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###
### Running command:
###
###   /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD check --install=check:S4Vectors.install-out.txt --library=/home/hpages/bbs-3.18-bioc-R41/R/site-library --timings S4Vectors_0.40.2.tar.gz
###
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* using log directory ‘/home/hpages/bbs-3.18-bioc-R41/meat/S4Vectors.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘S4Vectors/DESCRIPTION’ ... OK
* this is package ‘S4Vectors’ version ‘0.40.2’
* 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
* 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 loading without being on the library search path ... 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 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 '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        16.819  0.539  17.360
TransposedDataFrame-class  5.170  0.167   5.337
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 ERROR
Running the tests in ‘tests/run_unitTests.R’ failed.
Last 13 lines of output:
  
  Error in BiocGenerics:::testPackage("S4Vectors") : 
    unit tests failed for package S4Vectors
  Calls: <Anonymous> -> <Anonymous>
  In addition: 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
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘RleTricks.Rmd’ using ‘UTF-8’... OK
  ‘S4QuickOverview.Rnw’ using ‘UTF-8’... OK
  ‘S4VectorsOverview.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 WARNINGs, 3 NOTEs
See
  ‘/home/hpages/bbs-3.18-bioc-R41/meat/S4Vectors.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD INSTALL S4Vectors
###
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* installing to library ‘/home/hpages/bbs-3.18-bioc-R41/R/site-library’
* installing *source* package ‘S4Vectors’ ...
** using staged installation
** libs
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c AEbufs.c -o AEbufs.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c DataFrame_class.c -o DataFrame_class.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Hits_class.c -o Hits_class.o
In file included from /home/hpages/bbs-3.18-bioc-R41/R/include/Rdefines.h:42,
                 from ../inst/include/S4Vectors_defines.h:18,
                 from S4Vectors.h:1,
                 from Hits_class.c:4:
Hits_class.c: In function ‘Hits_new’:
/home/hpages/bbs-3.18-bioc-R41/R/include/Rinternals.h:1549:33: warning: ‘revmap’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1549 | #define defineVar               Rf_defineVar
      |                                 ^~~~~~~~~~~~
Hits_class.c:216:19: note: ‘revmap’ was declared here
  216 |         SEXP ans, revmap, symbol;
      |                   ^~~~~~
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c LLint_class.c -o LLint_class.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c List_class.c -o List_class.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Rle_class.c -o Rle_class.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c Rle_utils.c -o Rle_utils.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c SEXP_utils.c -o SEXP_utils.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c SimpleList_class.c -o SimpleList_class.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c anyMissing.c -o anyMissing.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c character_utils.c -o character_utils.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c eval_utils.c -o eval_utils.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c hash_utils.c -o hash_utils.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c integer_utils.c -o integer_utils.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c logical_utils.c -o logical_utils.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/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/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c raw_utils.c -o raw_utils.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c safe_arithm.c -o safe_arithm.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/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/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c subsetting_utils.c -o subsetting_utils.o
gcc -I"/home/hpages/bbs-3.18-bioc-R41/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c vector_utils.c -o vector_utils.o
gcc -shared -L/home/hpages/bbs-3.18-bioc-R41/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/hpages/bbs-3.18-bioc-R41/R/lib -lR
installing to /home/hpages/bbs-3.18-bioc-R41/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’
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
   ‘RleTricks.Rmd’ using ‘UTF-8’ 
   ‘S4QuickOverview.Rnw’ using ‘UTF-8’ 
   ‘S4VectorsOverview.Rnw’ using ‘UTF-8’ 
** 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 version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 objects are masked from 'package:base':

    I, expand.grid, unname

[1] TRUE
> S4Vectors:::.test()
Timing stopped at: 0.1 0 0.1
Error in as.POSIXlt.numeric(c(123123, 124235235, 96546546)) : 
  'origin' must be supplied
Timing stopped at: 0.53 0 0.53
Error in as.POSIXlt.numeric(c(123123, 124235235, 96546546)) : 
  'origin' must be supplied
Loading required package: GenomeInfoDb


RUNIT TEST PROTOCOL -- Fri Mar  8 16:16:24 2024 
*********************************************** 
Number of test functions: 74 
Number of errors: 2 
Number of failures: 0 

 
1 Test Suite : 
S4Vectors RUnit Tests - 74 test functions, 2 errors, 0 failures
ERROR in test_DataFrame_construction: Error in as.POSIXlt.numeric(c(123123, 124235235, 96546546)) : 
  'origin' must be supplied
ERROR in test_DataFrame_replace: Error in as.POSIXlt.numeric(c(123123, 124235235, 96546546)) : 
  'origin' must be supplied

Test files with failing tests

   test_DataFrame-class.R 
     test_DataFrame_construction 
     test_DataFrame_replace 


Error in BiocGenerics:::testPackage("S4Vectors") : 
  unit tests failed for package S4Vectors
Calls: <Anonymous> -> <Anonymous>
In addition: 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
Execution halted