Re: [R-pkg-devel] Can't reproduce re-building vignettes error in CRAN R CMD check

[Uwe Ligges]

This is probbaly a race condition, please resubmit.

Best,
Uwe Ligges

On 22.11.2017 16:49, Devin Incerti wrote:

Hi,

I have successfully run R CMD check for my package hesim (source
) on OSX sierra,
CentOS, Ubuntu 14.04 (on travis-ci), and win-builder (devel and
release). However, when I submitted to CRAN I received the warning:

* checking re-building of vignette outputs ... [3s] WARNING
Error in re-building vignettes:
   ...
Error: processing vignette 'cea-vignette.Rmd' failed with diagnostics:
DLL 'stringi' not found: maybe not installed for this architecture?
Execution halted

I'm stumped by this and can't recreate it. Any ideas on how to
eliminate this warning?

Thanks

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[R-pkg-devel] Errors in the pre-test after submitting the R package

[Tan, Senren]

Dear all,



I have been developing an R package using Rcpp to call C++ functions that use 
the C subroutine library 'fftw3' that implements fast Fourier transform 
algorithm. Since I have the C library 'fftw3' installed on my laptop (running 
MacOS), when I checked my developed package using R CMD CHECK --as-cran, I 
could pass all the checks with no errors or warnings.



However, when I submitted the package to CRAN, during the pre-test, I 
encountered an error. I was wondering whether this error came from the absence 
of the 'fftw3' C library on the checking machine? Or maybe I have made some 
mistakes in the Makevars.win file?



I have done some search on how to use the external C library in R packages with 
Rcpp.

Here is what I have provided in the Makevars.win file:



PKG_CPPFLAGS = -I$(LIB_FFTW)/include

CXX = g++

PKG_CXXFLAGS = -std=c++11

PKG_LIBS = -L$(LIB_FFTW)/lib -lfftw3





Could you please advise me on what to do?



Here is the error message:



* installing *source* package 'KSgeneral' ...

** libs



*** arch - i386

d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -I"D:/RCompile/recent/R/include" 
-DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include 
-I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   
-I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -pedantic -O2 -Wall  
-mtune=core2 -c RcppExports.cpp -o RcppExports.o

d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -I"D:/RCompile/recent/R/include" 
-DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include 
-I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   
-I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -pedantic -O2 -Wall  
-mtune=core2 -c cont_ks_dist.cpp -o cont_ks_dist.o

d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -I"D:/RCompile/recent/R/include" 
-DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include 
-I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   
-I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -pedantic -O2 -Wall  
-mtune=core2 -c crossprob_new.cc -o crossprob_new.o

d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -I"D:/RCompile/recent/R/include" 
-DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include 
-I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   
-I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -pedantic -O2 -Wall  
-mtune=core2 -c fftw_wrappers.cc -o fftw_wrappers.o

d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -I"D:/RCompile/recent/R/include" 
-DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include 
-I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   
-I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -pedantic -O2 -Wall  
-mtune=core2 -c fftwconvolver.cc -o fftwconvolver.o

d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -I"D:/RCompile/recent/R/include" 
-DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include 
-I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   
-I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -pedantic -O2 -Wall  
-mtune=core2 -c one_sided_noncrossing_probability.cc -o 
one_sided_noncrossing_probability.o

d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -I"D:/RCompile/recent/R/include" 
-DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include 
-I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   
-I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -pedantic -O2 -Wall  
-mtune=core2 -c one_sided_noncrossing_probability_n2.cc -o 
one_sided_noncrossing_probability_n2.o

d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -I"D:/RCompile/recent/R/include" 
-DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include 
-I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   
-I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -pedantic -O2 -Wall  
-mtune=core2 -c one_sided_noncrossing_probability_n2logn.cc -o 
one_sided_noncrossing_probability_n2logn.o

d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -I"D:/RCompile/recent/R/include" 
-DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include 
-I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   
-I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -pedantic -O2 -Wall  
-mtune=core2 -c poisson_pmf.cc -o poisson_pmf.o

d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -I"D:/RCompile/recent/R/include" 
-DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include 
-I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   
-I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -pedantic -O2 -Wall  
-mtune=core2 -c read_boundaries_file.cc -o read_boundaries_file.o

d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -I"D:/RCompile/recent/R/include" 
-DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include 
-I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   
-I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -pedantic -O2 -Wall  
-mtune=core2 -c string_utils.cc -o string_utils.o

d:/Compiler/gcc-4.9.3/mingw_32/bin/g++  -I"D:/RCompile/recent/R/include" 
-DNDEBUG -Id:/Rcompile/CRANpkg/extralibs215/local215/include 
-I"d:/RCompile/CRANpkg/lib/3.5/Rcpp/include"   
-I"d:/Compiler/gcc-4.9.3/local330/include"  -std=c++11   -pedantic -O2 -Wall  
-mtune=core2 -c two_sided_noncrossing_probability.cc -o 

Re: [R-pkg-devel] Errors in the pre-test after submitting the R package

[Dirk Eddelbuettel]

On 27 November 2017 at 21:24, Tan, Senren wrote:
| I have been developing an R package using Rcpp to call C++ functions that use 
the C subroutine library 'fftw3' that implements fast Fourier transform 
algorithm. Since I have the C library 'fftw3' installed on my laptop (running 
MacOS), when I checked my developed package using R CMD CHECK --as-cran, I 
could pass all the checks with no errors or warnings.
| 
| However, when I submitted the package to CRAN, during the pre-test, I 
encountered an error. I was wondering whether this error came from the absence 
of the 'fftw3' C library on the checking machine? Or maybe I have made some 
mistakes in the Makevars.win file?
| 
| I have done some search on how to use the external C library in R packages 
with Rcpp.
| 
| Here is what I have provided in the Makevars.win file:
| 
| PKG_CPPFLAGS = -I$(LIB_FFTW)/include
| CXX = g++
| PKG_CXXFLAGS = -std=c++11
| PKG_LIBS = -L$(LIB_FFTW)/lib -lfftw3
| 
| Could you please advise me on what to do?

Look at what other packages do. _Many_ packages deploy Rcpp to connect to
other external packages. That is how Rcpp started: to connect to QuantLib. I
also have packages connecting to the GSL, helped with one connecting to
nlopt, was involved with one connecting to PostgreSQL and probably several
more I now forget.  Jeroen has probably a dozen more too (xml2, curl,
poppler, v8, rmariadb, ... come to mind).  Look around some more. I also
think CRAN already _has_ packages interfacing the FFTW.  Plus, you can of
course connec to external libraries without using Rcpp. Lots of other
packages do that too.

Also read Writing R Extensions more carefully as the case is covered.  The
"bad" news is that you may need to learn to work with autoconf to create
configure, or re-invent it in shell how Jeroen does it, or rely on pkg-config
as I often, or ... do whatever it takes to _detect_ when fttw3 is not present.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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