Hervé Pagès
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/XVector |
| git_branch: master |
| git_last_commit: 7d8ff35 |
| git_last_commit_date: 2021-10-26 12:08:07 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:59 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the XVector package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2083/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| XVector 0.35.0 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: XVector |
| Version: 0.35.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL XVector |
| StartedAt: 2022-03-17 15:34:14 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 15:35:29 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 75.2 seconds |
| RetCode: 0 |
| Status: OK |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL XVector
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'XVector' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c R_init_XVector.c -o R_init_XVector.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c SharedDouble_class.c -o SharedDouble_class.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c SharedInteger_class.c -o SharedInteger_class.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c SharedVector_class.c -o SharedVector_class.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c XDouble_class.c -o XDouble_class.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c XInteger_class.c -o XInteger_class.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c XRawList_comparison.c -o XRawList_comparison.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c XRaw_class.c -o XRaw_class.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c XVector_class.c -o XVector_class.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c io_utils.c -o io_utils.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c slice_methods.c -o slice_methods.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c vector_copy.c -o vector_copy.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include" -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 -LD:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-XVector/00new/XVector/libs/x64
** 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
XIntegerViews-class html
XRawList-class html
XRawList-comparison html
XVector-class html
XVector-internals html
XVectorList-class html
compact-methods html
intra-range-methods html
reverse-methods html
slice-methods html
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
* DONE (XVector)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'pathVar' is missing or broken
done