[R] cygwin1.dll problems when installing packages from source

Duncan Murdoch murdoch.duncan at gmail.com
Sat Jun 3 12:57:03 CEST 2017


On 03/06/2017 6:31 AM, Vivek Sutradhara wrote:
> Hi all,
> I am having some problems in updating some packages from source. I start
> with :
> install.packages("Boom",lib="C:/RownLib",type="source")
>
> I get the following error message :

Do you have multiple copies of cygwin1.dll?

Duncan Murdoch

>
> * installing *source* package 'Boom' ...
> ** package 'Boom' successfully unpacked and MD5 sums checked
> ** libs
>
> *** arch - i386
> c:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R/R-34~1.0/include"
> -I. -I../inst/include -IBmath -Imath/cephes -DNO_BOOST_THREADS
> -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE -I"C:/RownLib/BH/include"
> -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -mtune=core2
> -c Models/Bart/Bart.cpp -o Models/Bart/Bart.o
>       0 [main] make (3304) c:\Rtools\bin\make.exe: *** fatal error -
> cygheap base mismatch detected - 0xD57408/0xC47408.
> This problem is probably due to using incompatible versions of the cygwin DLL.
> Search for cygwin1.dll using the Windows Start->Find/Search facility
> and delete all but the most recent version.  The most recent version *should*
> reside in x:\cygwin\bin, where 'x' is the drive on which you have
> installed the cygwin distribution.  Rebooting is also suggested if you
> are unable to find another cygwin DLL.
>       0 [main] make 9868 fork: child -1 - forked process 3304 died
> unexpectedly, retry 0, exit code 0xC0000142, errno 11
> make: vfork: Resource temporarily unavailable
> c:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R/R-34~1.0/include"
> -I. -I../inst/include -IBmath -Imath/cephes -DNO_BOOST_THREADS
> -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE -I"C:/RownLib/BH/include"
> -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -mtune=core2
> -c Models/Bart/GaussianBartModel.cpp -o
> Models/Bart/GaussianBartModel.o
>       0 [main] make (5256) c:\Rtools\bin\make.exe: *** fatal error -
> cygheap base mismatch detected - 0xD57408/0xEB7408.
> This problem is probably due to using incompatible versions of the cygwin DLL.
> Search for cygwin1.dll using the Windows Start->Find/Search facility
> and delete all but the most recent version.  The most recent version *should*
> reside in x:\cygwin\bin, where 'x' is the drive on which you have
> installed the cygwin distribution.  Rebooting is also suggested if you
> are unable to find another cygwin DLL.
>   31956 [main] make 9868 fork: child -1 - forked process 5256 died
> unexpectedly, retry 0, exit code 0xC0000142, errno 11
> make: vfork: Resource temporarily unavailable
> c:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R/R-34~1.0/include"
> -I. -I../inst/include -IBmath -Imath/cephes -DNO_BOOST_THREADS
> -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE -I"C:/RownLib/BH/include"
> -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -mtune=core2
> -c Models/Bart/GaussianLinearBartModel.cpp -o
> Models/Bart/GaussianLinearBartModel.o
>       0 [main] make (2308) c:\Rtools\bin\make.exe: *** fatal error -
> cygheap base mismatch detected - 0xD57408/0xDB7408.
> This problem is probably due to using incompatible versions of the cygwin DLL.
> Search for cygwin1.dll using the Windows Start->Find/Search facility
> and delete all but the most recent version.  The most recent version *should*
> reside in x:\cygwin\bin, where 'x' is the drive on which you have
> installed the cygwin distribution.  Rebooting is also suggested if you
> are unable to find another cygwin DLL.
>   65040 [main] make 9868 fork: child -1 - forked process 2308 died
> unexpectedly, retry 0, exit code 0xC0000142, errno 11
> make: vfork: Resource temporarily unavailable
> c:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/R/R-34~1.0/include"
> -I. -I../inst/include -IBmath -Imath/cephes -DNO_BOOST_THREADS
> -DNO_BOOST_FILESYSTEM -DADD_ -DRLANGUAGE -I"C:/RownLib/BH/include"
> -I"d:/Compiler/gcc-4.9.3/local330/include"     -O2 -Wall  -mtune=core2
> -c Models/Bart/LogitBartModel.cpp -o Models/Bart/LogitBartModel.o
>       0 [main] sh (1836) C:\Rtools\bin\sh.exe: *** fatal error -
> cygheap base mismatch detected - 0xD57408/0xDD7408.
> This problem is probably due to using incompatible versions of the cygwin DLL.
> Search for cygwin1.dll using the Windows Start->Find/Search facility
> and delete all but the most recent version.  The most recent version *should*
> reside in x:\cygwin\bin, where 'x' is the drive on which you have
> installed the cygwin distribution.  Rebooting is also suggested if you
> are unable to find another cygwin DLL.
> make: *** [Models/Bart/LogitBartModel.o] Error 127
> Warning: running command 'make -f "Makevars" -f
> "C:/R/R-34~1.0/etc/i386/Makeconf" -f
> "C:/R/R-34~1.0/share/make/winshlib.mk" -f
> "C:/Users/john/Documents/.R/Makevars" CXX='$(CXX11) $(CXX11STD)'
> CXXFLAGS='$(CXX11FLAGS)' CXXPICFLAGS='$(CXX11PICFLAGS)'
> SHLIB_LDFLAGS='$(SHLIB_CXX11LDFLAGS)' SHLIB_LD='$(SHLIB_CXX11LD)'
> SHLIB="Boom.dll" ' had status 2
> ERROR: compilation failed for package 'Boom'
> * removing 'C:/RownLib/Boom'
> * restoring previous 'C:/RownLib/Boom'
> Warning in install.packages :
>   running command '"C:/R/R-34~1.0/bin/x64/R" CMD INSTALL -l
> "C:\RownLib" C:\TMP\Rtmpegxnel/downloaded_packages/Boom_0.7.tar.gz'
> had status 1
> Warning in install.packages :
>   installation of package ‘Boom’ had non-zero exit status
>
>
>> sessionInfo()R version 3.4.0 (2017-04-21)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows >= 8 x64 (build 9200)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=Swedish_Sweden.1252  LC_CTYPE=Swedish_Sweden.1252
> LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C
> [5] LC_TIME=Swedish_Sweden.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
>  [1] shiny_1.0.3     compiler_3.4.0  R6_2.2.1        htmltools_0.3.6
> tools_3.4.0     withr_1.0.2     Rcpp_0.12.11    memoise_1.1.0
>  [9] git2r_0.18.0    digest_0.6.12   xtable_1.8-2    httpuv_1.3.3
> mime_0.5        ghit_0.2.17     devtools_1.13.2
>
> On checking, I have confirmed that the only location of
> cygwin1.dll is :
> C:\Rtools\bin
>
> I have not had any similiar problems before prior R3.4. The only new
> installation that I have done recently is python with
> Anaconda2. But I can't see any cygwin1.dll there. I wonder what
> the problem is. I will appreciate any help that I can get.
>
> Thanks,
>
> Vivek
>
> 	[[alternative HTML version deleted]]
>
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