XVector 0.28.0
Hervé Pagès
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/XVector |
| Branch: RELEASE_3_11 |
| Last Commit: 8bda737 |
| Last Changed Date: 2020-04-27 14:34:32 -0400 (Mon, 27 Apr 2020) |
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | NA | |
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/XVector_0.28.0.tar.gz && rm -rf XVector.buildbin-libdir && mkdir XVector.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=XVector.buildbin-libdir XVector_0.28.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL XVector_0.28.0.zip && rm XVector_0.28.0.tar.gz XVector_0.28.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'XVector' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/XVector.buildbin-libdir/00LOCK-XVector/00new/XVector/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'XVector'
finding HTML links ... done
OnDiskRaw-class html
XDoubleViews-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpS8gmcn/R.INSTALL13ec28982bba/XVector/man/XDoubleViews-class.Rd:37: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpS8gmcn/R.INSTALL13ec28982bba/XVector/man/XDoubleViews-class.Rd:38: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpS8gmcn/R.INSTALL13ec28982bba/XVector/man/XDoubleViews-class.Rd:39: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
XIntegerViews-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpS8gmcn/R.INSTALL13ec28982bba/XVector/man/XIntegerViews-class.Rd:37: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpS8gmcn/R.INSTALL13ec28982bba/XVector/man/XIntegerViews-class.Rd:38: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpS8gmcn/R.INSTALL13ec28982bba/XVector/man/XIntegerViews-class.Rd:39: file link 'Views' in package 'IRanges' does not exist and so has been treated as a topic
XRawList-class html
XRawList-comparison html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpS8gmcn/R.INSTALL13ec28982bba/XVector/man/XRawList-comparison.Rd:106: missing file link 'Ranges-comparison'
XVector-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpS8gmcn/R.INSTALL13ec28982bba/XVector/man/XVector-class.Rd:58: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpS8gmcn/R.INSTALL13ec28982bba/XVector/man/XVector-class.Rd:75: file link 'XString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpS8gmcn/R.INSTALL13ec28982bba/XVector/man/XVector-class.Rd:134: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic
XVector-internals html
XVectorList-class html
compact-methods html
intra-range-methods html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpS8gmcn/R.INSTALL13ec28982bba/XVector/man/intra-range-methods.Rd:19: file link 'narrow' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpS8gmcn/R.INSTALL13ec28982bba/XVector/man/intra-range-methods.Rd:19: file link 'threebands' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpS8gmcn/R.INSTALL13ec28982bba/XVector/man/intra-range-methods.Rd:38: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpS8gmcn/R.INSTALL13ec28982bba/XVector/man/intra-range-methods.Rd:65: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic
reverse-methods html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpS8gmcn/R.INSTALL13ec28982bba/XVector/man/reverse-methods.Rd:48: file link 'endoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
slice-methods html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpS8gmcn/R.INSTALL13ec28982bba/XVector/man/slice-methods.Rd:14: file link 'slice' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpS8gmcn/R.INSTALL13ec28982bba/XVector/man/slice-methods.Rd:53: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
updateObject-methods html
view-summarization-methods html
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'XVector' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/XVector.buildbin-libdir/XVector/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'XVector' as XVector_0.28.0.zip
* DONE (XVector)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'XVector' successfully unpacked and MD5 sums checked