date:20230516

Re: [R-pkg-devel] help fixing CRAN package sos

2023-05-16 Thread Uwe Ligges





On 16.05.2023 01:46, Spencer Graves wrote:

Hello, All:


   The sos package is failing some CRAN checks, complaining:[1]


LaTeX errors:
! Missing $ inserted.

     $
l.303 {\tt pspline_
    checker} in the



I can only guess this is part of the response you got from some sos 
request? I cannot reproduce it currently.


So check:
Does your package pass check if some function names including an 
underscore in the name is retunred from an sos request?


Best,
Uwe Ligges







! Emergency stop.

     $
l.303 {\tt pspline_
    checker} in the
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'sos.Rnw'


   I can NOT replicate these locally nor with GitHub action, and I 
failed to find 'psp' in 'sos.Rnw'.[2]  This raises two issue:



OBVIOUS:  What can I do to fix this error, or at least to understand it 
better?



SUBTLE:  How can I configure "github action", so it can replicate the 
errors reported on CRAN?



   Thanks,
   Spencer


[1]


https://cran.r-project.org


[2]


https://github.com/sbgraves237/sos


 Forwarded Message 
Subject: Re: CRAN package sos
Date: Sun, 14 May 2023 14:46:06 +0100
From: Prof Brian Ripley 
Reply-To: CRAN 
To: Spencer Graves 
CC: c...@r-project.org




On 12/05/2023 13:03, Spencer Graves wrote:

Hello, All:


You have just spammed my personal email address, contrary to the CRAN 
policy and done so deliberately and/or recklessly, overriding the 
Reply-To header.


   Is MASS being withdrawn along with multiple other packages 
(mgcv, survival, boot, lattice)?


Not so.  And that was a failure to do your own homework as you should 
have looked on CRAN to see that they are still available.


Further

options(repos=c(CRAN="http://cran.cnr.berkeley.edu";))

does not respect the user's choice of repository: that seems to make 
re-making it unreasonably slow.  On my very fast MacBook Pro


* checking re-building of vignette outputs ...^R
  [26s/265s] OK

so it is waiting 90% of the time.


   That's responsible for 3 of the 4 'warnings' listed there.  The 
warning for r-devel-linux-x86_64-fedora-gcc says "LaTeX errors:
! Missing $ inserted ... Fatal error occurred, no output PDF file 
produced! ... Vignette re-building failed."



   These all sound to me like operating system errors.  If there's 
something here I should do, I could use help in understanding what.


Do read the message -- it is a LaTeX error in the LaTeX code your 
package's vignettes generates.


    LaTeX errors:
     ! Missing $ inserted.
     
  $
     l.303 {\tt pspline_
  checker} in the
     ! Emergency stop.
     
  $
     l.303 {\tt pspline_
  checker} in the
     ! ==> Fatal error occurred, no output PDF file produced!

Underlines need to be escaped in LaTeX.  And as your results depend on 
Internet downloads,


"Packages which use Internet resources should fail gracefully with an 
informative message if the resource is not available or has changed (and 
not give a check warning nor error)."


applies: you need to anticipate that the results might include underlines.




   Thanks,
   Spencer Graves
m:  1-408-655-4567


On 5/12/23 1:38 AM, Prof Brian Ripley wrote:

Dear maintainer,

Please see the problems shown on
.

Please correct before 2023-05-26 to safely retain your package on CRAN.

The CRAN Team




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Re: [R-pkg-devel] help fixing CRAN package sos

2023-05-16 Thread Spencer Graves

On 5/16/23 6:06 AM, Uwe Ligges wrote:

On 16.05.2023 01:46, Spencer Graves wrote:

Hello, All:

   The sos package is failing some CRAN checks, complaining:[1]

LaTeX errors:
! Missing $ inserted.

 $
l.303 {\tt pspline_
    checker} in the

I can only guess this is part of the response you got from some sos 
request? I cannot reproduce it currently.

So check:
Does your package pass check if some function names including an 
underscore in the name is returned from an sos request?

Hi, Uwe et al.:

  Thanks, Uwe, for your reply.

	  It's complaining about something in a vignette that has been part of 
the package since it appeared in The R Journal in Volume 1/2 in 2009.  I 
received an email from Prof. Ripley complaining that it reported 
problems ("WARN") on some of the CRAN checks.  When I asked, Prof. 
Ripley reply's reply included:

>>  l.303 {\tt pspline_
>>   checker} in the
>>  ! ==> Fatal error occurred, no output PDF file produced!
>>
>> Underlines need to be escaped in LaTeX.  And as your results depend on
>> Internet downloads,
>>
>> "Packages which use Internet resources should fail gracefully with an
>> informative message if the resource is not available or has changed
>> (and not give a check warning nor error)."
>>
>> applies: you need to anticipate that the results might include
>> underlines.

	  I don't know how to detect, let alone fix the "Underlines" that "need 
to be escaped in LaTeX."

	  Regarding the other issue that "Packages which use Internet resources 
should fail gracefully with an informative message if the resource is 
not available or has changed (and not give a check warning nor error)", 
I assume I should wrap in "try" all tests in *.Rd files that access the 
Internet and make sure that they don't fail "R CMD check" if the 
Internet is not available.

  Comments?
  Thanks again,
  Spencer Graves

p.s.  Yesterday I remember I got "WARN" on three of six CRAN checks 
against r-devel on different platforms and NOTE on four of the seven 
other CRAN checks.  Today I see "WARN" on only two.  If I just wait, 
these "WARN" problems may go away by themselves.  However, Prof. Ripley 
gave me other problems to fix, and I want to support our kind, smart and 
generous English professor.

Best,
Uwe Ligges

! Emergency stop.

 $
l.303 {\tt pspline_
    checker} in the
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'sos.Rnw'

   I can NOT replicate these locally nor with GitHub action, and I 
failed to find 'psp' in 'sos.Rnw'.[2]  This raises two issue:

OBVIOUS:  What can I do to fix this error, or at least to understand 
it better?

SUBTLE:  How can I configure "github action", so it can replicate the 
errors reported on CRAN?

   Thanks,
   Spencer

[1]

https://cran.r-project.org

[2]

https://github.com/sbgraves237/sos

 Forwarded Message 
Subject: Re: CRAN package sos
Date: Sun, 14 May 2023 14:46:06 +0100
From: Prof Brian Ripley 
Reply-To: CRAN 
To: Spencer Graves 
CC: c...@r-project.org

On 12/05/2023 13:03, Spencer Graves wrote:

Hello, All:

You have just spammed my personal email address, contrary to the CRAN 
policy and done so deliberately and/or recklessly, overriding the 
Reply-To header.

   Is MASS being withdrawn along with multiple other packages 
(mgcv, survival, boot, lattice)?

Not so.  And that was a failure to do your own homework as you should 
have looked on CRAN to see that they are still available.

Further

options(repos=c(CRAN="http://cran.cnr.berkeley.edu";))

does not respect the user's choice of repository: that seems to make 
re-making it unreasonably slow.  On my very fast MacBook Pro

* checking re-building of vignette outputs ...^R
  [26s/265s] OK

so it is waiting 90% of the time.

   That's responsible for 3 of the 4 'warnings' listed there.  
The warning for r-devel-linux-x86_64-fedora-gcc says "LaTeX errors:
! Missing $ inserted ... Fatal error occurred, no output PDF file 
produced! ... Vignette re-building failed."

   These all sound to me like operating system errors.  If 
there's something here I should do, I could use help in understanding 
what.

Do read the message -- it is a LaTeX error in the LaTeX code your 
package's vignettes generates.

    LaTeX errors:
 ! Missing $ inserted.

  $
 l.303 {\tt pspline_
  checker} in the
 ! Emergency stop.

  $
 l.303 {\tt pspline_
  checker} in the
 ! ==> Fatal error occurred, no output PDF file produced!

Underlines need to be escaped in LaTeX.  And as your results depend on 
Internet downloads,

"Packages which use Internet resources should fail gracefully with an 
informative message if the resource is not available or has changed 
(and not give a check warning nor error)."

applies: you need to anticipate

Re: [R-pkg-devel] help fixing CRAN package sos

2023-05-16 Thread Uwe Ligges

On 16.05.2023 14:02, Spencer Graves wrote:

On 5/16/23 6:06 AM, Uwe Ligges wrote:

On 16.05.2023 01:46, Spencer Graves wrote:

Hello, All:

   The sos package is failing some CRAN checks, complaining:[1]

LaTeX errors:
! Missing $ inserted.

 $
l.303 {\tt pspline_
    checker} in the

I can only guess this is part of the response you got from some sos 
request? I cannot reproduce it currently.

So check:
Does your package pass check if some function names including an 
underscore in the name is returned from an sos request?

Hi, Uwe et al.:

   Thanks, Uwe, for your reply.

   It's complaining about something in a vignette that has been part 
of the package since it appeared in The R Journal in Volume 1/2 in 
2009.  I received an email from Prof. Ripley complaining that it 
reported problems ("WARN") on some of the CRAN checks.  When I asked, 
Prof. Ripley reply's reply included:

 >>  l.303 {\tt pspline_
 >>   checker} in the
 >>  ! ==> Fatal error occurred, no output PDF file produced!
 >>
 >> Underlines need to be escaped in LaTeX.  And as your results depend on
 >> Internet downloads,
 >>
 >> "Packages which use Internet resources should fail gracefully with an
 >> informative message if the resource is not available or has changed
 >> (and not give a check warning nor error)."
 >>
 >> applies: you need to anticipate that the results might include
 >> underlines.

   I don't know how to detect, let alone fix the "Underlines" that 
"need to be escaped in LaTeX."

If you receive an output, postprocess it via

gsub("_", "_", output)

   Regarding the other issue that "Packages which use Internet 
resources should fail gracefully with an informative message if the 
resource is not available or has changed (and not give a check warning 
nor error)", I assume I should wrap in "try" all tests in *.Rd files 
that access the Internet and make sure that they don't fail "R CMD 
check" if the Internet is not available.

Yes.

Best,
Uwe Ligges

   Comments?
   Thanks again,
   Spencer Graves

p.s.  Yesterday I remember I got "WARN" on three of six CRAN checks 
against r-devel on different platforms and NOTE on four of the seven 
other CRAN checks.  Today I see "WARN" on only two.  If I just wait, 
these "WARN" problems may go away by themselves.  However, Prof. Ripley 
gave me other problems to fix, and I want to support our kind, smart and 
generous English professor.

Best,
Uwe Ligges

! Emergency stop.

 $
l.303 {\tt pspline_
    checker} in the
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'sos.Rnw'

   I can NOT replicate these locally nor with GitHub action, and 
I failed to find 'psp' in 'sos.Rnw'.[2]  This raises two issue:

OBVIOUS:  What can I do to fix this error, or at least to understand 
it better?

SUBTLE:  How can I configure "github action", so it can replicate the 
errors reported on CRAN?

   Thanks,
   Spencer

[1]

https://cran.r-project.org

[2]

https://github.com/sbgraves237/sos

 Forwarded Message 
Subject: Re: CRAN package sos
Date: Sun, 14 May 2023 14:46:06 +0100
From: Prof Brian Ripley 
Reply-To: CRAN 
To: Spencer Graves 
CC: c...@r-project.org

On 12/05/2023 13:03, Spencer Graves wrote:

Hello, All:

You have just spammed my personal email address, contrary to the CRAN 
policy and done so deliberately and/or recklessly, overriding the 
Reply-To header.

   Is MASS being withdrawn along with multiple other packages 
(mgcv, survival, boot, lattice)?

Not so.  And that was a failure to do your own homework as you should 
have looked on CRAN to see that they are still available.

Further

options(repos=c(CRAN="http://cran.cnr.berkeley.edu";))

does not respect the user's choice of repository: that seems to make 
re-making it unreasonably slow.  On my very fast MacBook Pro

* checking re-building of vignette outputs ...^R
  [26s/265s] OK

so it is waiting 90% of the time.

   That's responsible for 3 of the 4 'warnings' listed there. 
The warning for r-devel-linux-x86_64-fedora-gcc says "LaTeX errors:
! Missing $ inserted ... Fatal error occurred, no output PDF file 
produced! ... Vignette re-building failed."

   These all sound to me like operating system errors.  If 
there's something here I should do, I could use help in 
understanding what.

Do read the message -- it is a LaTeX error in the LaTeX code your 
package's vignettes generates.

    LaTeX errors:
 ! Missing $ inserted.

  $
 l.303 {\tt pspline_
  checker} in the
 ! Emergency stop.

  $
 l.303 {\tt pspline_
  checker} in the
 ! ==> Fatal error occurred, no output PDF file produced!

Underlines need to be escaped in LaTeX.  And as your results depend 
on Internet downloads,

"Packages which use Internet resources should fail gracefully

[R-pkg-devel] Problems with devtools::build() in R

2023-05-16 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 how to fix the issue(s)?

Thanks!

Cheers,

Jarrett

[[alternative HTML version deleted]]

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Re: [R-pkg-devel] Problems with devtools::build() in R

2023-05-16 Thread Jeff Newmiller

Your mistake is confusing a tool designed for _iterative development_ for a 
tool designed for _delivery_.

Use R CMD build the way WRE says you should.

On May 16, 2023 9:07:05 AM PDT, Jarrett Phillips  
wrote:
>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 how to fix the issue(s)?
>
>Thanks!
>
>Cheers,
>
>Jarrett
>
>   [[alternative HTML version deleted]]
>
>__
>R-package-devel@r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-package-devel

-- 
Sent from my phone. Please excuse my brevity.

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[R-pkg-devel] Are the CRAN macOS builders down?

2023-05-16 Thread Dirk Eddelbuettel



Simon,

As a follow-up to the cmake questions (and me now knowing I have to tell R
where cmake is on macOS), I uploaded a new package last Thursday. It has long
built everywhere on CRAN, but not on macOS.  Ditto for another package update
from Sunday (RcppSimdJson) which also has not been touched.

Should I adjust my expectations that this can take a week or longer on macOS,
or did a few builds fall off the wagon?

Thanks as always for looking after that architecture.

Best,  Dirk

-- 
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [R-pkg-devel] Problems with devtools::build() in R

2023-05-16 Thread Ivan Krylov

В Tue, 16 May 2023 12:07:05 -0400
Jarrett Phillips  пишет:

>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

> I've also installed `Homebrew` and `gfortran`, verifying via typing
> in the Terminal.

Was it the Homebrew build of gfortran, or the one from
? Does this happen if you run R CMD
build  in the Terminal instead of devtools::build()?

It might be that you need this specific R.home('etc')build, or you
might have to adjust some paths in file.path(R.home('etc'),
'Makeconf'). A different build of gfortran may be not compatible with
the one used to compile R.

If you don't get a useful answer here, consider asking at
r-sig-...@r-project.org, because this seems to be a Mac-specific
problem.

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] Problems with devtools::build() in R

2023-05-16 Thread Serguei Sokol


Le 16/05/2023 à 18:07, Jarrett Phillips a écrit :

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 how to fix the issue(s)?

Try to add in /src/Makevars:

PKG_LIBS=$(FLIBS)

Best,
Serguei.

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Re: [R-pkg-devel] Problems with devtools::build() in R

2023-05-16 Thread Duncan Murdoch


On 16/05/2023 12:07 p.m., Jarrett Phillips wrote:

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 how to fix the issue(s)?


You don't say how you installed gfortran, but it sounds as though you 
installed Homebrew's build of it.  You should install the tools as 
available from https://mac.r-project.org/tools/.


Duncan Murdoch

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Re: [R-pkg-devel] Problems with devtools::build() in R

2023-05-16 Thread Jarrett Phillips

Hi Duncan,

I actually installed gfortran from

https://github.com/fxcoudert/gfortran-for-macOS/releases

but I can instead install from the URL you provide.

Hopefully this fixes the problem.

I will respond here if there are still issues.

Thanks.

Cheers,

Jarrett


On Tue, May 16, 2023 at 12:39 PM Duncan Murdoch 
wrote:

> On 16/05/2023 12:07 p.m., Jarrett Phillips wrote:
> > 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 how to fix the issue(s)?
>
> You don't say how you installed gfortran, but it sounds as though you
> installed Homebrew's build of it.  You should install the tools as
> available from https://mac.r-project.org/tools/.
>
> Duncan Murdoch
>
>

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Re: [R-pkg-devel] Problems with devtools::build() in R

2023-05-16 Thread Dirk Eddelbuettel



On 16 May 2023 at 18:32, Serguei Sokol wrote:
| Try to add in /src/Makevars:
| 
| PKG_LIBS=$(FLIBS)

Good catch. For every RcppArmadillo package we recommend (and inject if you
use the RcppArmadillo.package.skeleton() helper) (and omit the earlier
comment lines)

  PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
  PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

Source file (with addded comments) is at
https://github.com/RcppCore/RcppArmadillo/blob/master/inst/skeleton/Makevars
or in your friendly neighborhood RcppArmadillo installation as
system.file("skeleton", "Makevars", package="RcppArmadillo")

Dirk

-- 
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [R-pkg-devel] Problems with devtools::build() in R

2023-05-16 Thread Jarrett Phillips

Installing from the URL you provide, as well as doing R CMD build HACSim as
suggested by @JeffNewmiller fails.

When trying the latter solution, I get the same error as the one provided
in my original post.

Any thoughts?





On Tue, May 16, 2023 at 12:52 PM Jarrett Phillips <
phillipsjarre...@gmail.com> wrote:

> Hi Duncan,
>
> I actually installed gfortran from
>
> https://github.com/fxcoudert/gfortran-for-macOS/releases
>
> but I can instead install from the URL you provide.
>
> Hopefully this fixes the problem.
>
> I will respond here if there are still issues.
>
> Thanks.
>
> Cheers,
>
> Jarrett
>
>
> On Tue, May 16, 2023 at 12:39 PM Duncan Murdoch 
> wrote:
>
>> On 16/05/2023 12:07 p.m., Jarrett Phillips wrote:
>> > 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 how to fix the issue(s)?
>>
>> You don't say how you installed gfortran, but it sounds as though you
>> installed Homebrew's build of it.  You should install the tools as
>> available from https://mac.r-project.org/tools/.
>>
>> Duncan Murdoch
>>
>>

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Re: [R-pkg-devel] Problems with devtools::build() in R

2023-05-16 Thread Gábor Csárdi

Seems like you are on R 4.2.x, so you could try this one:
https://github.com/R-macos/gcc-darwin-arm64/releases

Gabor

On Tue, May 16, 2023 at 7:16 PM Jarrett Phillips
 wrote:
>
> Installing from the URL you provide, as well as doing R CMD build HACSim as
> suggested by @JeffNewmiller fails.
>
> When trying the latter solution, I get the same error as the one provided
> in my original post.
>
> Any thoughts?
>
>
>
>
>
> On Tue, May 16, 2023 at 12:52 PM Jarrett Phillips <
> phillipsjarre...@gmail.com> wrote:
>
> > Hi Duncan,
> >
> > I actually installed gfortran from
> >
> > https://github.com/fxcoudert/gfortran-for-macOS/releases
> >
> > but I can instead install from the URL you provide.
> >
> > Hopefully this fixes the problem.
> >
> > I will respond here if there are still issues.
> >
> > Thanks.
> >
> > Cheers,
> >
> > Jarrett
> >
> >
> > On Tue, May 16, 2023 at 12:39 PM Duncan Murdoch 
> > wrote:
> >
> >> On 16/05/2023 12:07 p.m., Jarrett Phillips wrote:
> >> > 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 how to fix the issue(s)?
> >>
> >> You don't say how you installed gfortran, but it sounds as though you
> >> installed Homebrew's build of it.  You should instal

Re: [R-pkg-devel] Problems with devtools::build() in R

2023-05-16 Thread Duncan Murdoch

On 16/05/2023 1:14 p.m., Jarrett Phillips wrote:
Installing from the URL you provide, as well as doing R CMD build HACSim 
as suggested by @JeffNewmiller fails.

When trying the latter solution, I get the same error as the one 
provided in my original post.

Any thoughts?

Did you try Serguei's suggestion?

On 16/05/2023 12:32 p.m., Serguei Sokol wrote:
> Try to add in /src/Makevars:
>
> PKG_LIBS=$(FLIBS)

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Re: [R-pkg-devel] Problems with devtools::build() in R

2023-05-16 Thread Jarrett Phillips

On Tue, May 16, 2023 at 2:00 PM Jarrett Phillips 
wrote:

> Yes, in addition to doing what @DirkEddelbuettel suggests. I keep getting
> the same error...
>
> On Tue, May 16, 2023 at 1:47 PM Duncan Murdoch 
> wrote:
>
>> On 16/05/2023 1:14 p.m., Jarrett Phillips wrote:
>> > Installing from the URL you provide, as well as doing R CMD
>> build HACSim
>> > as suggested by @JeffNewmiller fails.
>> >
>> > When trying the latter solution, I get the same error as the one
>> > provided in my original post.
>> >
>> > Any thoughts?
>>
>> Did you try Serguei's suggestion?
>>
>> On 16/05/2023 12:32 p.m., Serguei Sokol wrote:
>>  > Try to add in /src/Makevars:
>>  >
>>  > PKG_LIBS=$(FLIBS)
>>
>

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Re: [R-pkg-devel] Problems with devtools::build() in R

2023-05-16 Thread Duncan Murdoch

I don't know what the issue would be.  I just tried

  remotes::install_github("jphill01/HACSim.R")

and it worked fine, but I think that's not the same version that you are 
working with.

Duncan Murdoch

On 16/05/2023 2:01 p.m., Jarrett Phillips wrote:

On Tue, May 16, 2023 at 2:00 PM Jarrett Phillips 
mailto:phillipsjarre...@gmail.com>> wrote:

Yes, in addition to doing what @DirkEddelbuettel suggests. I keep
getting the same error...

On Tue, May 16, 2023 at 1:47 PM Duncan Murdoch
mailto:murdoch.dun...@gmail.com>> wrote:

On 16/05/2023 1:14 p.m., Jarrett Phillips wrote:
 > Installing from the URL you provide, as well as doing R CMD
build HACSim
 > as suggested by @JeffNewmiller fails.
 >
 > When trying the latter solution, I get the same error as the one
 > provided in my original post.
 >
 > Any thoughts?

Did you try Serguei's suggestion?

On 16/05/2023 12:32 p.m., Serguei Sokol wrote:
  > Try to add in /src/Makevars:
  >
  > PKG_LIBS=$(FLIBS)

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Re: [R-pkg-devel] Problems with devtools::build() in R

2023-05-16 Thread Jarrett Phillips

Strange... the GitHub repo is up to date and that's what I'm trying to
bundle up for a CRAN update. So, I'm thinking it's some kind of a system
issue (I recently purchased a new MacBook Pro)..

I'll investigate.

Thanks!

On Tue, May 16, 2023 at 2:09 PM Duncan Murdoch 
wrote:

> I don't know what the issue would be.  I just tried
>
>remotes::install_github("jphill01/HACSim.R")
>
> and it worked fine, but I think that's not the same version that you are
> working with.
>
> Duncan Murdoch
>
> On 16/05/2023 2:01 p.m., Jarrett Phillips wrote:
> >
> >
> > On Tue, May 16, 2023 at 2:00 PM Jarrett Phillips
> > mailto:phillipsjarre...@gmail.com>> wrote:
> >
> > Yes, in addition to doing what @DirkEddelbuettel suggests. I keep
> > getting the same error...
> >
> > On Tue, May 16, 2023 at 1:47 PM Duncan Murdoch
> > mailto:murdoch.dun...@gmail.com>> wrote:
> >
> > On 16/05/2023 1:14 p.m., Jarrett Phillips wrote:
> >  > Installing from the URL you provide, as well as doing R CMD
> > build HACSim
> >  > as suggested by @JeffNewmiller fails.
> >  >
> >  > When trying the latter solution, I get the same error as the
> one
> >  > provided in my original post.
> >  >
> >  > Any thoughts?
> >
> > Did you try Serguei's suggestion?
> >
> > On 16/05/2023 12:32 p.m., Serguei Sokol wrote:
> >   > Try to add in /src/Makevars:
> >   >
> >   > PKG_LIBS=$(FLIBS)
> >
>
>

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Re: [R-pkg-devel] Problems with devtools::build() in R

2023-05-16 Thread Duncan Murdoch


I'm using R 4.3.0, newer than you, so that might affect things.

Duncan

On 16/05/2023 2:48 p.m., Jarrett Phillips wrote:
Strange... the GitHub repo is up to date and that's what I'm trying to 
bundle up for a CRAN update. So, I'm thinking it's some kind of a system 
issue (I recently purchased a new MacBook Pro)..


I'll investigate.

Thanks!

On Tue, May 16, 2023 at 2:09 PM Duncan Murdoch > wrote:


I don't know what the issue would be.  I just tried

    remotes::install_github("jphill01/HACSim.R")

and it worked fine, but I think that's not the same version that you
are
working with.

Duncan Murdoch

On 16/05/2023 2:01 p.m., Jarrett Phillips wrote:
 >
 >
 > On Tue, May 16, 2023 at 2:00 PM Jarrett Phillips
 > mailto:phillipsjarre...@gmail.com>
>> wrote:
 >
 >     Yes, in addition to doing what @DirkEddelbuettel suggests. I keep
 >     getting the same error...
 >
 >     On Tue, May 16, 2023 at 1:47 PM Duncan Murdoch
 >     mailto:murdoch.dun...@gmail.com>
>>
wrote:
 >
 >         On 16/05/2023 1:14 p.m., Jarrett Phillips wrote:
 >          > Installing from the URL you provide, as well as doing
R CMD
 >         build HACSim
 >          > as suggested by @JeffNewmiller fails.
 >          >
 >          > When trying the latter solution, I get the same error
as the one
 >          > provided in my original post.
 >          >
 >          > Any thoughts?
 >
 >         Did you try Serguei's suggestion?
 >
 >         On 16/05/2023 12:32 p.m., Serguei Sokol wrote:
 >           > Try to add in /src/Makevars:
 >           >
 >           > PKG_LIBS=$(FLIBS)
 >



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Re: [R-pkg-devel] Are the CRAN macOS builders down?

2023-05-16 Thread Simon Urbanek

Dirk,

builds are immediate, so it is a matter of seconds for most packages. I don't 
see any issues on the Mac Builder server.
If you have a problem, please be more specific and include the check link 
returned at submission.

Cheers,
Simon
 

> On 17/05/2023, at 4:27 AM, Dirk Eddelbuettel  wrote:
> 
> 
> Simon,
> 
> As a follow-up to the cmake questions (and me now knowing I have to tell R
> where cmake is on macOS), I uploaded a new package last Thursday. It has long
> built everywhere on CRAN, but not on macOS.  Ditto for another package update
> from Sunday (RcppSimdJson) which also has not been touched.
> 
> Should I adjust my expectations that this can take a week or longer on macOS,
> or did a few builds fall off the wagon?
> 
> Thanks as always for looking after that architecture.
> 
> Best,  Dirk
> 
> -- 
> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
> 

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Re: [R-pkg-devel] Are the CRAN macOS builders down?

2023-05-16 Thread Dirk Eddelbuettel



Simon:

On 17 May 2023 at 07:57, Simon Urbanek wrote:
| builds are immediate, so it is a matter of seconds for most packages. I don't 
see any issues on the Mac Builder server.
| If you have a problem, please be more specific and include the check link 
returned at submission.

I was talking about _CRAN uploads_. To be as specific as you asked:

 - crc32c on CRAN since May 11, all systems apart from macOS built but all
   macOS builds missing
   https://cran.r-project.org/web/checks/check_results_crc32c.html

 - RcppSimdJson on CRAN since May 14, six linux + windows builds made, two
   linux builds and all macOS missing
   https://cran.r-project.org/web/checks/check_results_RcppSimdJson.html

So no builds on macOS for either of my uploads to CRAN. Can you comment?

Dirk

| Cheers,
| Simon
|  
| 
| > On 17/05/2023, at 4:27 AM, Dirk Eddelbuettel  wrote:
| > 
| > 
| > Simon,
| > 
| > As a follow-up to the cmake questions (and me now knowing I have to tell R
| > where cmake is on macOS), I uploaded a new package last Thursday. It has 
long
| > built everywhere on CRAN, but not on macOS.  Ditto for another package 
update
| > from Sunday (RcppSimdJson) which also has not been touched.
| > 
| > Should I adjust my expectations that this can take a week or longer on 
macOS,
| > or did a few builds fall off the wagon?
| > 
| > Thanks as always for looking after that architecture.
| > 
| > Best,  Dirk
| > 
| > -- 
| > dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
| > 
| 

-- 
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Re: [R-pkg-devel] Are the CRAN macOS builders down?

2023-05-16 Thread Simon Urbanek

Dirk,

thanks, ok, now I get what you meant. This has nothing to do with CRAN uploads 
(which are handled in Vienna) this was about specific macOS builds. The arm64 
Big Sur build machine had apparently issues. I have re-started the arm64 builds 
so they should catch up in a few hours.

Thanks,
Simon


> On 17/05/2023, at 8:39 AM, Dirk Eddelbuettel  wrote:
> 
> 
> Simon:
> 
> On 17 May 2023 at 07:57, Simon Urbanek wrote:
> | builds are immediate, so it is a matter of seconds for most packages. I 
> don't see any issues on the Mac Builder server.
> | If you have a problem, please be more specific and include the check link 
> returned at submission.
> 
> I was talking about _CRAN uploads_. To be as specific as you asked:
> 
> - crc32c on CRAN since May 11, all systems apart from macOS built but all
>   macOS builds missing
>   https://cran.r-project.org/web/checks/check_results_crc32c.html
> 
> - RcppSimdJson on CRAN since May 14, six linux + windows builds made, two
>   linux builds and all macOS missing
>   https://cran.r-project.org/web/checks/check_results_RcppSimdJson.html
> 
> So no builds on macOS for either of my uploads to CRAN. Can you comment?
> 
> Dirk
> 
> | Cheers,
> | Simon
> |  
> | 
> | > On 17/05/2023, at 4:27 AM, Dirk Eddelbuettel  wrote:
> | > 
> | > 
> | > Simon,
> | > 
> | > As a follow-up to the cmake questions (and me now knowing I have to tell R
> | > where cmake is on macOS), I uploaded a new package last Thursday. It has 
> long
> | > built everywhere on CRAN, but not on macOS.  Ditto for another package 
> update
> | > from Sunday (RcppSimdJson) which also has not been touched.
> | > 
> | > Should I adjust my expectations that this can take a week or longer on 
> macOS,
> | > or did a few builds fall off the wagon?
> | > 
> | > Thanks as always for looking after that architecture.
> | > 
> | > Best,  Dirk
> | > 
> | > -- 
> | > dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
> | > 
> | 
> 
> -- 
> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
> 

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Re: [R-pkg-devel] Are the CRAN macOS builders down?

2023-05-16 Thread Dirk Eddelbuettel



On 17 May 2023 at 10:39, Simon Urbanek wrote:
| Dirk,
| 
| thanks, ok, now I get what you meant. This has nothing to do with CRAN 
uploads (which are handled in Vienna) this was about specific macOS builds. The 
arm64 Big Sur build machine had apparently issues. I have re-started the arm64 
builds so they should catch up in a few hours.

Thanks but as I noted _all other non-arm64 macOS machines are also lagging_
and now for about five days -- which is why wrote the email.

But good to know you are on it now!

Dirk

| 
| Thanks,
| Simon
| 
| 
| > On 17/05/2023, at 8:39 AM, Dirk Eddelbuettel  wrote:
| > 
| > 
| > Simon:
| > 
| > On 17 May 2023 at 07:57, Simon Urbanek wrote:
| > | builds are immediate, so it is a matter of seconds for most packages. I 
don't see any issues on the Mac Builder server.
| > | If you have a problem, please be more specific and include the check link 
returned at submission.
| > 
| > I was talking about _CRAN uploads_. To be as specific as you asked:
| > 
| > - crc32c on CRAN since May 11, all systems apart from macOS built but all
| >   macOS builds missing
| >   https://cran.r-project.org/web/checks/check_results_crc32c.html
| > 
| > - RcppSimdJson on CRAN since May 14, six linux + windows builds made, two
| >   linux builds and all macOS missing
| >   https://cran.r-project.org/web/checks/check_results_RcppSimdJson.html
| > 
| > So no builds on macOS for either of my uploads to CRAN. Can you comment?
| > 
| > Dirk
| > 
| > | Cheers,
| > | Simon
| > |  
| > | 
| > | > On 17/05/2023, at 4:27 AM, Dirk Eddelbuettel  wrote:
| > | > 
| > | > 
| > | > Simon,
| > | > 
| > | > As a follow-up to the cmake questions (and me now knowing I have to 
tell R
| > | > where cmake is on macOS), I uploaded a new package last Thursday. It 
has long
| > | > built everywhere on CRAN, but not on macOS.  Ditto for another package 
update
| > | > from Sunday (RcppSimdJson) which also has not been touched.
| > | > 
| > | > Should I adjust my expectations that this can take a week or longer on 
macOS,
| > | > or did a few builds fall off the wagon?
| > | > 
| > | > Thanks as always for looking after that architecture.
| > | > 
| > | > Best,  Dirk
| > | > 
| > | > -- 
| > | > dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
| > | > 
| > | 
| > 
| > -- 
| > dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
| > 
| 

-- 
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Re: [R-pkg-devel] Problems with devtools::build() in R

2023-05-16 Thread Jarrett Phillips

Hi Dirk,

I wonder if my problem is related to the question you posed about the CRAN
macOS builders being down. If it is, then according to @Simon Urbanek, this
should be resolved in a few hours.

Can you confirm?

Thanks.

Cheers,

Jarrett

On Tue, May 16, 2023 at 1:11 PM Dirk Eddelbuettel  wrote:

>
> On 16 May 2023 at 18:32, Serguei Sokol wrote:
> | Try to add in /src/Makevars:
> |
> | PKG_LIBS=$(FLIBS)
>
> Good catch. For every RcppArmadillo package we recommend (and inject if you
> use the RcppArmadillo.package.skeleton() helper) (and omit the earlier
> comment lines)
>
>   PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
>   PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
>
> Source file (with addded comments) is at
>
> https://github.com/RcppCore/RcppArmadillo/blob/master/inst/skeleton/Makevars
> or in your friendly neighborhood RcppArmadillo installation as
> system.file("skeleton", "Makevars", package="RcppArmadillo")
>
> Dirk
>
> --
> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>

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Re: [R-pkg-devel] Problems with devtools::build() in R

2023-05-16 Thread Dirk Eddelbuettel



Hi Jarrett

On 16 May 2023 at 19:06, Jarrett Phillips wrote:
| I wonder if my problem is related to the question you posed about the CRAN
| macOS builders being down. If it is, then according to @Simon Urbanek, this
| should be resolved in a few hours.
| 
| Can you confirm? 

Oh, maybe -- were you trying at Simon's macbuilder? I thought you were doing
this locally on your machine.  If it was Simon's and if that box had hickups
then yes that could indeed be related.

Dirk

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Re: [R-pkg-devel] Problems with devtools::build() in R

2023-05-16 Thread Jarrett Phillips

Actually, no, only locally… but so far all proposed solutions have failed.

On Tue, May 16, 2023 at 7:11 PM Dirk Eddelbuettel  wrote:

>
> Hi Jarrett
>
> On 16 May 2023 at 19:06, Jarrett Phillips wrote:
> | I wonder if my problem is related to the question you posed about the
> CRAN
> | macOS builders being down. If it is, then according to @Simon Urbanek,
> this
> | should be resolved in a few hours.
> |
> | Can you confirm?
>
> Oh, maybe -- were you trying at Simon's macbuilder? I thought you were
> doing
> this locally on your machine.  If it was Simon's and if that box had
> hickups
> then yes that could indeed be related.
>
> Dirk
>
> --
> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>

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Re: [R-pkg-devel] help fixing CRAN package sos

Re: [R-pkg-devel] help fixing CRAN package sos

Re: [R-pkg-devel] help fixing CRAN package sos

[R-pkg-devel] Problems with devtools::build() in R

Re: [R-pkg-devel] Problems with devtools::build() in R

[R-pkg-devel] Are the CRAN macOS builders down?

Re: [R-pkg-devel] Problems with devtools::build() in R

Re: [R-pkg-devel] Problems with devtools::build() in R

Re: [R-pkg-devel] Problems with devtools::build() in R

Re: [R-pkg-devel] Problems with devtools::build() in R

Re: [R-pkg-devel] Problems with devtools::build() in R

Re: [R-pkg-devel] Problems with devtools::build() in R

Re: [R-pkg-devel] Problems with devtools::build() in R

Re: [R-pkg-devel] Problems with devtools::build() in R

Re: [R-pkg-devel] Problems with devtools::build() in R

Re: [R-pkg-devel] Problems with devtools::build() in R

Re: [R-pkg-devel] Problems with devtools::build() in R

Re: [R-pkg-devel] Problems with devtools::build() in R

Re: [R-pkg-devel] Are the CRAN macOS builders down?

Re: [R-pkg-devel] Are the CRAN macOS builders down?

Re: [R-pkg-devel] Are the CRAN macOS builders down?

Re: [R-pkg-devel] Are the CRAN macOS builders down?

Re: [R-pkg-devel] Problems with devtools::build() in R

Re: [R-pkg-devel] Problems with devtools::build() in R

Re: [R-pkg-devel] Problems with devtools::build() in R

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