BioC 3.3: INSTALL report for XVector on windows2.bioconductor.org

Package: XVector

Version: 0.11.0

Command: C:\cygwin64\bin\curl.exe -O http://linux2.bioconductor.org/BBS/3.3/bioc/src/contrib/XVector_0.11.0.tar.gz && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch XVector_0.11.0.tar.gz && rm XVector_0.11.0.tar.gz

StartedAt: 2015-10-26 21:05:55 -0400 (Mon, 26 Oct 2015)

EndedAt: 2015-10-26 21:06:17 -0400 (Mon, 26 Oct 2015)

EllapsedTime: 22.3 seconds

RetCode: 0

Status:  OK

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### Running command:
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###   C:\cygwin64\bin\curl.exe -O http://linux2.bioconductor.org/BBS/3.3/bioc/src/contrib/XVector_0.11.0.tar.gz && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch XVector_0.11.0.tar.gz && rm XVector_0.11.0.tar.gz
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install for i386

* installing to library 'c:/biocbld/bbs-3.3-bioc/R/library'
* installing *source* package 'XVector' ...
** libs
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_XVector.c -o R_init_XVector.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c SharedDouble_class.c -o SharedDouble_class.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c SharedInteger_class.c -o SharedInteger_class.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c SharedRaw_class.c -o SharedRaw_class.o
SharedRaw_class.c: In function 'SharedRaw_read_complexes_from_subscript':
SharedRaw_class.c:364:13: warning: variable 'src_tag' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c SharedVector_class.c -o SharedVector_class.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c XRawList_comparison.c -o XRawList_comparison.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c XVectorList_class.c -o XVectorList_class.o
XVectorList_class.c: In function '_new_XRawList_from_CharAEAE':
XVectorList_class.c:466:33: warning: 'lkup_length' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c XVector_class.c -o XVector_class.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c io_utils.c -o io_utils.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c slice_methods.c -o slice_methods.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c vector_copy.c -o vector_copy.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c view_summarization_methods.c -o view_summarization_methods.o
view_summarization_methods.c: In function 'get_which_min_from_Ints_holder':
view_summarization_methods.c:219:36: warning: 'cur_min' may be used uninitialized in this function [-Wuninitialized]
view_summarization_methods.c: In function 'get_which_min_from_Doubles_holder':
view_summarization_methods.c:246:36: warning: 'cur_min' may be used uninitialized in this function [-Wuninitialized]
view_summarization_methods.c: In function 'get_which_max_from_Ints_holder':
view_summarization_methods.c:269:36: warning: 'cur_max' may be used uninitialized in this function [-Wuninitialized]
view_summarization_methods.c: In function 'get_which_max_from_Doubles_holder':
view_summarization_methods.c:296:36: warning: 'cur_max' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -shared -s -static-libgcc -o XVector.dll tmp.def IRanges_stubs.o Ocopy_byteblocks.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XRawList_comparison.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -LC:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -Lc:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to c:/biocbld/bbs-3.3-bioc/R/library/XVector/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'toString' from package 'base' in package 'XVector'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

install for x64

* installing to library 'c:/biocbld/bbs-3.3-bioc/R/library'
* installing *source* package 'XVector' ...
** libs
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_XVector.c -o R_init_XVector.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c SharedDouble_class.c -o SharedDouble_class.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c SharedInteger_class.c -o SharedInteger_class.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c SharedRaw_class.c -o SharedRaw_class.o
SharedRaw_class.c: In function 'SharedRaw_read_complexes_from_subscript':
SharedRaw_class.c:364:13: warning: variable 'src_tag' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c SharedVector_class.c -o SharedVector_class.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c XRawList_comparison.c -o XRawList_comparison.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c XVectorList_class.c -o XVectorList_class.o
XVectorList_class.c: In function '_new_XRawList_from_CharAEAE':
XVectorList_class.c:466:33: warning: 'lkup_length' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c XVector_class.c -o XVector_class.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c io_utils.c -o io_utils.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c slice_methods.c -o slice_methods.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c vector_copy.c -o vector_copy.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"c:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c view_summarization_methods.c -o view_summarization_methods.o
view_summarization_methods.c: In function 'get_which_min_from_Ints_holder':
view_summarization_methods.c:219:36: warning: 'cur_min' may be used uninitialized in this function [-Wuninitialized]
view_summarization_methods.c: In function 'get_which_min_from_Doubles_holder':
view_summarization_methods.c:246:36: warning: 'cur_min' may be used uninitialized in this function [-Wuninitialized]
view_summarization_methods.c: In function 'get_which_max_from_Ints_holder':
view_summarization_methods.c:269:36: warning: 'cur_max' may be used uninitialized in this function [-Wuninitialized]
view_summarization_methods.c: In function 'get_which_max_from_Doubles_holder':
view_summarization_methods.c:296:36: warning: 'cur_max' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -shared -s -static-libgcc -o XVector.dll tmp.def IRanges_stubs.o Ocopy_byteblocks.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XRawList_comparison.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -LC:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -Lc:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to c:/biocbld/bbs-3.3-bioc/R/library/XVector/libs/x64
** testing if installed package can be loaded
* DONE (XVector)