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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:IRanges.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings IRanges_2.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/IRanges.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IRanges/DESCRIPTION’ ... OK
* this is package ‘IRanges’ version ‘2.45.0’
* 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 ‘IRanges’ can be installed ... OK
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
setCompressedListSummaryMethod : <anonymous>: no visible binding for
  global variable ‘C_fun’
setCompressedListWhichSummaryMethod : def: no visible binding for
  global variable ‘C_fun’
Undefined global functions or variables:
  C_fun
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'IntegerRangesList-class.Rd':
  ‘[IRanges]{RangesList}’

Missing link(s) in Rd file 'intra-range-methods.Rd':
  ‘RangesList’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AtomicList-class.Rd: List-class
  AtomicList-utils.Rd: unstrsplit
  CompressedHitsList-class.Rd: HitsList
  CompressedList-class.Rd: List
  DataFrameList-class.Rd: DataFrame-class, List-class
  Grouping-class.Rd: List
  IPosRanges-comparison.Rd: Hits
  NCList-class.Rd: Hits
  RleViews-class.Rd: Rle, Rle-class
  Views-class.Rd: Vector, Vector-class
  ViewsList-class.Rd: List-class
  coverage-methods.Rd: Rle
  extractList.Rd: Vector, List
  extractListFragments.Rd: List
  intra-range-methods.Rd: RangesList
  reverse-methods.Rd: revElements
  seqapply.Rd: List, Vector
  slice-methods.Rd: Rle
  view-summarization-methods.Rd: List, Rle
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘%poutside%’ ‘%pover%’ ‘%pwithin%’ ‘cvg’ ‘heads’ ‘slidingIRanges’
  ‘slidingViews’ ‘tails’ ‘windows’
Undocumented S4 classes:
  ‘BaseManyToManyGrouping’ ‘Pos’ ‘CompressedIntegerRangesList’
  ‘IPosList’ ‘CompressedRangesList’ ‘SimpleIPosList’ ‘RangesList’
  ‘CompressedPosList’ ‘CompressedIPosList’ ‘Ranges’ ‘SimplePosList’
  ‘PosList’ ‘SimpleRangesList’
Undocumented S4 methods:
  generic 'anyDuplicated' and siglist 'RangesNSBS'
  generic 'as.factor' and siglist 'ManyToOneGrouping'
  generic 'as.integer' and siglist 'NormalIRanges'
  generic 'as.integer' and siglist 'Pos'
  generic 'as.integer' and siglist 'RangesNSBS'
  generic 'cbind' and siglist 'Rle'
  generic 'cbind' and siglist 'RleList'
  generic 'chartr' and siglist 'ANY,ANY,CharacterList'
  generic 'chartr' and siglist 'ANY,ANY,RleList'
  generic 'coerce' and siglist 'ANY,IPosRanges'
  generic 'coerce' and siglist 'AtomicList,RleViews'
  generic 'coerce' and siglist 'IPosRanges,CompressedIntegerList'
  generic 'coerce' and siglist 'IPosRanges,IntegerList'
  generic 'coerce' and siglist 'IRanges,IPosList'
  generic 'coerce' and siglist 'IntegerRanges,CompressedIPosList'
  generic 'coerce' and siglist 'IntegerRanges,IPosList'
  generic 'coerce' and siglist 'PartitioningByEnd,PartitioningMap'
  generic 'coerce' and siglist 'factor,ManyToOneGrouping'
  generic 'commonColnames<-' and siglist 'SplitDataFrameList'
  generic 'cvg' and siglist 'IntegerRanges'
  generic 'cvg' and siglist 'IntegerRangesList'
  generic 'endsWith' and siglist 'CharacterList'
  generic 'endsWith' and siglist 'RleList'
  generic 'extractROWS' and siglist 'CompressedList,ANY'
  generic 'extractROWS' and siglist 'IPos,ANY'
  generic 'extractROWS' and siglist 'MaskCollection,ANY'
  generic 'extractROWS' and siglist 'NormalIRanges,ANY'
  generic 'extractROWS' and siglist 'Partitioning,ANY'
  generic 'extractROWS' and siglist 'Rle,RangesNSBS'
  generic 'extractROWS' and siglist 'vector_OR_factor,RangesNSBS'
  generic 'getListElement' and siglist 'CompressedList'
  generic 'getListElement' and siglist 'CompressedNormalIRangesList'
  generic 'getListElement' and siglist 'H2LGrouping'
  generic 'getListElement' and siglist 'MaskCollection'
  generic 'getListElement' and siglist 'NCLists'
  generic 'getListElement' and siglist 'Partitioning'
  generic 'getListElement' and siglist 'Views'
  generic 'gsub' and siglist 'ANY,ANY,CharacterList'
  generic 'gsub' and siglist 'ANY,ANY,RleList'
  generic 'ifelse2' and siglist 'ANY,List,List'
  generic 'is.unsorted' and siglist 'CompressedIntegerList'
  generic 'is.unsorted' and siglist 'CompressedLogicalList'
  generic 'is.unsorted' and siglist 'CompressedNumericList'
  generic 'isNormal' and siglist 'IntegerRanges'
  generic 'length' and siglist 'RangesNSBS'
  generic 'nchar' and siglist 'CharacterList'
  generic 'nchar' and siglist 'RleList'
  generic 'pcompareRecursively' and siglist 'IPosRanges'
  generic 'relist' and siglist 'grouping,missing'
  generic 'replaceROWS' and siglist 'IRanges'
  generic 'replaceROWS' and siglist 'NormalIRanges'
  generic 'slidingWindows' and siglist 'IntegerRanges'
  generic 'startsWith' and siglist 'CharacterList'
  generic 'startsWith' and siglist 'RleList'
  generic 'sub' and siglist 'ANY,ANY,CharacterList'
  generic 'sub' and siglist 'ANY,ANY,RleList'
  generic 'tile' and siglist 'IntegerRanges'
  generic 'tolower' and siglist 'CharacterList'
  generic 'tolower' and siglist 'RleList'
  generic 'toupper' and siglist 'CharacterList'
  generic 'toupper' and siglist 'RleList'
  generic 'updateObject' and siglist 'CompressedList'
  generic 'updateObject' and siglist 'IPosRanges'
  generic 'whichFirstNotNormal' and siglist 'IntegerRanges'
  generic 'windows' and siglist 'list_OR_List'
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 ... WARNING
Documented arguments not in \usage in Rd file 'nearest-methods.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘IRanges-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IPos-class
> ### Title: IPos objects
> ### Aliases: class:IPos IPos-class IPos parallel_slot_names,IPos-method
> ###   class:UnstitchedIPos UnstitchedIPos-class UnstitchedIPos
> ###   parallel_slot_names,UnstitchedIPos-method class:StitchedIPos
> ###   StitchedIPos-class StitchedIPos updateObject,IPos-method pos
> ###   pos,UnstitchedIPos-method pos,IPos-method
> ###   length,UnstitchedIPos-method length,IPos-method names,IPos-method
> ###   names<-,IPos-method coerce,UnstitchedIPos,StitchedIPos-method
> ###   coerce,StitchedIPos,UnstitchedIPos-method
> ###   coerce,IntegerRanges,UnstitchedIPos-method
> ###   coerce,IntegerRanges,StitchedIPos-method
> ###   coerce,IntegerRanges,IPos-method coerce,ANY,UnstitchedIPos-method
> ###   coerce,ANY,StitchedIPos-method coerce,ANY,IPos-method
> ###   as.data.frame.IPos as.data.frame,IPos-method extractROWS,IPos-method
> ###   summary.IPos summary,IPos-method show,IPos-method
> ###   bindROWS,IPos-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> showClass("IPos")  # shows the known subclasses
Virtual Class "IPos" [package "IRanges"]

Slots:
                                                                              
Name:              NAMES       elementType   elementMetadata          metadata
Class: character_OR_NULL         character DataFrame_OR_NULL              list

Extends: 
Class "Pos", directly
Class "IPosRanges", directly
Class "IntegerRanges", by class "IPosRanges", distance 2
Class "Ranges", by class "IPosRanges", distance 3
Class "List", by class "IPosRanges", distance 4
Class "Vector", by class "IPosRanges", distance 5
Class "list_OR_List", by class "IPosRanges", distance 5
Class "Annotated", by class "IPosRanges", distance 6
Class "vector_OR_Vector", by class "IPosRanges", distance 6
Class "IntegerRanges_OR_missing", by class "IntegerRanges", distance 3

Known Subclasses: "UnstitchedIPos", "StitchedIPos"
> 
> ## ---------------------------------------------------------------------
> ## BASIC EXAMPLES
> ## ---------------------------------------------------------------------
> 
> ## Example 1:
> ipos1a <- IPos(c(44:53, 5:10, 2:5))
> ipos1a  # unstitched
UnstitchedIPos object with 20 positions and 0 metadata columns:
             pos
       <integer>
   [1]        44
   [2]        45
   [3]        46
   [4]        47
   [5]        48
   ...       ...
  [16]        10
  [17]         2
  [18]         3
  [19]         4
  [20]         5
> 
> length(ipos1a)
[1] 20
> pos(ipos1a)  # same as 'start(ipos1a)' and 'end(ipos1a)'
 [1] 44 45 46 47 48 49 50 51 52 53  5  6  7  8  9 10  2  3  4  5
> as.character(ipos1a)
 [1] "44" "45" "46" "47" "48" "49" "50" "51" "52" "53" "5"  "6"  "7"  "8"  "9" 
[16] "10" "2"  "3"  "4"  "5" 
> as.data.frame(ipos1a)
   pos
1   44
2   45
3   46
4   47
5   48
6   49
7   50
8   51
9   52
10  53
11   5
12   6
13   7
14   8
15   9
16  10
17   2
18   3
19   4
20   5
> as(ipos1a, "IRanges")
IRanges object with 20 ranges and 0 metadata columns:
           start       end     width
       <integer> <integer> <integer>
   [1]        44        44         1
   [2]        45        45         1
   [3]        46        46         1
   [4]        47        47         1
   [5]        48        48         1
   ...       ...       ...       ...
  [16]        10        10         1
  [17]         2         2         1
  [18]         3         3         1
  [19]         4         4         1
  [20]         5         5         1
> as.data.frame(as(ipos1a, "IRanges"))
   start end width
1     44  44     1
2     45  45     1
3     46  46     1
4     47  47     1
5     48  48     1
6     49  49     1
7     50  50     1
8     51  51     1
9     52  52     1
10    53  53     1
11     5   5     1
12     6   6     1
13     7   7     1
14     8   8     1
15     9   9     1
16    10  10     1
17     2   2     1
18     3   3     1
19     4   4     1
20     5   5     1
> ipos1a[9:17]
UnstitchedIPos object with 9 positions and 0 metadata columns:
            pos
      <integer>
  [1]        52
  [2]        53
  [3]         5
  [4]         6
  [5]         7
  [6]         8
  [7]         9
  [8]        10
  [9]         2
> 
> ipos1b <- IPos(c(44:53, 5:10, 2:5), stitch=TRUE)
> ipos1b  # stitched
StitchedIPos object with 20 positions and 0 metadata columns:
             pos
       <integer>
   [1]        44
   [2]        45
   [3]        46
   [4]        47
   [5]        48
   ...       ...
  [16]        10
  [17]         2
  [18]         3
  [19]         4
  [20]         5
> 
> ## 'ipos1a' and 'ipos1b' are semantically equivalent, only their
> ## internal representations differ:
> all(ipos1a == ipos1b)
[1] TRUE
> 
> ipos1c <- IPos(c("44-53", "5-10", "2-5"))
> ipos1c  # stitched
StitchedIPos object with 20 positions and 0 metadata columns:
             pos
       <integer>
   [1]        44
   [2]        45
   [3]        46
   [4]        47
   [5]        48
   ...       ...
  [16]        10
  [17]         2
  [18]         3
  [19]         4
  [20]         5
> 
> identical(ipos1b, ipos1c)
[1] TRUE
> 
> ## Example 2:
> my_pos <- IRanges(c(1, 6, 12, 17), c(5, 10, 16, 20))
> ipos2 <- IPos(my_pos)
> ipos2  # stitched
StitchedIPos object with 19 positions and 0 metadata columns:
             pos
       <integer>
   [1]         1
   [2]         2
   [3]         3
   [4]         4
   [5]         5
   ...       ...
  [15]        16
  [16]        17
  [17]        18
  [18]        19
  [19]        20
> 
> ## Example 3:
> ipos3A <- ipos3B <- IPos(c("1-15000", "15400-88700"))
> npos <- length(ipos3A)
> 
> mcols(ipos3A)$sample <- Rle("sA")
> sA_counts <- sample(10, npos, replace=TRUE)
> mcols(ipos3A)$counts <- sA_counts
> 
> mcols(ipos3B)$sample <- Rle("sB")
> sB_counts <- sample(10, npos, replace=TRUE)
> mcols(ipos3B)$counts <- sB_counts
> 
> ipos3 <- c(ipos3A, ipos3B)
> ipos3
StitchedIPos object with 176602 positions and 2 metadata columns:
                 pos | sample    counts
           <integer> |  <Rle> <integer>
       [1]         1 |     sA         9
       [2]         2 |     sA         4
       [3]         3 |     sA         7
       [4]         4 |     sA         1
       [5]         5 |     sA         2
       ...       ... .    ...       ...
  [176598]     88696 |     sB         5
  [176599]     88697 |     sB        10
  [176600]     88698 |     sB         4
  [176601]     88699 |     sB         8
  [176602]     88700 |     sB         3
> 
> ## ---------------------------------------------------------------------
> ## MEMORY USAGE
> ## ---------------------------------------------------------------------
> 
> ## Coercion to IRanges works on a StitchedIPos object...
> ipos4 <- IPos(c("1-125000", "135000-575000"))
> ir4 <- as(ipos4, "IRanges")
> ir4
IRanges object with 565001 ranges and 0 metadata columns:
               start       end     width
           <integer> <integer> <integer>
       [1]         1         1         1
       [2]         2         2         1
       [3]         3         3         1
       [4]         4         4         1
       [5]         5         5         1
       ...       ...       ...       ...
  [564997]    574996    574996         1
  [564998]    574997    574997         1
  [564999]    574998    574998         1
  [565000]    574999    574999         1
  [565001]    575000    575000         1
> ## ... but is generally not a good idea:
> object.size(ipos4)
2904 bytes
> object.size(ir4)  # 1652 times bigger than the StitchedIPos object!
4521560 bytes
> 
> ## Shuffling the order of the positions impacts memory usage:
> ipos4r <- rev(ipos4)
> object.size(ipos4r)
4522904 bytes
> ipos4s <- sample(ipos4)
> object.size(ipos4s)
4522888 bytes
> 
> ## If one anticipates a lot of shuffling of the positions,
> ## then an UnstitchedIPos object should be used instead:
> ipos4b <- as(ipos4, "UnstitchedIPos")
> object.size(ipos4b)  # initial size is bigger than stitched version
2261400 bytes
> object.size(rev(ipos4b))  # size didn't change
2261400 bytes
> object.size(sample(ipos4b))  # size didn't change
2261400 bytes
> 
> ## AN IMPORTANT NOTE: In the worst situations, IPos still performs
> ## as good as an IRanges object.
> object.size(as(ipos4r, "IRanges"))  # same size as 'ipos4r'
4521560 bytes
> object.size(as(ipos4s, "IRanges"))  # same size as 'ipos4s'
4521560 bytes
> 
> ## Best case scenario is when the object is strictly sorted (i.e.
> ## positions are in strict ascending order).
> ## This can be checked with:
> is.unsorted(ipos4, strict=TRUE)  # 'ipos4' is strictly sorted
[1] FALSE
> 
> ## ---------------------------------------------------------------------
> ## USING MEMORY-EFFICIENT METADATA COLUMNS
> ## ---------------------------------------------------------------------
> ## In order to keep memory usage as low as possible, it is recommended
> ## to use a memory-efficient representation of the metadata columns that
> ## we want to set on the object. Rle's are particularly well suited for
> ## this, especially if the metadata columns contain long runs of
> ## identical values. This is the case for example if we want to use an
> ## IPos object to represent the coverage of sequencing reads along a
> ## chromosome.
> 
> ## Example 5:
> library(pasillaBamSubset)
> library(Rsamtools)  # for the BamFile() constructor function
Loading required package: GenomeInfoDb
Loading required package: Seqinfo
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Error: package or namespace load failed for ‘Rsamtools’:
 class "Seqinfo" is not exported by 'namespace:GenomeInfoDb'
Execution halted
* 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:
  1 Test Suite : 
  IRanges RUnit Tests - 104 test functions, 1 error, 0 failures
  ERROR in test_DataFrameList_transform: Error in argname %notin% names(sys.call(which)) : 
    could not find function "%notin%"
  
  Test files with failing tests
  
     test_DataFrameList.R 
       test_DataFrameList_transform 
  
  
  Error in BiocGenerics:::testPackage("IRanges") : 
    unit tests failed for package IRanges
  Calls: <Anonymous> -> <Anonymous>
  Execution halted
* 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 ERRORs, 3 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/IRanges.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL IRanges
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘IRanges’ ...
** this is package ‘IRanges’ version ‘2.45.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c CompressedList_class.c -o CompressedList_class.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c Grouping_class.c -o Grouping_class.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c IPosRanges_comparison.c -o IPosRanges_comparison.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c IRanges_class.c -o IRanges_class.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c IRanges_constructor.c -o IRanges_constructor.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c NCList.c -o NCList.o
NCList.c:1303:13: warning: ‘NCList_get_y_overlaps_rec’ defined but not used [-Wunused-function]
 1303 | static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~
NCList.c:203:22: warning: ‘next_top_down’ defined but not used [-Wunused-function]
  203 | static const NCList *next_top_down(NCListWalkingStack *stack,
      |                      ^~~~~~~~~~~~~
NCList.c: In function ‘C_find_overlaps_in_groups_NCList’:
NCList.c:1782:24: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized]
 1782 |                 return ans;
      |                        ^~~
NCList.c:1751:14: note: ‘ans’ was declared here
 1751 |         SEXP ans;
      |              ^~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c R_init_IRanges.c -o R_init_IRanges.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c Ranges_class.c -o Ranges_class.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c RleViews_summarization.c -o RleViews_summarization.o
In function ‘viewWhichMaxs_int_RleViews’,
    inlined from ‘viewWhichMaxs_RleViews’ at RleViews_summarization.c:579:3,
    inlined from ‘C_summarize_RleViews’ at RleViews_summarization.c:694:9:
RleViews_summarization.c:325:54: warning: ‘max’ may be used uninitialized [-Wmaybe-uninitialized]
  325 |                         if (!max_is_initialized || v > max) {
      |                                                    ~~^~~~~
RleViews_summarization.c: In function ‘C_summarize_RleViews’:
RleViews_summarization.c:316:21: note: ‘max’ was declared here
  316 |                 int max;  /* uninitialized */
      |                     ^~~
In function ‘viewWhichMins_int_RleViews’,
    inlined from ‘viewWhichMins_RleViews’ at RleViews_summarization.c:546:3,
    inlined from ‘C_summarize_RleViews’ at RleViews_summarization.c:686:9:
RleViews_summarization.c:293:54: warning: ‘min’ may be used uninitialized [-Wmaybe-uninitialized]
  293 |                         if (!min_is_initialized || v < min) {
      |                                                    ~~^~~~~
RleViews_summarization.c: In function ‘C_summarize_RleViews’:
RleViews_summarization.c:284:21: note: ‘min’ was declared here
  284 |                 int min;  /* uninitialized */
      |                     ^~~
In function ‘viewMaxs_int_RleViews’,
    inlined from ‘viewMaxs_RleViews’ at RleViews_summarization.c:443:3,
    inlined from ‘C_summarize_RleViews’ at RleViews_summarization.c:665:9:
RleViews_summarization.c:67:54: warning: ‘max’ may be used uninitialized [-Wmaybe-uninitialized]
   67 |                         if (!max_is_initialized || v > max) {
      |                                                    ~~^~~~~
RleViews_summarization.c: In function ‘C_summarize_RleViews’:
RleViews_summarization.c:54:21: note: ‘max’ was declared here
   54 |                 int max;  /* uninitialized */
      |                     ^~~
In function ‘viewMins_int_RleViews’,
    inlined from ‘viewMins_RleViews’ at RleViews_summarization.c:413:3,
    inlined from ‘C_summarize_RleViews’ at RleViews_summarization.c:660:9:
RleViews_summarization.c:36:54: warning: ‘min’ may be used uninitialized [-Wmaybe-uninitialized]
   36 |                         if (!min_is_initialized || v < min) {
      |                                                    ~~^~~~~
RleViews_summarization.c: In function ‘C_summarize_RleViews’:
RleViews_summarization.c:23:21: note: ‘min’ was declared here
   23 |                 int min;  /* uninitialized */
      |                     ^~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c coverage_methods.c -o coverage_methods.o
In function ‘shift_and_clip_ranges’,
    inlined from ‘compute_coverage_from_IRanges_holder’ at coverage_methods.c:609:12:
coverage_methods.c:579:35: warning: ‘x_end’ may be used uninitialized [-Wmaybe-uninitialized]
  579 |         if (*out_ranges_are_tiles && x_end != cvg_len)
      |             ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
coverage_methods.c: In function ‘compute_coverage_from_IRanges_holder’:
coverage_methods.c:495:28: note: ‘x_end’ was declared here
  495 |             i, j, x_start, x_end, shift_elt, tmp;
      |                            ^~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c extractListFragments.c -o extractListFragments.o
extractListFragments.c: In function ‘C_find_partition_overlaps’:
extractListFragments.c:85:25: warning: ‘split_partitions_buf’ may be used uninitialized [-Wmaybe-uninitialized]
   85 |                         IntAE_insert_at(split_partitions_buf,
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   86 |                                 IntAE_get_nelt(split_partitions_buf),
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   87 |                                 q_prev_end);
      |                                 ~~~~~~~~~~~
extractListFragments.c:35:16: note: ‘split_partitions_buf’ was declared here
   35 |         IntAE *split_partitions_buf;
      |                ^~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function ‘reduce_ranges.isra’:
inter_range_methods.c:154:39: warning: ‘gapwidth’ may be used uninitialized [-Wmaybe-uninitialized]
  154 |                                 delta += gapwidth;
      |                                 ~~~~~~^~~~~~~~~~~
inter_range_methods.c:102:38: note: ‘gapwidth’ was declared here
  102 |             append_or_drop, max_end, gapwidth, delta, width_inc;
      |                                      ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security -c thread_control.c -o thread_control.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_summarization.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o thread_control.o -fopenmp -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-IRanges/00new/IRanges/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘startsWith’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘endsWith’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’
** 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 (IRanges)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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Platform: aarch64-unknown-linux-gnu

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> require("IRanges") || stop("unable to load IRanges package")
Loading required package: IRanges
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

Loading required package: S4Vectors
Loading required package: stats4

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
> IRanges:::.test()
Timing stopped at: 0.017 0.004 0.02
Error in argname %notin% names(sys.call(which)) : 
  could not find function "%notin%"
In addition: Warning messages:
1: In recycleListElements(e1, en) :
  Some element lengths are not multiples of their corresponding element length in e1
2: In x + y :
  longer object length is not a multiple of shorter object length
3: In recycleListElements(e1, en) :
  Some element lengths are not multiples of their corresponding element length in e1
4: In x + y :
  longer object length is not a multiple of shorter object length


RUNIT TEST PROTOCOL -- Fri Apr 17 04:29:02 2026 
*********************************************** 
Number of test functions: 104 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
IRanges RUnit Tests - 104 test functions, 1 error, 0 failures
ERROR in test_DataFrameList_transform: Error in argname %notin% names(sys.call(which)) : 
  could not find function "%notin%"

Test files with failing tests

   test_DataFrameList.R 
     test_DataFrameList_transform 


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