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### Running command:
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### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/IRanges_2.24.1.tar.gz && rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IRanges.buildbin-libdir IRanges_2.24.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL IRanges_2.24.1.zip && rm IRanges_2.24.1.tar.gz IRanges_2.24.1.zip
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% 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 255k 100 255k 0 0 11.2M 0 --:--:-- --:--:-- --:--:-- 11.8M
install for i386
* installing *source* package 'IRanges' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-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
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/AtomicList-class.Rd:307: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
AtomicList-utils html
CompressedHitsList-class html
CompressedList-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/CompressedList-class.Rd:38: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/CompressedList-class.Rd:39: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/CompressedList-class.Rd:44: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/CompressedList-class.Rd:49: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/CompressedList-class.Rd:50: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/CompressedList-class.Rd:60: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/CompressedList-class.Rd:66: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/CompressedList-class.Rd:81: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/CompressedList-class.Rd:84: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/CompressedList-class.Rd:87: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/CompressedList-class.Rd:89: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/CompressedList-class.Rd:95: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/CompressedList-class.Rd:100: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/CompressedList-class.Rd:105: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/CompressedList-class.Rd:110: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/CompressedList-class.Rd:118: file link 'classNameForDisplay' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/CompressedList-class.Rd:124: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/CompressedList-class.Rd:127: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
DataFrameList-class html
Grouping-class html
Hits-class-leftovers html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/Hits-class-leftovers.Rd:29: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/Hits-class-leftovers.Rd:58: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
IPos-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/IPos-class.Rd:124: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/IPos-class.Rd:194: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/IPos-class.Rd:211: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
IPosRanges-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/IPosRanges-class.Rd:200: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/IPosRanges-class.Rd:225: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/IPosRanges-class.Rd:225: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/IPosRanges-class.Rd:226: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/IPosRanges-class.Rd:226: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/IPosRanges-class.Rd:227: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
IPosRanges-comparison html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/IPosRanges-comparison.Rd:164: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
IRanges-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/IRanges-class.Rd:97: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/IRanges-class.Rd:120: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
IRanges-constructor html
IRanges-internals html
IRanges-utils html
IRangesList-class html
IntegerRanges-class html
IntegerRangesList-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/IntegerRangesList-class.Rd:76: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/IntegerRangesList-class.Rd:76: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/IntegerRangesList-class.Rd:77: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/IntegerRangesList-class.Rd:77: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
MaskCollection-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/MaskCollection-class.Rd:206: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
NCList-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/NCList-class.Rd:81: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/NCList-class.Rd:101: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/NCList-class.Rd:102: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/NCList-class.Rd:110: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/NCList-class.Rd:126: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/NCList-class.Rd:128: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/NCList-class.Rd:131: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
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RangedSelection-class html
Rle-class-leftovers html
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RleViews-class html
RleViewsList-class html
Vector-class-leftovers html
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Views-class html
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ViewsList-class html
coverage-methods html
extractList html
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Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/extractList.Rd:150: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
extractListFragments html
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Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/extractListFragments.Rd:79: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/extractListFragments.Rd:80: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/extractListFragments.Rd:87: file link 'relistToClass' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/extractListFragments.Rd:104: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/extractListFragments.Rd:104: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/extractListFragments.Rd:107: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
findOverlaps-methods html
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Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/findOverlaps-methods.Rd:58: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/findOverlaps-methods.Rd:58: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/findOverlaps-methods.Rd:169: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/findOverlaps-methods.Rd:177: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/findOverlaps-methods.Rd:189: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/findOverlaps-methods.Rd:189: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/findOverlaps-methods.Rd:247: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/findOverlaps-methods.Rd:247: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/findOverlaps-methods.Rd:255: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/findOverlaps-methods.Rd:256: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/findOverlaps-methods.Rd:287: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/findOverlaps-methods.Rd:287: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/findOverlaps-methods.Rd:291: file link 'findOverlaps,GenomicRanges,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/findOverlaps-methods.Rd:293: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/findOverlaps-methods.Rd:293: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
inter-range-methods html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/inter-range-methods.Rd:266: file link 'endoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
intra-range-methods html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/intra-range-methods.Rd:94: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/intra-range-methods.Rd:102: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/intra-range-methods.Rd:123: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/intra-range-methods.Rd:136: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/intra-range-methods.Rd:146: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/intra-range-methods.Rd:160: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/intra-range-methods.Rd:188: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/intra-range-methods.Rd:251: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/intra-range-methods.Rd:252: file link 'promoters,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/intra-range-methods.Rd:297: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/intra-range-methods.Rd:307: file link 'endoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
multisplit html
nearest-methods html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/nearest-methods.Rd:148: file link 'breakTies' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/nearest-methods.Rd:174: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/nearest-methods.Rd:175: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/nearest-methods.Rd:188: file link 'precede,GenomicRanges,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
range-squeezers html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:15: file link 'granges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:16: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:19: file link 'granges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:20: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:21: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:32: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:33: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:34: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:35: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:36: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:37: file link 'Pairs' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:63: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:64: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:77: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:93: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:96: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:97: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/range-squeezers.Rd:98: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
read.Mask html
reverse-methods html
seqapply html
setops-methods html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/setops-methods.Rd:91: file link 'Pairs' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/setops-methods.Rd:116: file link 'Pairs' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEr37md/R.INSTALL9e0126b571f/IRanges/man/setops-methods.Rd:165: file link 'mendoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IRanges' as IRanges_2.24.1.zip
* DONE (IRanges)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'IRanges' successfully unpacked and MD5 sums checked
