Package: XVector

Version: 0.24.0

Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/XVector_0.24.0.tar.gz && rm -rf XVector.buildbin-libdir && mkdir XVector.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=XVector.buildbin-libdir XVector_0.24.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL XVector_0.24.0.zip && rm XVector_0.24.0.tar.gz XVector_0.24.0.zip

StartedAt: 2019-10-15 19:24:03 -0400 (Tue, 15 Oct 2019)

EndedAt: 2019-10-15 19:25:33 -0400 (Tue, 15 Oct 2019)

EllapsedTime: 90.0 seconds

RetCode: 0

Status:  OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/XVector_0.24.0.tar.gz && rm -rf XVector.buildbin-libdir && mkdir XVector.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=XVector.buildbin-libdir XVector_0.24.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL XVector_0.24.0.zip && rm XVector_0.24.0.tar.gz XVector_0.24.0.zip
###
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install for i386

* installing *source* package 'XVector' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c RDS_random_access.c -o RDS_random_access.o
RDS_random_access.c: In function 'RDS_read_character_vector':
RDS_random_access.c:305:2: warning: unknown conversion type character 't' in format [-Wformat=]
  PRINTIFVERBOSE2("object length: %td", ans_len);
  ^
RDS_random_access.c:305:2: warning: too many arguments for format [-Wformat-extra-args]
RDS_random_access.c: In function 'RDS_read_atomic_vector':
RDS_random_access.c:335:2: warning: unknown conversion type character 't' in format [-Wformat=]
  PRINTIFVERBOSE2("object length: %td", ans_len);
  ^
RDS_random_access.c:335:2: warning: too many arguments for format [-Wformat-extra-args]
RDS_random_access.c: In function 'RDS_read_list':
RDS_random_access.c:379:2: warning: unknown conversion type character 't' in format [-Wformat=]
  PRINTIFVERBOSE2("object length: %td", ans_len);
  ^
RDS_random_access.c:379:2: warning: too many arguments for format [-Wformat-extra-args]
RDS_random_access.c: In function 'RDS_extract_subarray':
RDS_random_access.c:796:18: warning: unused variable 'ans' [-Wunused-variable]
  SEXP subscript, ans;
                  ^
RDS_random_access.c:793:11: warning: variable 'x_type' set but not used [-Wunused-but-set-variable]
  SEXPTYPE x_type;
           ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_XVector.c -o R_init_XVector.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c SharedDouble_class.c -o SharedDouble_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c SharedInteger_class.c -o SharedInteger_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c SharedRaw_class.c -o SharedRaw_class.o
SharedRaw_class.c: In function 'SharedRaw_read_complexes_from_subscript':
SharedRaw_class.c:396:13: warning: variable 'src_tag' set but not used [-Wunused-but-set-variable]
  SEXP dest, src_tag;
             ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c SharedVector_class.c -o SharedVector_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c XDouble_class.c -o XDouble_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c XInteger_class.c -o XInteger_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c XRawList_comparison.c -o XRawList_comparison.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c XRaw_class.c -o XRaw_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c XVectorList_class.c -o XVectorList_class.o
XVectorList_class.c: In function '_new_XRawList_from_CharAEAE':
XVectorList_class.c:459:3: warning: 'lkup_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
   _Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1,
   ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c XVector_class.c -o XVector_class.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c io_utils.c -o io_utils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c slice_methods.c -o slice_methods.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c vector_copy.c -o vector_copy.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -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:219:31: warning: 'cur_min' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (which_min == NA_INTEGER || x < cur_min) {
                               ^
view_summarization_methods.c: In function 'get_which_min_from_Doubles_holder':
view_summarization_methods.c:246:31: warning: 'cur_min' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (which_min == NA_INTEGER || x < cur_min) {
                               ^
view_summarization_methods.c: In function 'get_which_max_from_Ints_holder':
view_summarization_methods.c:269:31: warning: 'cur_max' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (which_max == NA_INTEGER || x > cur_max) {
                               ^
view_summarization_methods.c: In function 'get_which_max_from_Doubles_holder':
view_summarization_methods.c:296:31: warning: 'cur_max' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (which_max == NA_INTEGER || x > cur_max) {
                               ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o XVector.dll tmp.def IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XDouble_class.o XInteger_class.o XRawList_comparison.o XRaw_class.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/XVector.buildbin-libdir/00LOCK-XVector/00new/XVector/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'XVector'
    finding HTML links ... done
    OnDiskRaw-class                         html  
    XDoubleViews-class                      html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwzuV4J/R.INSTALL13dc32e15b7/XVector/man/XDoubleViews-class.Rd:37: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwzuV4J/R.INSTALL13dc32e15b7/XVector/man/XDoubleViews-class.Rd:38: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwzuV4J/R.INSTALL13dc32e15b7/XVector/man/XDoubleViews-class.Rd:39: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
    XIntegerViews-class                     html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwzuV4J/R.INSTALL13dc32e15b7/XVector/man/XIntegerViews-class.Rd:37: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwzuV4J/R.INSTALL13dc32e15b7/XVector/man/XIntegerViews-class.Rd:38: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwzuV4J/R.INSTALL13dc32e15b7/XVector/man/XIntegerViews-class.Rd:39: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
    XRawList-class                          html  
    XRawList-comparison                     html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwzuV4J/R.INSTALL13dc32e15b7/XVector/man/XRawList-comparison.Rd:106: missing file link 'Ranges-comparison'
    XVector-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwzuV4J/R.INSTALL13dc32e15b7/XVector/man/XVector-class.Rd:58: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwzuV4J/R.INSTALL13dc32e15b7/XVector/man/XVector-class.Rd:75: file link 'XString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwzuV4J/R.INSTALL13dc32e15b7/XVector/man/XVector-class.Rd:134: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic
    XVector-internals                       html  
    XVectorList-class                       html  
    compact-methods                         html  
    intra-range-methods                     html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwzuV4J/R.INSTALL13dc32e15b7/XVector/man/intra-range-methods.Rd:19: file link 'narrow' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwzuV4J/R.INSTALL13dc32e15b7/XVector/man/intra-range-methods.Rd:19: file link 'threebands' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwzuV4J/R.INSTALL13dc32e15b7/XVector/man/intra-range-methods.Rd:38: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwzuV4J/R.INSTALL13dc32e15b7/XVector/man/intra-range-methods.Rd:65: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic
    reverse-methods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwzuV4J/R.INSTALL13dc32e15b7/XVector/man/reverse-methods.Rd:48: file link 'endoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
    slice-methods                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwzuV4J/R.INSTALL13dc32e15b7/XVector/man/slice-methods.Rd:14: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpwzuV4J/R.INSTALL13dc32e15b7/XVector/man/slice-methods.Rd:53: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
    updateObject-methods                    html  
    view-summarization-methods              html  
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'XVector' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c RDS_random_access.c -o RDS_random_access.o
RDS_random_access.c: In function 'RDS_read_character_vector':
RDS_random_access.c:305:2: warning: unknown conversion type character 't' in format [-Wformat=]
  PRINTIFVERBOSE2("object length: %td", ans_len);
  ^
RDS_random_access.c:305:2: warning: too many arguments for format [-Wformat-extra-args]
RDS_random_access.c: In function 'RDS_read_atomic_vector':
RDS_random_access.c:335:2: warning: unknown conversion type character 't' in format [-Wformat=]
  PRINTIFVERBOSE2("object length: %td", ans_len);
  ^
RDS_random_access.c:335:2: warning: too many arguments for format [-Wformat-extra-args]
RDS_random_access.c: In function 'RDS_read_list':
RDS_random_access.c:379:2: warning: unknown conversion type character 't' in format [-Wformat=]
  PRINTIFVERBOSE2("object length: %td", ans_len);
  ^
RDS_random_access.c:379:2: warning: too many arguments for format [-Wformat-extra-args]
RDS_random_access.c: In function 'RDS_extract_subarray':
RDS_random_access.c:796:18: warning: unused variable 'ans' [-Wunused-variable]
  SEXP subscript, ans;
                  ^
RDS_random_access.c:793:11: warning: variable 'x_type' set but not used [-Wunused-but-set-variable]
  SEXPTYPE x_type;
           ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_XVector.c -o R_init_XVector.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c SharedDouble_class.c -o SharedDouble_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c SharedInteger_class.c -o SharedInteger_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c SharedRaw_class.c -o SharedRaw_class.o
SharedRaw_class.c: In function 'SharedRaw_read_complexes_from_subscript':
SharedRaw_class.c:396:13: warning: variable 'src_tag' set but not used [-Wunused-but-set-variable]
  SEXP dest, src_tag;
             ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c SharedVector_class.c -o SharedVector_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c XDouble_class.c -o XDouble_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c XInteger_class.c -o XInteger_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c XRawList_comparison.c -o XRawList_comparison.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c XRaw_class.c -o XRaw_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c XVectorList_class.c -o XVectorList_class.o
XVectorList_class.c: In function '_new_XRawList_from_CharAEAE':
XVectorList_class.c:459:3: warning: 'lkup_length' may be used uninitialized in this function [-Wmaybe-uninitialized]
   _Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1,
   ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c XVector_class.c -o XVector_class.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c io_utils.c -o io_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c slice_methods.c -o slice_methods.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c vector_copy.c -o vector_copy.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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:219:31: warning: 'cur_min' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (which_min == NA_INTEGER || x < cur_min) {
                               ^
view_summarization_methods.c: In function 'get_which_min_from_Doubles_holder':
view_summarization_methods.c:246:31: warning: 'cur_min' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (which_min == NA_INTEGER || x < cur_min) {
                               ^
view_summarization_methods.c: In function 'get_which_max_from_Ints_holder':
view_summarization_methods.c:269:31: warning: 'cur_max' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (which_max == NA_INTEGER || x > cur_max) {
                               ^
view_summarization_methods.c: In function 'get_which_max_from_Doubles_holder':
view_summarization_methods.c:296:31: warning: 'cur_max' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (which_max == NA_INTEGER || x > cur_max) {
                               ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o XVector.dll tmp.def IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XDouble_class.o XInteger_class.o XRawList_comparison.o XRaw_class.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/XVector.buildbin-libdir/XVector/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'XVector' as XVector_0.24.0.zip
* DONE (XVector)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'XVector' successfully unpacked and MD5 sums checked