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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:S4Vectors.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings S4Vectors_0.45.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/S4Vectors.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* 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 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
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 10.6  0.373  10.974
* 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 re-building of vignette outputs ... OK
* 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.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL S4Vectors
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘S4Vectors’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c AEbufs.c -o AEbufs.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c DataFrame_class.c -o DataFrame_class.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c Hits_class.c -o Hits_class.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/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/bbs-3.21-bioc/R/include/Rinternals.h:919:33: warning: ‘revmap’ may be used uninitialized [-Wmaybe-uninitialized]
  919 | #define defineVar               Rf_defineVar
Hits_class.c:241:9: note: in expansion of macro ‘defineVar’
  241 |         defineVar(install(translateChar(symbol)), revmap, revmap_envir);
      |         ^~~~~~~~~
Hits_class.c:216:19: note: ‘revmap’ was declared here
  216 |         SEXP ans, revmap, symbol;
      |                   ^~~~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c LLint_class.c -o LLint_class.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c List_class.c -o List_class.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c Rle_class.c -o Rle_class.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c Rle_utils.c -o Rle_utils.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c SEXP_utils.c -o SEXP_utils.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c SimpleList_class.c -o SimpleList_class.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c anyMissing.c -o anyMissing.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c character_utils.c -o character_utils.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c eval_utils.c -o eval_utils.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c hash_utils.c -o hash_utils.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c integer_utils.c -o integer_utils.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c logical_utils.c -o logical_utils.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c map_ranges_to_runs.c -o map_ranges_to_runs.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c raw_utils.c -o raw_utils.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c safe_arithm.c -o safe_arithm.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -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/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c subsetting_utils.c -o subsetting_utils.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -c vector_utils.c -o vector_utils.o
gcc -shared -L/home/biocbuild/bbs-3.21-bioc/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/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/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)

R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

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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
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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 Dec 12 05:49:44 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 
  7.937   0.337   8.268