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

Vivek Sutradhara viveksutra at gmail.com
Sat Jun 3 14:14:52 CEST 2017


Hi,
I have now re-installed Rtools. This has solved my problem.

Even previously, Rtools was the first on the path. However, thanks a lot
for this help. I can now move on.
Thanks,
Vivek

2017-06-03 13:09 GMT+02:00 Duncan Murdoch <murdoch.duncan at gmail.com>:

> 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_p
>> ackages/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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