Hervé Pagès
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/S4Vectors |
| git_branch: RELEASE_3_17 |
| git_last_commit: 6878c63 |
| git_last_commit_date: 2023-09-22 13:25:00 -0400 (Fri, 22 Sep 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:11 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1797/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| S4Vectors 0.38.2 (landing page) Hervé Pagès
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the S4Vectors 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. |
| Package: S4Vectors |
| Version: 0.38.2 |
| 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_0.38.2.tar.gz |
| StartedAt: 2023-10-18 21:15:44 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 21:18:59 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 194.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: S4Vectors.Rcheck |
| Warnings: 3 |
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### Running command:
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### /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_0.38.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/S4Vectors.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 ‘S4Vectors/DESCRIPTION’ ... OK
* this is package ‘S4Vectors’ version ‘0.38.2’
* 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: ‘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 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 ... 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 ... WARNING
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* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object '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 'max' and siglist 'NSBS'
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 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 10.186 0.691 19.171
TransposedDataFrame-class 4.854 0.190 7.750
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run_unitTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-arm64/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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c AEbufs.c -o AEbufs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DataFrame_class.c -o DataFrame_class.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Hits_class.c -o Hits_class.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LLint_class.c -o LLint_class.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c List_class.c -o List_class.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_S4Vectors.c -o R_init_S4Vectors.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rle_class.c -o Rle_class.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rle_utils.c -o Rle_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SEXP_utils.c -o SEXP_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SimpleList_class.c -o SimpleList_class.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c anyMissing.c -o anyMissing.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c character_utils.c -o character_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c eval_utils.c -o eval_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hash_utils.c -o hash_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c integer_utils.c -o integer_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c logical_utils.c -o logical_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c map_ranges_to_runs.c -o map_ranges_to_runs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c raw_utils.c -o raw_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c safe_arithm.c -o safe_arithm.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c subsetting_utils.c -o subsetting_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vector_utils.c -o vector_utils.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 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/4.3-arm64/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’
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 4.3.1 (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("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, sort, 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 Oct 18 21:18:30 2023
***********************************************
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
11.220 0.332 20.518
S4Vectors.Rcheck/S4Vectors-Ex.timings
| name | user | system | elapsed | |
| Annotated-class | 0.871 | 0.041 | 1.606 | |
| DataFrame-class | 0.237 | 0.016 | 0.409 | |
| DataFrame-combine | 0.346 | 0.011 | 0.546 | |
| DataFrame-comparison | 0.087 | 0.004 | 0.135 | |
| DataFrame-utils | 0.221 | 0.003 | 0.372 | |
| DataFrameFactor-class | 0.068 | 0.003 | 0.122 | |
| Factor-class | 0.217 | 0.009 | 0.402 | |
| FilterRules-class | 0.112 | 0.003 | 0.196 | |
| Hits-class | 0.081 | 0.004 | 0.149 | |
| Hits-comparison | 0.034 | 0.002 | 0.069 | |
| Hits-setops | 0.116 | 0.004 | 0.204 | |
| HitsList-class | 0.086 | 0.003 | 0.134 | |
| LLint-class | 0.029 | 0.004 | 0.050 | |
| List-class | 0.546 | 0.018 | 0.863 | |
| List-utils | 0.087 | 0.005 | 0.146 | |
| Pairs-class | 0.048 | 0.001 | 0.076 | |
| RectangularData-class | 0.001 | 0.000 | 0.003 | |
| Rle-class | 0.070 | 0.003 | 0.113 | |
| Rle-runstat | 0.155 | 0.006 | 0.285 | |
| Rle-utils | 0.018 | 0.001 | 0.037 | |
| SimpleList-class | 0.029 | 0.003 | 0.058 | |
| TransposedDataFrame-class | 4.854 | 0.190 | 7.750 | |
| Vector-class | 0.001 | 0.001 | 0.002 | |
| Vector-comparison | 0.067 | 0.007 | 0.127 | |
| Vector-merge | 0.663 | 0.046 | 1.193 | |
| Vector-setops | 0 | 0 | 0 | |
| aggregate-methods | 0.114 | 0.007 | 0.206 | |
| character-utils | 0.003 | 0.002 | 0.009 | |
| expand-methods | 0.471 | 0.021 | 0.837 | |
| integer-utils | 0.000 | 0.001 | 0.002 | |
| isSorted | 0.004 | 0.001 | 0.007 | |
| shiftApply-methods | 10.186 | 0.691 | 19.171 | |
| splitAsList | 0.081 | 0.004 | 0.146 | |
| stack-methods | 0.069 | 0.003 | 0.124 | |
| zip-methods | 0.017 | 0.001 | 0.027 | |