| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:43 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 2198/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| XVector 0.39.0 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
| Package: XVector |
| Version: 0.39.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL XVector |
| StartedAt: 2023-04-12 01:35:11 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 01:35:31 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 20.2 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL XVector
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘XVector’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c RDS_random_access.c -o RDS_random_access.o
RDS_random_access.c: In function ‘RDS_extract_subarray’:
RDS_random_access.c:796:18: warning: unused variable ‘ans’ [-Wunused-variable]
796 | SEXP subscript, ans;
| ^~~
RDS_random_access.c:793:11: warning: variable ‘x_type’ set but not used [-Wunused-but-set-variable]
793 | SEXPTYPE x_type;
| ^~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c R_init_XVector.c -o R_init_XVector.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c SharedDouble_class.c -o SharedDouble_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c SharedInteger_class.c -o SharedInteger_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -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]
396 | SEXP dest, src_tag;
| ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c SharedVector_class.c -o SharedVector_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XDouble_class.c -o XDouble_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XInteger_class.c -o XInteger_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XRawList_comparison.c -o XRawList_comparison.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XRaw_class.c -o XRaw_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -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]
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);
| ~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVector_class.c -o XVector_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c io_utils.c -o io_utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c slice_methods.c -o slice_methods.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c vector_copy.c -o vector_copy.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -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]
219 | 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]
246 | 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]
269 | 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]
296 | if (which_max == NA_INTEGER || x > cur_max) {
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o XVector.so 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 -lz -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-XVector/00new/XVector/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (XVector)