed
 ---
 Exit status: 1
 stdout & stderr: 
 ---
Type .Last.error to see the more details.

`clang` is installed (since I am able to run the code within my package)
and I've verified by typing `gcc` in the Mac Terminal. I've also installed
`Homebrew` and `gfortran`, verifying via typing in the Terminal.

Any idea on what's going on and how to fix the issue(s)?

Thanks!

Cheers,

Jarrett

P.S. - I've asked on the R package dev list and after trying a number of
solutions was suggested to try here as it seems to be a macOS issue.

[[alternative HTML version deleted]]

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

Re: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

Re: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

Re: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

Re: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

Re: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

Re: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

Re: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

Re: [R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

[R-SIG-Mac] Problems compiling with R CMD build and devtools::build()

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