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### Running command:
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###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings geneXtendeR_1.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/geneXtendeR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* 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 ‘geneXtendeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geneXtendeR’ version ‘1.30.0’
* 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 ‘geneXtendeR’ can be installed ... WARNING
Found the following significant warnings:
  annotate.c:159:79: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  annotate.c:191:87: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  annotate.c:199:87: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  annotate.c:208:87: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  annotate.c:228:83: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
  extract_peaks.c:202:79: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=]
See ‘/home/biocbuild/bbs-3.19-bioc/meat/geneXtendeR.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data      5.8Mb
    doc       1.9Mb
    extdata   3.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘rtracklayer’
A package should be listed in only one of these fields.
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘BiocStyle’ ‘SnowballC’ ‘org.Rn.eg.db’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.geneXtender: no visible binding for global variable ‘type’
.geneXtender: no visible binding for global variable ‘seqid’
.geneXtender: no visible binding for global variable ‘gene_id’
.geneXtender: no visible binding for global variable ‘gene_name’
annotate_n: no visible binding for global variable ‘..I’
annotate_n: no visible binding for global variable ‘seqid’
diffGO: no visible binding for global variable ‘rat’
gene_annotate: no visible global function definition for ‘.’
gene_annotate: no visible binding for global variable
  ‘Distance-of-Gene-to-Nearest-Peak’
gene_annotate: no visible global function definition for ‘sd’
gene_annotate: no visible binding for global variable ‘Chromosome’
gene_annotate: no visible binding for global variable ‘Gene-Start’
gene_annotate: no visible binding for global variable ‘Gene-End’
gene_annotate: no visible binding for global variable ‘Gene-ID’
gene_annotate: no visible binding for global variable ‘Gene-Name’
gene_annotate: no visible binding for global variable
  ‘Peaks-on-Gene-Body’
gene_annotate: no visible binding for global variable
  ‘Number-of-Peaks-Associated-with-Gene’
gene_lookup: no visible binding for global variable ‘gene_name_id’
gene_lookup: no visible binding for global variable ‘gene_id’
gene_lookup : internal_find: no visible binding for global variable
  ‘Chromosome’
gene_lookup : internal_find: no visible binding for global variable
  ‘distance’
gene_lookup : internal_find: no visible global function definition for
  ‘na.omit’
gene_lookup: no visible binding for global variable ‘..I’
gene_lookup: no visible binding for global variable ‘distance’
makeWordCloud: no visible binding for global variable ‘rat’
meanPeakLength: no visible binding for global variable ‘rat’
peaksInput: no visible binding for global variable ‘chr’
peaksInput: no visible global function definition for ‘na.omit’
peaksMerge: no visible binding for global variable ‘chr’
peaksMerge: no visible binding for global variable ‘g’
peaksMerge: no visible global function definition for ‘.’
plotWordFreq : geneXtender: no visible binding for global variable
  ‘type’
plotWordFreq : geneXtender: no visible binding for global variable
  ‘seqid’
plotWordFreq : geneXtender: no visible binding for global variable
  ‘gene_id’
plotWordFreq : geneXtender: no visible binding for global variable
  ‘gene_name’
Undefined global functions or variables:
  . ..I Chromosome Distance-of-Gene-to-Nearest-Peak Gene-End Gene-ID
  Gene-Name Gene-Start Number-of-Peaks-Associated-with-Gene
  Peaks-on-Gene-Body chr distance g gene_id gene_name gene_name_id
  na.omit rat sd seqid type
Consider adding
  importFrom("stats", "na.omit", "sd")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... WARNING
  LazyData DB of 5.8 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... 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’ ... NOTE
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/geneXtendeR.Rnw’
(Is a VignetteBuilder field missing?)
* checking examples ... ERROR
Running examples in ‘geneXtendeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeNetwork
> ### Title: Makes gene-GO networks
> ### Aliases: makeNetwork
> 
> ### ** Examples
> 
> library(rtracklayer)
> rat <- readGFF("ftp://ftp.ensembl.org/pub/release-84/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.84.gtf.gz")
trying URL 'ftp://ftp.ensembl.org/pub/release-84/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.84.gtf.gz'
Content type 'unknown' length 11705191 bytes (11.2 MB)
==================================================
Warning in download.file(fp, filepath2[i]) :
  URL 'ftp://ftp.ensembl.org/pub/release-84/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.84.gtf.gz': status was 'Failure when receiving data from the peer'
Error in download.file(fp, filepath2[i]) : 
  cannot open URL 'ftp://ftp.ensembl.org/pub/release-84/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.84.gtf.gz'
Calls: readGFF ... <Anonymous> -> .normarg_input_filepath -> download.file
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’