##############################################################################
##############################################################################
###
### Running command:
###
### 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
###
##############################################################################
##############################################################################
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/RtmpgrlGxz/R.INSTALL7fe0322c3a4b/IRanges/man/intra-range-methods.Rd:94: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpgrlGxz/R.INSTALL7fe0322c3a4b/IRanges/man/intra-range-methods.Rd:102: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpgrlGxz/R.INSTALL7fe0322c3a4b/IRanges/man/intra-range-methods.Rd:123: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpgrlGxz/R.INSTALL7fe0322c3a4b/IRanges/man/intra-range-methods.Rd:136: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpgrlGxz/R.INSTALL7fe0322c3a4b/IRanges/man/intra-range-methods.Rd:146: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpgrlGxz/R.INSTALL7fe0322c3a4b/IRanges/man/intra-range-methods.Rd:160: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpgrlGxz/R.INSTALL7fe0322c3a4b/IRanges/man/intra-range-methods.Rd:188: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpgrlGxz/R.INSTALL7fe0322c3a4b/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)
