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This page was generated on 2024-12-09 11:47 -0500 (Mon, 09 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4749
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4461
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4411
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4366
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4241
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 1815/2272HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
S4Vectors 0.45.2  (landing page)
Hervé Pagès
Snapshot Date: 2024-12-08 13:40 -0500 (Sun, 08 Dec 2024)
git_url: https://git.bioconductor.org/packages/S4Vectors
git_branch: devel
git_last_commit: 336e71e
git_last_commit_date: 2024-11-15 05:42:26 -0500 (Fri, 15 Nov 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for S4Vectors on kunpeng2

To the developers/maintainers of the S4Vectors package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/S4Vectors.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: S4Vectors
Version: 0.45.2
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:S4Vectors.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings S4Vectors_0.45.2.tar.gz
StartedAt: 2024-12-09 09:33:17 -0000 (Mon, 09 Dec 2024)
EndedAt: 2024-12-09 09:35:19 -0000 (Mon, 09 Dec 2024)
EllapsedTime: 122.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: S4Vectors.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:S4Vectors.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings S4Vectors_0.45.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/S4Vectors.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (conda-forge gcc 14.2.0-1) 14.2.0
    GNU Fortran (conda-forge gcc 14.2.0-1) 14.2.0
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘S4Vectors/DESCRIPTION’ ... OK
* this is package ‘S4Vectors’ version ‘0.45.2’
* 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 ‘S4Vectors’ can be installed ... OK
* used C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘data.table:::as.data.frame.data.table’
  ‘stats:::na.exclude.data.frame’ ‘stats:::na.omit.data.frame’
  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 ... NOTE
evalSeparately,FilterRules : <anonymous>: no visible global function
  definition for ‘.’
Undefined global functions or variables:
  .
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'Vector-comparison.Rd':
  ‘[IRanges]{IntegerRanges-comparison}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘I’ ‘head.LLint’ ‘pcompareRecursively’ ‘sort.List’ ‘t.HitsList’
  ‘tail.LLint’ ‘unname’ ‘window.LLint’
Undocumented S4 methods:
  generic '!' and siglist 'List'
  generic '<=' and siglist 'List,List'
  generic '<=' and siglist 'List,list'
  generic '<=' and siglist 'list,List'
  generic '==' and siglist 'List,List'
  generic '==' and siglist 'List,list'
  generic '==' and siglist 'list,List'
  generic '[' and siglist 'LLint'
  generic '[<-' and siglist 'Rle'
  generic 'anyNA' and siglist 'List'
  generic 'by' and siglist 'Vector'
  generic 'countMatches' and siglist 'ANY'
  generic 'do.call' and siglist 'ANY,List'
  generic 'duplicated' and siglist 'List'
  generic 'eval' and siglist 'expression,Vector'
  generic 'eval' and siglist 'language,Vector'
  generic 'extractROWS' and siglist 'LLint,ANY'
  generic 'extractROWS' and siglist 'LLint,NSBS'
  generic 'extractROWS' and siglist 'LLint,RangeNSBS'
  generic 'extractROWS' and siglist 'Vector,ANY'
  generic 'filterRules' and siglist 'FilterResults'
  generic 'from' and siglist 'HitsList'
  generic 'getListElement' and siglist 'SimpleList'
  generic 'grep' and siglist 'ANY,Rle'
  generic 'grepl' and siglist 'ANY,Rle'
  generic 'head' and siglist 'LLint'
  generic 'is.na' and siglist 'List'
  generic 'is.unsorted' and siglist 'List'
  generic 'match' and siglist 'List,List'
  generic 'match' and siglist 'List,Vector'
  generic 'match' and siglist 'List,list'
  generic 'match' and siglist 'List,vector'
  generic 'match' and siglist 'list,List'
  generic 'mergeROWS' and siglist 'ANY'
  generic 'mergeROWS' and siglist 'Vector'
  generic 'normalizeSingleBracketReplacementValue' and siglist
    'DataFrame'
  generic 'normalizeSingleBracketReplacementValue' and siglist 'List'
  generic 'order' and siglist 'List'
  generic 'pcompare' and siglist 'List,List'
  generic 'pcompare' and siglist 'List,list'
  generic 'pcompare' and siglist 'list,List'
  generic 'pcompareRecursively' and siglist 'List'
  generic 'pcompareRecursively' and siglist 'list'
  generic 'rank' and siglist 'List'
  generic 'rep.int' and siglist 'LLint'
  generic 'replaceROWS' and siglist 'ANY'
  generic 'replaceROWS' and siglist 'Rle'
  generic 'replaceROWS' and siglist 'Vector'
  generic 'sameAsPreviousROW' and siglist 'Rle'
  generic 'sameAsPreviousROW' and siglist 'atomic'
  generic 'sameAsPreviousROW' and siglist 'complex'
  generic 'sameAsPreviousROW' and siglist 'integer'
  generic 'sameAsPreviousROW' and siglist 'numeric'
  generic 'sort' and siglist 'List'
  generic 'splitAsList' and siglist 'ANY'
  generic 'splitAsList' and siglist 'SortedByQueryHits'
  generic 'summary' and siglist 'FilterResults'
  generic 't' and siglist 'Pairs'
  generic 'tail' and siglist 'LLint'
  generic 'to' and siglist 'HitsList'
  generic 'unique' and siglist 'List'
  generic 'unique' and siglist 'SimpleList'
  generic 'window' and siglist 'LLint'
  generic 'with' and siglist 'Vector'
  generic 'xtabs' and siglist 'Vector'
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 compiled code ... NOTE
Note: information on .o files is not available
File ‘S4Vectors/libs/S4Vectors.so’:
  Found non-API calls to R: ‘PRENV’, ‘R_PromiseExpr’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
shiftApply-methods        23.464  0.255  23.757
TransposedDataFrame-class  6.363  0.164   6.540
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/S4Vectors.Rcheck/00check.log’
for details.


Installation output

S4Vectors.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL S4Vectors
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘S4Vectors’ ...
** using staged installation
** libs
using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c AEbufs.c -o AEbufs.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c DataFrame_class.c -o DataFrame_class.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c Hits_class.c -o Hits_class.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c LLint_class.c -o LLint_class.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c List_class.c -o List_class.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c Rle_class.c -o Rle_class.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c Rle_utils.c -o Rle_utils.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c SEXP_utils.c -o SEXP_utils.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c SimpleList_class.c -o SimpleList_class.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c anyMissing.c -o anyMissing.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c character_utils.c -o character_utils.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c eval_utils.c -o eval_utils.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c hash_utils.c -o hash_utils.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c integer_utils.c -o integer_utils.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c logical_utils.c -o logical_utils.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c map_ranges_to_runs.c -o map_ranges_to_runs.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c raw_utils.c -o raw_utils.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c safe_arithm.c -o safe_arithm.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c sort_utils.c -o sort_utils.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c subsetting_utils.c -o subsetting_utils.o
gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -c vector_utils.c -o vector_utils.o
gcc -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-S4Vectors/00new/S4Vectors/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘normalizeSingleBracketReplacementValue’ with signature ‘"List"’: no definition for class “List”
Creating a new generic function for ‘unname’ in package ‘S4Vectors’
Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’
Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’
in method for ‘coerce’ with signature ‘"Hits","DFrame"’: no definition for class “DFrame”
Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘S4Vectors’
in method for ‘coerce’ with signature ‘"data.table","DFrame"’: no definition for class “data.table”
Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (S4Vectors)

Tests output

S4Vectors.Rcheck/tests/run_unitTests.Rout


R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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("S4Vectors") || stop("unable to load S4Vectors package")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

[1] TRUE
> S4Vectors:::.test()
Loading required package: GenomeInfoDb


RUNIT TEST PROTOCOL -- Mon Dec  9 09:35:12 2024 
*********************************************** 
Number of test functions: 74 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
S4Vectors RUnit Tests - 74 test functions, 0 errors, 0 failures
Number of test functions: 74 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In combineUniqueCols(X, Y, Z, use.names = FALSE) :
  different values in multiple instances of column 'dup', ignoring this column
  in DFrame 2
2: In combineUniqueCols(X, Y, Z) :
  different values for shared rows in multiple instances of column 'dup',
  ignoring this column in DFrame 2
3: In combineUniqueCols(x, y2) :
  different values for shared rows in multiple instances of column 'X',
  ignoring this column in DFrame 2
> 
> proc.time()
   user  system elapsed 
 12.535   0.259  12.736 

Example timings

S4Vectors.Rcheck/S4Vectors-Ex.timings

nameusersystemelapsed
Annotated-class0.9950.0201.016
DataFrame-class0.2800.0040.284
DataFrame-combine0.3560.0160.373
DataFrame-comparison0.0970.0040.101
DataFrame-utils0.2300.0000.229
DataFrameFactor-class0.0720.0000.073
Factor-class0.2150.0040.220
FilterRules-class0.1220.0000.123
Hits-class0.0790.0000.080
Hits-comparison0.0380.0000.037
Hits-setops0.1310.0000.131
HitsList-class0.090.000.09
LLint-class0.0280.0040.031
List-class0.6190.0000.621
List-utils0.0930.0040.097
Pairs-class0.0510.0000.051
RectangularData-class000
Rle-class0.0780.0040.082
Rle-runstat0.1810.0000.182
Rle-utils0.0210.0000.021
SimpleList-class0.0310.0000.030
TransposedDataFrame-class6.3630.1646.540
Vector-class0.0020.0000.002
Vector-comparison0.0660.0040.070
Vector-merge0.6550.0400.697
Vector-setops000
aggregate-methods0.0970.0180.115
character-utils0.0000.0020.003
expand-methods0.4250.0330.459
integer-utils0.0000.0000.001
isSorted0.0040.0000.004
shiftApply-methods23.464 0.25523.757
show-utils0.0280.0000.027
splitAsList0.0840.0000.084
stack-methods0.0630.0000.063
zip-methods0.0180.0000.018