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### Running command:
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###   /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings GenomicRanges_1.53.1.tar.gz
###
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* using log directory ‘/home/hpages/bbs-3.18-bioc-testing/meat/GenomicRanges.Rcheck’
* using R version 4.3.0 Patched (2023-05-23 r84466)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0
    GNU Fortran (Ubuntu 12.2.0-17ubuntu1) 12.2.0
* running under: Ubuntu 23.04
* using session charset: UTF-8
* checking for file ‘GenomicRanges/DESCRIPTION’ ... OK
* this is package ‘GenomicRanges’ version ‘1.53.1’
* 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 (Ubuntu 12.2.0-17ubuntu1) 12.2.0’
* 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
genomicvars              47.825  3.272  51.102
GPos-class               40.715  5.568  46.306
makeGRangesFromDataFrame  0.806  0.026   9.111
* 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 ...
  ‘GenomicRangesIntroduction.Rmd’ using ‘UTF-8’... OK
  ‘ExtendingGenomicRanges.Rnw’ using ‘UTF-8’... OK
  ‘GRanges_and_GRangesList_slides.Rnw’ using ‘UTF-8’... OK
  ‘GenomicRangesHOWTOs.Rnw’ using ‘UTF-8’... OK
  ‘Ten_things_slides.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/hpages/bbs-3.18-bioc-testing/meat/GenomicRanges.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/hpages/bbs-3.18-bioc/R/bin/R CMD INSTALL GenomicRanges
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* installing to library ‘/home/hpages/bbs-3.18-bioc-testing/Rlibs’
* installing *source* package ‘GenomicRanges’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0’
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/S4Vectors/include' -I'/home/hpages/bbs-3.18-bioc-testing/Rlibs/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c transcript_utils.c -o transcript_utils.o
In function ‘tloc2rloc’,
    inlined from ‘tlocs2rlocs’ at transcript_utils.c:208:26:
transcript_utils.c:143:45: warning: ‘end’ may be used uninitialized [-Wmaybe-uninitialized]
  143 |         return on_minus_strand ? end - tloc : start + tloc;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
transcript_utils.c: In function ‘tlocs2rlocs’:
transcript_utils.c:120:31: note: ‘end’ was declared here
  120 |         int nexons, j, start, end, width;
      |                               ^~~
In function ‘tloc2rloc’,
    inlined from ‘tlocs2rlocs’ at transcript_utils.c:208:26:
transcript_utils.c:143:45: warning: ‘start’ may be used uninitialized [-Wmaybe-uninitialized]
  143 |         return on_minus_strand ? end - tloc : start + tloc;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
transcript_utils.c: In function ‘tlocs2rlocs’:
transcript_utils.c:120:24: note: ‘start’ was declared here
  120 |         int nexons, j, start, end, width;
      |                        ^~~~~
gcc -shared -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o
installing to /home/hpages/bbs-3.18-bioc-testing/Rlibs/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 4.3.0 Patched (2023-05-23 r84466) -- "Already Tomorrow"
Copyright (C) 2023 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("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 Jun  1 13:12:23 2023 
*********************************************** 
Number of test functions: 73 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicRanges RUnit Tests - 73 test functions, 0 errors, 0 failures
Number of test functions: 73 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 45.397   0.223  45.605