Hervé Pagès
| Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/XVector |
| git_branch: devel |
| git_last_commit: 3fa081b |
| git_last_commit_date: 2024-12-19 13:39:26 -0500 (Thu, 19 Dec 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-04 11:42 -0500 (Sat, 04 Jan 2025).
| 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" | 4756 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4475 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4435 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4383 |
| 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 2265/2275 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| XVector 0.47.1 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ERROR | OK | ERROR | ERROR | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 0.47.1 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:XVector.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings XVector_0.47.1.tar.gz |
| StartedAt: 2025-01-04 06:29:46 -0500 (Sat, 04 Jan 2025) |
| EndedAt: 2025-01-04 06:29:51 -0500 (Sat, 04 Jan 2025) |
| EllapsedTime: 5.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: XVector.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:XVector.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings XVector_0.47.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/XVector.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'XVector/DESCRIPTION' ... OK
* this is package 'XVector' version '0.47.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'XVector' can be installed ... ERROR
Installation failed.
See 'E:/biocbuild/bbs-3.21-bioc/meat/XVector.Rcheck/00install.out' for details.
* DONE
Status: 1 ERROR
See
'E:/biocbuild/bbs-3.21-bioc/meat/XVector.Rcheck/00check.log'
for details.
XVector.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL XVector
###
##############################################################################
##############################################################################
* 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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 -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
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: io_utils.o:io_utils.c:(.text+0x154): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: io_utils.o:io_utils.c:(.text+0x28d): undefined reference to `gzopen'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: io_utils.o:io_utils.c:(.text+0x494): undefined reference to `gzgets'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: io_utils.o:io_utils.c:(.text+0x54a): undefined reference to `gztell'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: io_utils.o:io_utils.c:(.text+0x687): undefined reference to `gzputs'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: io_utils.o:io_utils.c:(.text+0x715): undefined reference to `gzputc'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: io_utils.o:io_utils.c:(.text+0x29): undefined reference to `gzclose'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: io_utils.o:io_utils.c:(.text+0x410): undefined reference to `gzread'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: io_utils.o:io_utils.c:(.text+0x5bd): undefined reference to `gzseek'
C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: io_utils.o:io_utils.c:(.text+0x61e): undefined reference to `gzrewind'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'XVector'
* removing 'E:/biocbuild/bbs-3.21-bioc/R/library/XVector'
* restoring previous 'E:/biocbuild/bbs-3.21-bioc/R/library/XVector'