############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/XVector_0.32.0.tar.gz && rm -rf XVector.buildbin-libdir && mkdir XVector.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=XVector.buildbin-libdir XVector_0.32.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL XVector_0.32.0.zip && rm XVector_0.32.0.tar.gz XVector_0.32.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 68968 100 68968 0 0 440k 0 --:--:-- --:--:-- --:--:-- 443k install for i386 * installing *source* package 'XVector' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RDS_random_access.c -o RDS_random_access.o RDS_random_access.c: In function 'RDS_read_character_vector': RDS_random_access.c:305:18: warning: unknown conversion type character 't' in format [-Wformat=] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c:305:18: warning: too many arguments for format [-Wformat-extra-args] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c:305:18: warning: unknown conversion type character 't' in format [-Wformat=] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c:305:18: warning: too many arguments for format [-Wformat-extra-args] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c: In function 'RDS_read_atomic_vector': RDS_random_access.c:335:18: warning: unknown conversion type character 't' in format [-Wformat=] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c:335:18: warning: too many arguments for format [-Wformat-extra-args] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c:335:18: warning: unknown conversion type character 't' in format [-Wformat=] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c:335:18: warning: too many arguments for format [-Wformat-extra-args] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c: In function 'RDS_read_list': RDS_random_access.c:379:18: warning: unknown conversion type character 't' in format [-Wformat=] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c:379:18: warning: too many arguments for format [-Wformat-extra-args] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c:379:18: warning: unknown conversion type character 't' in format [-Wformat=] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c:379:18: warning: too many arguments for format [-Wformat-extra-args] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ 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:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_XVector.c -o R_init_XVector.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SharedDouble_class.c -o SharedDouble_class.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SharedInteger_class.c -o SharedInteger_class.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SharedVector_class.c -o SharedVector_class.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XDouble_class.c -o XDouble_class.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XInteger_class.c -o XInteger_class.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XRawList_comparison.c -o XRawList_comparison.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XRaw_class.c -o XRaw_class.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (char *) dest.ptr, dest.length, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src->elts, CharAE_get_nelt(src), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ lkup0, lkup_length); ~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_class.c -o XVector_class.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io_utils.c -o io_utils.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c slice_methods.c -o slice_methods.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vector_copy.c -o vector_copy.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/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-3.13-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-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 XIntegerViews-class html XRawList-class html XRawList-comparison html XVector-class html XVector-internals html XVectorList-class html compact-methods html intra-range-methods html reverse-methods html slice-methods html 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:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RDS_random_access.c -o RDS_random_access.o RDS_random_access.c: In function 'RDS_read_character_vector': RDS_random_access.c:305:18: warning: unknown conversion type character 't' in format [-Wformat=] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c:305:18: warning: too many arguments for format [-Wformat-extra-args] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c:305:18: warning: unknown conversion type character 't' in format [-Wformat=] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c:305:18: warning: too many arguments for format [-Wformat-extra-args] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c: In function 'RDS_read_atomic_vector': RDS_random_access.c:335:18: warning: unknown conversion type character 't' in format [-Wformat=] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c:335:18: warning: too many arguments for format [-Wformat-extra-args] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c:335:18: warning: unknown conversion type character 't' in format [-Wformat=] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c:335:18: warning: too many arguments for format [-Wformat-extra-args] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c: In function 'RDS_read_list': RDS_random_access.c:379:18: warning: unknown conversion type character 't' in format [-Wformat=] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c:379:18: warning: too many arguments for format [-Wformat-extra-args] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c:379:18: warning: unknown conversion type character 't' in format [-Wformat=] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ RDS_random_access.c:379:18: warning: too many arguments for format [-Wformat-extra-args] PRINTIFVERBOSE2("object length: %td", ans_len); ^~~~~~~~~~~~~~~~~~~~ RDS_random_access.c:88:10: note: in definition of macro 'PRINTIFVERBOSE2' printf(format, value); \ ^~~~~~ 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:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_XVector.c -o R_init_XVector.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SharedDouble_class.c -o SharedDouble_class.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SharedInteger_class.c -o SharedInteger_class.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SharedVector_class.c -o SharedVector_class.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XDouble_class.c -o XDouble_class.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XInteger_class.c -o XInteger_class.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XRawList_comparison.c -o XRawList_comparison.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XRaw_class.c -o XRaw_class.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (char *) dest.ptr, dest.length, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src->elts, CharAE_get_nelt(src), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ lkup0, lkup_length); ~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_class.c -o XVector_class.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io_utils.c -o io_utils.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c slice_methods.c -o slice_methods.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c vector_copy.c -o vector_copy.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/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-3.13-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/XVector.buildbin-libdir/XVector/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'XVector' as XVector_0.32.0.zip * DONE (XVector) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'XVector' successfully unpacked and MD5 sums checked