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

[Vivek Sutradhara]

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 :

* 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

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