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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings GenomicRanges_1.54.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GenomicRanges.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicRanges/DESCRIPTION’ ... OK
* this is package ‘GenomicRanges’ version ‘1.54.1’
* 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 ‘GenomicRanges’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    SIGNIFICANT USER-VISIBLE CHANGES
  Cannot process chunk/lines:
    DEPRECATED AND DEFUNCT
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GenomicRanges-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genomicvars
> ### Title: Manipulating genomic variables
> ### Aliases: genomicvars genomicvariables coerce,RleList,GRanges-method
> ###   coerce,RleViewsList,GRanges-method bindAsGRanges mcolAsRleList
> ###   binnedAverage
> ### Keywords: manip
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## A. TWO WAYS TO REPRESENT A GENOMIC VARIABLE
> ## -----------------------------------------------------------------
> 
> ## 1) As a named RleList object
> ## ----------------------------
> ## Let's create a genomic variable in the "named RleList" form:
> library(BSgenome.Scerevisiae.UCSC.sacCer2)
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

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

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: ‘rtracklayer’

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

    FileForFormat

> set.seed(55)
> my_var <- RleList(
+     lapply(seqlengths(Scerevisiae),
+         function(seqlen) {
+             tmp <- sample(50L, seqlen, replace=TRUE) 
+             Rle(cumsum(tmp - rev(tmp)))
+         }
+     ),
+     compress=FALSE)
> my_var
RleList of length 18
$chrI
integer-Rle of length 230208 with 225554 runs
  Lengths:   1   1   1   1   1   1   1   1 ...   1   1   1   1   1   1   1   1
  Values :  -1   2  45   7  15  25  74  59 ...  74  25  15   7  45   2  -1   0

$chrII
integer-Rle of length 813178 with 796736 runs
  Lengths:    1    1    1    1    1    1    1 ...    1    1    1    1    1    1
  Values :  -44  -66  -75  -87  -88  -80 -109 ...  -88  -87  -75  -66  -44    0

$chrIII
integer-Rle of length 316617 with 310186 runs
  Lengths:   1   1   1   1   1   1   1   1 ...   1   1   1   1   1   1   1   1
  Values : -30 -33 -25 -50 -25 -37  -2 -44 ...  -2 -37 -25 -50 -25 -33 -30   0

$chrIV
integer-Rle of length 1531919 with 1501028 runs
  Lengths:    1    1    1    1    1    1    1 ...    1    1    1    1    1    1
  Values :   28   61   22   41   80   47   70 ...   80   41   22   61   28    0

$chrV
integer-Rle of length 576869 with 565604 runs
  Lengths:   1   1   1   1   1   1   1   1 ...   1   1   1   1   1   1   1   1
  Values :   5  19 -11 -29 -24 -13 -10 -21 ... -10 -13 -24 -29 -11  19   5   0

...
<13 more elements>
> 
> ## 2) As a metadata column on a disjoint GRanges object
> ## ----------------------------------------------------
> gr1 <- bindAsGRanges(my_var=my_var)
* 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: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/GenomicRanges.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL GenomicRanges
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘GenomicRanges’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-4.3.1/site-library/IRanges/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function ‘tlocs2rlocs’:
transcript_utils.c:143:38: warning: ‘end’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  143 |  return on_minus_strand ? end - tloc : start + tloc;
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
transcript_utils.c:120:24: note: ‘end’ was declared here
  120 |  int nexons, j, start, end, width;
      |                        ^~~
transcript_utils.c:143:38: warning: ‘start’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  143 |  return on_minus_strand ? end - tloc : start + tloc;
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
transcript_utils.c:120:17: note: ‘start’ was declared here
  120 |  int nexons, j, start, end, width;
      |                 ^~~~~
gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-GenomicRanges/00new/GenomicRanges/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (GenomicRanges)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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("GenomicRanges") || stop("unable to load GenomicRanges package")
Loading required package: GenomicRanges
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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
[1] TRUE
> GenomicRanges:::.test()


RUNIT TEST PROTOCOL -- Thu Nov  2 10:54:28 2023 
*********************************************** 
Number of test functions: 74 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicRanges RUnit Tests - 74 test functions, 0 errors, 0 failures
Number of test functions: 74 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 60.997   2.292  65.230