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

Duncan Murdoch murdoch.duncan at gmail.com
Sat Jun 3 13:09:43 CEST 2017


On 03/06/2017 7:00 AM, Vivek Sutradhara wrote:
> Hi,
> As far as I can see, no.
>
> On checking, I have confirmed that the only location of
> cygwin1.dll is :
> C:\Rtools\bin

I would re-install Rtools, and make sure C:\Rtools\bin appears first in 
your PATH.

Duncan Murdoch

>
> Thanks
> Vivek
>
> 2017-06-03 12:57 GMT+02:00 Duncan Murdoch <murdoch.duncan at gmail.com
> <mailto:murdoch.duncan at gmail.com>>:
>
>     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 <http://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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>
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