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This page was generated on 2023-10-20 09:38:15 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 2221/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XVector 0.40.0  (landing page)
Hervé Pagès
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/XVector
git_branch: RELEASE_3_17
git_last_commit: 875b4b4
git_last_commit_date: 2023-04-25 10:27:07 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for XVector on kjohnson2


To the developers/maintainers of the XVector package:
- 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.

raw results


Summary

Package: XVector
Version: 0.40.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:XVector.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings XVector_0.40.0.tar.gz
StartedAt: 2023-10-19 10:28:26 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 10:30:58 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 152.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: XVector.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:XVector.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings XVector_0.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/XVector.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XVector/DESCRIPTION’ ... OK
* this is package ‘XVector’ version ‘0.40.0’
* 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
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* 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 ... WARNING
checkRd: (5) XDoubleViews-class.Rd:51-58: \item in \describe must have non-empty label
checkRd: (5) XDoubleViews-class.Rd:59-64: \item in \describe must have non-empty label
checkRd: (5) XDoubleViews-class.Rd:65-68: \item in \describe must have non-empty label
checkRd: (5) XIntegerViews-class.Rd:51-58: \item in \describe must have non-empty label
checkRd: (5) XIntegerViews-class.Rd:59-64: \item in \describe must have non-empty label
checkRd: (5) XIntegerViews-class.Rd:65-68: \item in \describe must have non-empty label
checkRd: (5) XVector-class.Rd:87-106: \item in \describe must have non-empty label
checkRd: (5) XVector-class.Rd:107-123: \item in \describe must have non-empty label
* 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:
  ‘RdaCollection’ ‘RdsCollection’
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
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
reverse-methods 3.367  0.175   6.311
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/XVector.Rcheck/00check.log’
for details.



Installation output

XVector.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL XVector
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘XVector’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RDS_random_access.c -o RDS_random_access.o
RDS_random_access.c:793:11: warning: variable 'x_type' set but not used [-Wunused-but-set-variable]
        SEXPTYPE x_type;
                 ^
RDS_random_access.c:796:18: warning: unused variable 'ans' [-Wunused-variable]
        SEXP subscript, ans;
                        ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_XVector.c -o R_init_XVector.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c SharedDouble_class.c -o SharedDouble_class.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c SharedInteger_class.c -o SharedInteger_class.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c SharedRaw_class.c -o SharedRaw_class.o
SharedRaw_class.c:396:13: warning: variable 'src_tag' set but not used [-Wunused-but-set-variable]
        SEXP dest, src_tag;
                   ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c SharedVector_class.c -o SharedVector_class.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XDouble_class.c -o XDouble_class.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XInteger_class.c -o XInteger_class.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XRawList_comparison.c -o XRawList_comparison.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XRaw_class.c -o XRaw_class.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XVectorList_class.c -o XVectorList_class.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c XVector_class.c -o XVector_class.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c io_utils.c -o io_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c slice_methods.c -o slice_methods.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vector_copy.c -o vector_copy.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c view_summarization_methods.c -o view_summarization_methods.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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)

Tests output

XVector.Rcheck/tests/run_unitTests.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("XVector") || stop("unable to load XVector package")
Loading required package: XVector
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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, aperm, 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 object is masked from 'package:utils':

    findMatches

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 19 10:30:35 2023 
*********************************************** 
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 
  2.609   0.186   5.087 

Example timings

XVector.Rcheck/XVector-Ex.timings

nameusersystemelapsed
XDoubleViews-class0.0970.0090.200
XIntegerViews-class0.2810.0150.531
XRawList-comparison000
XVector-class0.0550.0050.106
compact-methods0.4980.0180.946
intra-range-methods0.0000.0010.001
reverse-methods3.3670.1756.311
slice-methods0.0270.0020.050
view-summarization-methods0.0260.0020.048