Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-08-21 11:46 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 1809/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
S4Vectors 0.43.2 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the S4Vectors package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org: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. |
Package: S4Vectors |
Version: 0.43.2 |
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_0.43.2.tar.gz |
StartedAt: 2024-08-21 08:43:41 -0000 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 08:45:44 -0000 (Wed, 21 Aug 2024) |
EllapsedTime: 123.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: S4Vectors.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### 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_0.43.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/S4Vectors.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * 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 ‘0.43.2’ * 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 (GCC) 10.3.1’ * 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 or links 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 * 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 26.659 0.087 26.794 TransposedDataFrame-class 6.251 0.151 6.414 * 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-3.20-bioc/meat/S4Vectors.Rcheck/00check.log’ for details.
S4Vectors.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL S4Vectors ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘S4Vectors’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c AEbufs.c -o AEbufs.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c DataFrame_class.c -o DataFrame_class.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c Hits_class.c -o Hits_class.o In file included from /home/biocbuild/R/R-4.4.1/include/Rdefines.h:41, from ../inst/include/S4Vectors_defines.h:18, from S4Vectors.h:1, from Hits_class.c:4: Hits_class.c: In function ‘Hits_new’: /home/biocbuild/R/R-4.4.1/include/Rinternals.h:895:20: warning: ‘revmap’ may be used uninitialized in this function [-Wmaybe-uninitialized] 895 | #define defineVar Rf_defineVar | ^~~~~~~~~~~~ Hits_class.c:216:12: note: ‘revmap’ was declared here 216 | SEXP ans, revmap, symbol; | ^~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c LLint_class.c -o LLint_class.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c List_class.c -o List_class.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c R_init_S4Vectors.c -o R_init_S4Vectors.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c Rle_class.c -o Rle_class.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c Rle_utils.c -o Rle_utils.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c SEXP_utils.c -o SEXP_utils.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c SimpleList_class.c -o SimpleList_class.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c anyMissing.c -o anyMissing.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c character_utils.c -o character_utils.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c eval_utils.c -o eval_utils.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c hash_utils.c -o hash_utils.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c integer_utils.c -o integer_utils.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c logical_utils.c -o logical_utils.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c map_ranges_to_runs.c -o map_ranges_to_runs.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c raw_utils.c -o raw_utils.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c safe_arithm.c -o safe_arithm.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c sort_utils.c -o sort_utils.o sort_utils.c:263:13: warning: ‘sort_uchar_array’ defined but not used [-Wunused-function] 263 | static void sort_uchar_array(unsigned char *x, int nelt, int desc) | ^~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c subsetting_utils.c -o subsetting_utils.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c vector_utils.c -o vector_utils.o gcc -shared -L/home/biocbuild/R/R-4.4.1/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-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/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’ Creating a generic function for ‘setequal’ from package ‘base’ 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)
S4Vectors.Rcheck/tests/run_unitTests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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 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, table, tapply, union, 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 -- Wed Aug 21 08:45:37 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 12.589 0.351 12.964
S4Vectors.Rcheck/S4Vectors-Ex.timings
name | user | system | elapsed | |
Annotated-class | 0.970 | 0.084 | 1.056 | |
DataFrame-class | 0.263 | 0.000 | 0.264 | |
DataFrame-combine | 0.351 | 0.004 | 0.355 | |
DataFrame-comparison | 0.079 | 0.004 | 0.083 | |
DataFrame-utils | 0.227 | 0.000 | 0.227 | |
DataFrameFactor-class | 0.066 | 0.000 | 0.066 | |
Factor-class | 0.227 | 0.000 | 0.227 | |
FilterRules-class | 0.124 | 0.000 | 0.124 | |
Hits-class | 0.096 | 0.028 | 0.124 | |
Hits-comparison | 0.031 | 0.052 | 0.083 | |
Hits-setops | 0.145 | 0.128 | 0.273 | |
HitsList-class | 0.094 | 0.040 | 0.135 | |
LLint-class | 0.034 | 0.004 | 0.039 | |
List-class | 0.572 | 0.012 | 0.585 | |
List-utils | 0.137 | 0.040 | 0.178 | |
Pairs-class | 0.051 | 0.000 | 0.051 | |
RectangularData-class | 0 | 0 | 0 | |
Rle-class | 0.078 | 0.000 | 0.078 | |
Rle-runstat | 0.174 | 0.012 | 0.186 | |
Rle-utils | 0.021 | 0.000 | 0.020 | |
SimpleList-class | 0.029 | 0.000 | 0.029 | |
TransposedDataFrame-class | 6.251 | 0.151 | 6.414 | |
Vector-class | 0.000 | 0.001 | 0.001 | |
Vector-comparison | 0.065 | 0.004 | 0.069 | |
Vector-merge | 0.621 | 0.052 | 0.674 | |
Vector-setops | 0 | 0 | 0 | |
aggregate-methods | 0.105 | 0.008 | 0.113 | |
character-utils | 0.003 | 0.000 | 0.003 | |
expand-methods | 0.45 | 0.00 | 0.45 | |
integer-utils | 0.001 | 0.000 | 0.001 | |
isSorted | 0.004 | 0.000 | 0.004 | |
shiftApply-methods | 26.659 | 0.087 | 26.794 | |
show-utils | 0.027 | 0.000 | 0.027 | |
splitAsList | 0.083 | 0.000 | 0.083 | |
stack-methods | 0.061 | 0.000 | 0.061 | |
zip-methods | 0.017 | 0.000 | 0.018 | |