Hervé Pagès
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/XVector |
| git_branch: devel |
| git_last_commit: 7fd9ca2 |
| git_last_commit_date: 2024-10-29 09:46:03 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:16 -0500 (Thu, 28 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2262/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| XVector 0.47.0 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the XVector package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/XVector.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: XVector |
| Version: 0.47.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL XVector |
| StartedAt: 2024-11-27 15:28:40 -0500 (Wed, 27 Nov 2024) |
| EndedAt: 2024-11-27 15:30:04 -0500 (Wed, 27 Nov 2024) |
| EllapsedTime: 83.2 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL XVector
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'XVector' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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:305:25: warning: unknown conversion type character 't' in format [-Wformat=]
305 | PRINTIFVERBOSE2("object length: %td", ans_len);
| ^~~~~~~~~~~~~~~~~~~~
RDS_random_access.c:88:24: note: in definition of macro 'PRINTIFVERBOSE2'
88 | printf(format, value); \
| ^~~~~~
RDS_random_access.c:305:42: note: format string is defined here
305 | PRINTIFVERBOSE2("object length: %td", ans_len);
| ^
RDS_random_access.c:305:25: warning: too many arguments for format [-Wformat-extra-args]
305 | PRINTIFVERBOSE2("object length: %td", ans_len);
| ^~~~~~~~~~~~~~~~~~~~
RDS_random_access.c:88:24: note: in definition of macro 'PRINTIFVERBOSE2'
88 | printf(format, value); \
| ^~~~~~
RDS_random_access.c: In function 'RDS_read_atomic_vector':
RDS_random_access.c:335:25: warning: unknown conversion type character 't' in format [-Wformat=]
335 | PRINTIFVERBOSE2("object length: %td", ans_len);
| ^~~~~~~~~~~~~~~~~~~~
RDS_random_access.c:88:24: note: in definition of macro 'PRINTIFVERBOSE2'
88 | printf(format, value); \
| ^~~~~~
RDS_random_access.c:335:42: note: format string is defined here
335 | PRINTIFVERBOSE2("object length: %td", ans_len);
| ^
RDS_random_access.c:335:25: warning: too many arguments for format [-Wformat-extra-args]
335 | PRINTIFVERBOSE2("object length: %td", ans_len);
| ^~~~~~~~~~~~~~~~~~~~
RDS_random_access.c:88:24: note: in definition of macro 'PRINTIFVERBOSE2'
88 | printf(format, value); \
| ^~~~~~
RDS_random_access.c: In function 'RDS_read_list':
RDS_random_access.c:379:25: warning: unknown conversion type character 't' in format [-Wformat=]
379 | PRINTIFVERBOSE2("object length: %td", ans_len);
| ^~~~~~~~~~~~~~~~~~~~
RDS_random_access.c:88:24: note: in definition of macro 'PRINTIFVERBOSE2'
88 | printf(format, value); \
| ^~~~~~
RDS_random_access.c:379:42: note: format string is defined here
379 | PRINTIFVERBOSE2("object length: %td", ans_len);
| ^
RDS_random_access.c:379:25: warning: too many arguments for format [-Wformat-extra-args]
379 | PRINTIFVERBOSE2("object length: %td", ans_len);
| ^~~~~~~~~~~~~~~~~~~~
RDS_random_access.c:88:24: note: in definition of macro 'PRINTIFVERBOSE2'
88 | printf(format, value); \
| ^~~~~~
RDS_random_access.c: In function 'RDS_extract_subarray':
RDS_random_access.c:796:25: warning: unused variable 'ans' [-Wunused-variable]
796 | SEXP subscript, ans;
| ^~~
RDS_random_access.c:793:18: warning: variable 'x_type' set but not used [-Wunused-but-set-variable]
793 | SEXPTYPE x_type;
| ^~~~~~
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_XVector.c -o R_init_XVector.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SharedDouble_class.c -o SharedDouble_class.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SharedInteger_class.c -o SharedInteger_class.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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:396:20: warning: variable 'src_tag' set but not used [-Wunused-but-set-variable]
396 | SEXP dest, src_tag;
| ^~~~~~~
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SharedVector_class.c -o SharedVector_class.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XDouble_class.c -o XDouble_class.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XInteger_class.c -o XInteger_class.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XRawList_comparison.c -o XRawList_comparison.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XRaw_class.c -o XRaw_class.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XVectorList_class.c -o XVectorList_class.o
XVectorList_class.c: In function '_new_XRawList_from_CharAEAE':
XVectorList_class.c:459:17: warning: 'lkup_length' may be used uninitialized [-Wmaybe-uninitialized]
459 | _Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
460 | (char *) dest.ptr, dest.length,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
461 | src->elts, CharAE_get_nelt(src),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
462 | lkup0, lkup_length);
| ~~~~~~~~~~~~~~~~~~~
XVectorList_class.c:434:13: note: 'lkup_length' was declared here
434 | int lkup_length, nelt, i;
| ^~~~~~~~~~~
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XVector_class.c -o XVector_class.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c io_utils.c -o io_utils.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c slice_methods.c -o slice_methods.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vector_copy.c -o vector_copy.o
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/include" -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/S4Vectors/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/IRanges/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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:219:45: warning: 'cur_min' may be used uninitialized [-Wmaybe-uninitialized]
219 | if (which_min == NA_INTEGER || x < cur_min) {
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
view_summarization_methods.c:208:19: note: 'cur_min' was declared here
208 | int xlen, cur_min, which_min, i, x;
| ^~~~~~~
view_summarization_methods.c: In function 'get_which_min_from_Doubles_holder':
view_summarization_methods.c:246:45: warning: 'cur_min' may be used uninitialized [-Wmaybe-uninitialized]
246 | if (which_min == NA_INTEGER || x < cur_min) {
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
view_summarization_methods.c:235:16: note: 'cur_min' was declared here
235 | double cur_min, x;
| ^~~~~~~
view_summarization_methods.c: In function 'get_which_max_from_Ints_holder':
view_summarization_methods.c:269:45: warning: 'cur_max' may be used uninitialized [-Wmaybe-uninitialized]
269 | if (which_max == NA_INTEGER || x > cur_max) {
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
view_summarization_methods.c:258:19: note: 'cur_max' was declared here
258 | int xlen, cur_max, which_max, i, x;
| ^~~~~~~
view_summarization_methods.c: In function 'get_which_max_from_Doubles_holder':
view_summarization_methods.c:296:45: warning: 'cur_max' may be used uninitialized [-Wmaybe-uninitialized]
296 | if (which_max == NA_INTEGER || x > cur_max) {
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
view_summarization_methods.c:285:16: note: 'cur_max' was declared here
285 | double cur_max, x;
| ^~~~~~~
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 -LE:/biocbuild/bbs-3.21-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-XVector/00new/XVector/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (XVector)