Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-11-28 12:17 -0500 (Thu, 28 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
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 1815/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
S4Vectors 0.45.2 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
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. |
Package: S4Vectors |
Version: 0.45.2 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:S4Vectors.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings S4Vectors_0.45.2.tar.gz |
StartedAt: 2024-11-28 01:51:55 -0500 (Thu, 28 Nov 2024) |
EndedAt: 2024-11-28 01:57:01 -0500 (Thu, 28 Nov 2024) |
EllapsedTime: 305.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: S4Vectors.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:S4Vectors.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings S4Vectors_0.45.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/S4Vectors.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: x86_64-apple-darwin20 * 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 12.7.6 * 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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: ‘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 ‘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 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 sizes of PDF files under ‘inst/doc’ ... OK * 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 7.876 1.004 8.916 * 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/S4Vectors.Rcheck/00check.log’ for details.
S4Vectors.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL S4Vectors ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘S4Vectors’ ... ** 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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c AEbufs.c -o AEbufs.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DataFrame_class.c -o DataFrame_class.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Hits_class.c -o Hits_class.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LLint_class.c -o LLint_class.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c List_class.c -o List_class.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_S4Vectors.c -o R_init_S4Vectors.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rle_class.c -o Rle_class.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rle_utils.c -o Rle_utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SEXP_utils.c -o SEXP_utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SimpleList_class.c -o SimpleList_class.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c anyMissing.c -o anyMissing.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c character_utils.c -o character_utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c eval_utils.c -o eval_utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hash_utils.c -o hash_utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c integer_utils.c -o integer_utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c logical_utils.c -o logical_utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c map_ranges_to_runs.c -o map_ranges_to_runs.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c raw_utils.c -o raw_utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c safe_arithm.c -o safe_arithm.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sort_utils.c -o sort_utils.o sort_utils.c:263:13: warning: unused function 'sort_uchar_array' [-Wunused-function] static void sort_uchar_array(unsigned char *x, int nelt, int desc) ^ 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c subsetting_utils.c -o subsetting_utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vector_utils.c -o vector_utils.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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)
S4Vectors.Rcheck/tests/run_unitTests.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 -- Thu Nov 28 01:56:49 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 7.414 0.261 7.696
S4Vectors.Rcheck/S4Vectors-Ex.timings
name | user | system | elapsed | |
Annotated-class | 0.621 | 0.034 | 0.656 | |
DataFrame-class | 0.166 | 0.015 | 0.181 | |
DataFrame-combine | 0.206 | 0.005 | 0.211 | |
DataFrame-comparison | 0.051 | 0.003 | 0.054 | |
DataFrame-utils | 0.116 | 0.001 | 0.118 | |
DataFrameFactor-class | 0.041 | 0.002 | 0.044 | |
Factor-class | 0.129 | 0.006 | 0.135 | |
FilterRules-class | 0.068 | 0.001 | 0.070 | |
Hits-class | 0.046 | 0.002 | 0.049 | |
Hits-comparison | 0.022 | 0.002 | 0.023 | |
Hits-setops | 0.074 | 0.002 | 0.076 | |
HitsList-class | 0.049 | 0.001 | 0.050 | |
LLint-class | 0.019 | 0.003 | 0.022 | |
List-class | 0.329 | 0.007 | 0.337 | |
List-utils | 0.055 | 0.003 | 0.058 | |
Pairs-class | 0.029 | 0.001 | 0.030 | |
RectangularData-class | 0.000 | 0.001 | 0.001 | |
Rle-class | 0.044 | 0.001 | 0.046 | |
Rle-runstat | 0.100 | 0.002 | 0.102 | |
Rle-utils | 0.011 | 0.001 | 0.012 | |
SimpleList-class | 0.019 | 0.002 | 0.021 | |
TransposedDataFrame-class | 3.934 | 0.181 | 4.130 | |
Vector-class | 0.001 | 0.001 | 0.002 | |
Vector-comparison | 0.044 | 0.006 | 0.050 | |
Vector-merge | 0.403 | 0.054 | 0.458 | |
Vector-setops | 0 | 0 | 0 | |
aggregate-methods | 0.072 | 0.011 | 0.083 | |
character-utils | 0.002 | 0.002 | 0.003 | |
expand-methods | 0.278 | 0.011 | 0.289 | |
integer-utils | 0.000 | 0.000 | 0.001 | |
isSorted | 0.002 | 0.001 | 0.003 | |
shiftApply-methods | 7.876 | 1.004 | 8.916 | |
show-utils | 0.019 | 0.003 | 0.022 | |
splitAsList | 0.046 | 0.002 | 0.048 | |
stack-methods | 0.037 | 0.002 | 0.039 | |
zip-methods | 0.009 | 0.000 | 0.010 | |