############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/IRanges_2.28.0.tar.gz && rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IRanges.buildbin-libdir IRanges_2.28.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL IRanges_2.28.0.zip && rm IRanges_2.28.0.tar.gz IRanges_2.28.0.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 72 257k 72 187k 0 0 384k 0 --:--:-- --:--:-- --:--:-- 383k 100 257k 100 257k 0 0 457k 0 --:--:-- --:--:-- --:--:-- 457k install for i386 * installing *source* package 'IRanges' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CompressedList_class.c -o CompressedList_class.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Grouping_class.c -o Grouping_class.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IPosRanges_comparison.c -o IPosRanges_comparison.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_class.c -o IRanges_class.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_constructor.c -o IRanges_constructor.o IRanges_constructor.c: In function 'solve_range': IRanges_constructor.c:43:22: warning: unknown conversion type character 'l' in format [-Wformat=] "the 'width' (%lld) inferred from the " ^ IRanges_constructor.c:43:6: warning: too many arguments for format [-Wformat-extra-args] "the 'width' (%lld) inferred from the " ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IRanges_constructor.c:66:22: warning: unknown conversion type character 'l' in format [-Wformat=] "the 'start' (%lld) inferred from the " ^ IRanges_constructor.c:66:6: warning: too many arguments for format [-Wformat-extra-args] "the 'start' (%lld) inferred from the " ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IRanges_constructor.c:86:20: warning: unknown conversion type character 'l' in format [-Wformat=] "the 'end' (%lld) inferred from the " ^ IRanges_constructor.c:86:6: warning: too many arguments for format [-Wformat-extra-args] "the 'end' (%lld) inferred from the " ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IRanges_constructor.c:98:5: warning: unknown conversion type character 'l' in format [-Wformat=] "the supplied 'width' (%d) doesn't match " ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IRanges_constructor.c:100:27: note: format string is defined here "'start' and 'end' (%lld)", width, tmp); ^ IRanges_constructor.c:98:5: warning: too many arguments for format [-Wformat-extra-args] "the supplied 'width' (%d) doesn't match " ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c NCList.c -o NCList.o NCList.c:1173:13: warning: 'NCList_get_y_overlaps_rec' defined but not used [-Wunused-function] static void NCList_get_y_overlaps_rec(const NCList *x_nclist, ^~~~~~~~~~~~~~~~~~~~~~~~~ NCList.c:202:22: warning: 'next_top_down' defined but not used [-Wunused-function] static const NCList *next_top_down(const NCList *nclist) ^~~~~~~~~~~~~ NCList.c: In function 'C_print_NCListAsINTSXP': NCList.c:674:23: warning: '%d' directive writing between 1 and 11 bytes into a region of size 8 [-Wformat-overflow=] sprintf(format, "%c0%d%c", '%', max_digits, 'd'); ^~ NCList.c:674:19: note: directive argument in the range [-2147483647, 2147483647] sprintf(format, "%c0%d%c", '%', max_digits, 'd'); ^~~~~~~~~ NCList.c:674:3: note: 'sprintf' output between 5 and 15 bytes into a destination of size 10 sprintf(format, "%c0%d%c", '%', max_digits, 'd'); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NCList.c: In function 'C_find_overlaps_in_groups_NCList': NCList.c:1546:7: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized] SEXP ans; ^~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_IRanges.c -o R_init_IRanges.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Ranges_class.c -o Ranges_class.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RleViews_utils.c -o RleViews_utils.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/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/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c coverage_methods.c -o coverage_methods.o coverage_methods.c: In function 'compute_coverage_from_IRanges_holder': coverage_methods.c:579:28: warning: 'x_end' may be used uninitialized in this function [-Wmaybe-uninitialized] if (*out_ranges_are_tiles && x_end != cvg_len) ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ coverage_methods.c:495:21: note: 'x_end' was declared here i, j, x_start, x_end, shift_elt, tmp; ^~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c extractListFragments.c -o extractListFragments.o extractListFragments.c: In function 'C_find_partition_overlaps': extractListFragments.c:66:5: warning: 'split_partitions_buf' may be used uninitialized in this function [-Wmaybe-uninitialized] IntAE_insert_at(split_partitions_buf, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IntAE_get_nelt(split_partitions_buf), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ q_prev_end); ~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c inter_range_methods.c -o inter_range_methods.o C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o IRanges.dll tmp.def CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'drop' from package 'base' in package 'IRanges' Creating a generic function for 'runmed' from package 'stats' in package 'IRanges' Creating a generic function for 'chartr' from package 'base' in package 'IRanges' Creating a generic function for 'toupper' from package 'base' in package 'IRanges' Creating a generic function for 'tolower' from package 'base' in package 'IRanges' Creating a generic function for 'sub' from package 'base' in package 'IRanges' Creating a generic function for 'gsub' from package 'base' in package 'IRanges' Creating a generic function for 'startsWith' from package 'base' in package 'IRanges' Creating a generic function for 'endsWith' from package 'base' in package 'IRanges' Creating a generic function for 'smoothEnds' from package 'stats' in package 'IRanges' Creating a new generic function for 'windows' in package 'IRanges' ** help *** installing help indices converting help for package 'IRanges' finding HTML links ... done AtomicList-class html finding level-2 HTML links ... done AtomicList-utils html CompressedHitsList-class html CompressedList-class html DataFrameList-class html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/help/ROWNAMES+2CDataFrameList-method.html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/help/nrow+2CDataFrameList-method.html Grouping-class html Hits-class-leftovers html IPos-class html IPosRanges-class html IPosRanges-comparison html IRanges-class html IRanges-constructor html IRanges-internals html IRanges-utils html IRangesList-class html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/help/coerce+2CList+2CCompressedIRangesList-method.html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/help/coerce+2CList+2CSimpleIRangesList-method.html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/help/coerce+2CList+2CIRangesList-method.html IntegerRanges-class html IntegerRangesList-class html MaskCollection-class html NCList-class html RangedSelection-class html Rle-class-leftovers html RleViews-class html RleViewsList-class html Vector-class-leftovers html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/help/window+3C-+2Cvector-method.html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/help/window+3C-.vector.html Views-class html ViewsList-class html coverage-methods html extractList html extractListFragments html findOverlaps-methods html inter-range-methods html intra-range-methods html Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpmMy0qG/R.INSTALL170021ce350f/IRanges/man/intra-range-methods.Rd:94: missing link 'RangesList' Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpmMy0qG/R.INSTALL170021ce350f/IRanges/man/intra-range-methods.Rd:102: missing link 'RangesList' Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpmMy0qG/R.INSTALL170021ce350f/IRanges/man/intra-range-methods.Rd:123: missing link 'RangesList' Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpmMy0qG/R.INSTALL170021ce350f/IRanges/man/intra-range-methods.Rd:136: missing link 'RangesList' Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpmMy0qG/R.INSTALL170021ce350f/IRanges/man/intra-range-methods.Rd:146: missing link 'RangesList' Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpmMy0qG/R.INSTALL170021ce350f/IRanges/man/intra-range-methods.Rd:160: missing link 'RangesList' Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpmMy0qG/R.INSTALL170021ce350f/IRanges/man/intra-range-methods.Rd:188: missing link 'RangesList' Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpmMy0qG/R.INSTALL170021ce350f/IRanges/man/intra-range-methods.Rd:297: missing link 'RangesList' multisplit html nearest-methods html range-squeezers html read.Mask html reverse-methods html seqapply html setops-methods html slice-methods html view-summarization-methods html ** building package indices ** installing vignettes ** 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 'IRanges' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CompressedList_class.c -o CompressedList_class.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Grouping_class.c -o Grouping_class.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IPosRanges_comparison.c -o IPosRanges_comparison.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_class.c -o IRanges_class.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_constructor.c -o IRanges_constructor.o IRanges_constructor.c: In function 'solve_range': IRanges_constructor.c:43:22: warning: unknown conversion type character 'l' in format [-Wformat=] "the 'width' (%lld) inferred from the " ^ IRanges_constructor.c:43:6: warning: too many arguments for format [-Wformat-extra-args] "the 'width' (%lld) inferred from the " ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IRanges_constructor.c:66:22: warning: unknown conversion type character 'l' in format [-Wformat=] "the 'start' (%lld) inferred from the " ^ IRanges_constructor.c:66:6: warning: too many arguments for format [-Wformat-extra-args] "the 'start' (%lld) inferred from the " ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IRanges_constructor.c:86:20: warning: unknown conversion type character 'l' in format [-Wformat=] "the 'end' (%lld) inferred from the " ^ IRanges_constructor.c:86:6: warning: too many arguments for format [-Wformat-extra-args] "the 'end' (%lld) inferred from the " ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IRanges_constructor.c:98:5: warning: unknown conversion type character 'l' in format [-Wformat=] "the supplied 'width' (%d) doesn't match " ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IRanges_constructor.c:100:27: note: format string is defined here "'start' and 'end' (%lld)", width, tmp); ^ IRanges_constructor.c:98:5: warning: too many arguments for format [-Wformat-extra-args] "the supplied 'width' (%d) doesn't match " ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c NCList.c -o NCList.o NCList.c:1173:13: warning: 'NCList_get_y_overlaps_rec' defined but not used [-Wunused-function] static void NCList_get_y_overlaps_rec(const NCList *x_nclist, ^~~~~~~~~~~~~~~~~~~~~~~~~ NCList.c:202:22: warning: 'next_top_down' defined but not used [-Wunused-function] static const NCList *next_top_down(const NCList *nclist) ^~~~~~~~~~~~~ NCList.c: In function 'C_print_NCListAsINTSXP': NCList.c:674:23: warning: '%d' directive writing between 1 and 11 bytes into a region of size 8 [-Wformat-overflow=] sprintf(format, "%c0%d%c", '%', max_digits, 'd'); ^~ NCList.c:674:19: note: directive argument in the range [-2147483647, 2147483647] sprintf(format, "%c0%d%c", '%', max_digits, 'd'); ^~~~~~~~~ NCList.c:674:3: note: 'sprintf' output between 5 and 15 bytes into a destination of size 10 sprintf(format, "%c0%d%c", '%', max_digits, 'd'); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_IRanges.c -o R_init_IRanges.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Ranges_class.c -o Ranges_class.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RleViews_utils.c -o RleViews_utils.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/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/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c coverage_methods.c -o coverage_methods.o coverage_methods.c: In function 'compute_coverage_from_IRanges_holder': coverage_methods.c:579:28: warning: 'x_end' may be used uninitialized in this function [-Wmaybe-uninitialized] if (*out_ranges_are_tiles && x_end != cvg_len) ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ coverage_methods.c:495:21: note: 'x_end' was declared here i, j, x_start, x_end, shift_elt, tmp; ^~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c extractListFragments.c -o extractListFragments.o extractListFragments.c: In function 'C_find_partition_overlaps': extractListFragments.c:66:5: warning: 'split_partitions_buf' may be used uninitialized in this function [-Wmaybe-uninitialized] IntAE_insert_at(split_partitions_buf, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IntAE_get_nelt(split_partitions_buf), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ q_prev_end); ~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/S4Vectors/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c inter_range_methods.c -o inter_range_methods.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o IRanges.dll tmp.def CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'IRanges' as IRanges_2.28.0.zip * DONE (IRanges) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'IRanges' successfully unpacked and MD5 sums checked