Hervé Pagès
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/XVector |
| git_branch: RELEASE_3_13 |
| git_last_commit: 300392d |
| git_last_commit_date: 2021-05-19 11:58:53 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:56 -0400 (Fri, 15 Oct 2021).
|
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 2033/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| XVector 0.32.0 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: XVector |
| Version: 0.32.0 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:XVector.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings XVector_0.32.0.tar.gz |
| StartedAt: 2021-10-14 12:03:46 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 12:04:44 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 57.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: XVector.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:XVector.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings XVector_0.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/XVector.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XVector/DESCRIPTION’ ... OK
* this is package ‘XVector’ version ‘0.32.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘XVector’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’ ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘BiocGenerics:::replaceSlots’ ‘BiocGenerics:::testPackage’
‘IRanges:::new_Views’ ‘IRanges:::solveUserSEWForSingleSeq’
‘S4Vectors:::anyMissing’ ‘S4Vectors:::prepare_objects_to_bind’
‘S4Vectors:::setDefaultSlotValue’ ‘S4Vectors:::toNumSnippet’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'XRawList-comparison.Rd':
‘[IRanges]{Ranges-comparison}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘RdaCollection’ ‘RdsCollection’ ‘open_input_files’ ‘rdaPath’
Undocumented S4 classes:
‘RdsCollection’ ‘RdaCollection’
Undocumented S4 methods:
generic '[[' and siglist 'RdaCollection'
generic 'coerce' and siglist 'XVector,Rle'
generic 'extractList' and siglist 'XVector,IntegerRanges'
generic 'extractROWS' and siglist 'RdsCollection,ANY'
generic 'extractROWS' and siglist 'XVector,ANY'
generic 'extractROWS' and siglist 'XVectorList,ANY'
generic 'getListElement' and siglist 'RdsCollection'
generic 'getListElement' and siglist 'XVectorList'
generic 'length' and siglist 'RdaCollection'
generic 'names' and siglist 'RdaCollection'
generic 'names' and siglist 'RdsCollection'
generic 'parallel_slot_names' and siglist 'RdsCollection'
generic 'path' and siglist 'RdsCollection'
generic 'rdaPath' and siglist 'RdaCollection'
generic 'relist' and siglist 'XVector,PartitioningByEnd'
generic 'relistToClass' and siglist 'XVector'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run_unitTests.R’
OK
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.13-bioc/meat/XVector.Rcheck/00check.log’
for details.
XVector.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL XVector
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘XVector’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c SharedDouble_class.c -o SharedDouble_class.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c SharedInteger_class.c -o SharedInteger_class.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c SharedVector_class.c -o SharedVector_class.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XDouble_class.c -o XDouble_class.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XInteger_class.c -o XInteger_class.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XRawList_comparison.c -o XRawList_comparison.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XRaw_class.c -o XRaw_class.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c XVector_class.c -o XVector_class.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c io_utils.c -o io_utils.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c slice_methods.c -o slice_methods.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -c vector_copy.c -o vector_copy.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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-3.13-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-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/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)
XVector.Rcheck/tests/run_unitTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.
> require("XVector") || stop("unable to load XVector package")
Loading required package: XVector
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
[1] TRUE
> XVector:::.test()
RUNIT TEST PROTOCOL -- Thu Oct 14 12:04:41 2021
***********************************************
Number of test functions: 8
Number of errors: 0
Number of failures: 0
1 Test Suite :
XVector RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
2.018 0.105 2.105
XVector.Rcheck/XVector-Ex.timings
| name | user | system | elapsed | |
| XDoubleViews-class | 0.080 | 0.004 | 0.084 | |
| XIntegerViews-class | 0.181 | 0.011 | 0.193 | |
| XRawList-comparison | 0 | 0 | 0 | |
| XVector-class | 0.038 | 0.000 | 0.038 | |
| compact-methods | 0.488 | 0.004 | 0.492 | |
| intra-range-methods | 0.001 | 0.000 | 0.001 | |
| reverse-methods | 2.662 | 0.111 | 2.778 | |
| slice-methods | 0.018 | 0.000 | 0.017 | |
| view-summarization-methods | 0.023 | 0.000 | 0.022 | |