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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:APAlyzer.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings APAlyzer_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/APAlyzer.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘APAlyzer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘APAlyzer’ version ‘1.24.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘APAlyzer’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... WARNING
'library' or 'require' call not declared from: ‘HybridMTest’
'library' or 'require' call to ‘HybridMTest’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.GTF2LE: no visible binding for global variable ‘group_name’
.GTF2refUTRraw: no visible binding for global variable ‘GENEID’
.annotatePASRegion: no visible global function definition for
  ‘queryHits’
APABox: no visible binding for global variable ‘APAreg’
APABox: no visible binding for global variable ‘RED’
APAVolcano: no visible binding for global variable ‘APAreg’
APAVolcano: no visible binding for global variable ‘color’
PASEXP_IPA: no visible global function definition for ‘Print’
ThreeMostPairBam: no visible global function definition for ‘Print’
download_testbam: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  APAreg GENEID Print RED color download.file group_name queryHits
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: download_testbam.Rd:7-8: Dropping empty section \arguments
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘APAlyzer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: download_testbam
> ### Title: download_testbam, download bam files of mouse testis and heart
> ### Aliases: download_testbam
> 
> ### ** Examples
> 
> 	download_testbam()
[1] "Download  Heart_rep1"
trying URL 'https://media.githubusercontent.com/media/RJWANGbioinfo/PAS_reference_RData_and_testing_data/master/bam/Heart_rep1.bam'
Content type 'application/octet-stream' length 358373738 bytes (341.8 MB)
==================================================
downloaded 341.8 MB

[1] "Download  Heart_rep2"
trying URL 'https://media.githubusercontent.com/media/RJWANGbioinfo/PAS_reference_RData_and_testing_data/master/bam/Heart_rep2.bam'
Content type 'application/octet-stream' length 341667659 bytes (325.8 MB)
==================================================
downloaded 325.8 MB

[1] "Download  Heart_rep3"
trying URL 'https://media.githubusercontent.com/media/RJWANGbioinfo/PAS_reference_RData_and_testing_data/master/bam/Heart_rep3.bam'
Content type 'application/octet-stream' length 384305345 bytes (366.5 MB)
==================================================
downloaded 366.5 MB

[1] "Download  Heart_rep4"
trying URL 'https://media.githubusercontent.com/media/RJWANGbioinfo/PAS_reference_RData_and_testing_data/master/bam/Heart_rep4.bam'
Content type 'application/octet-stream' length 364028034 bytes (347.2 MB)
==================================================
downloaded 347.2 MB

[1] "Download  Testis_rep1"
trying URL 'https://media.githubusercontent.com/media/RJWANGbioinfo/PAS_reference_RData_and_testing_data/master/bam/Testis_rep1.bam'
Content type 'application/octet-stream' length 341459693 bytes (325.6 MB)
=========
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
PASEXP_3UTR 16.004  3.484  26.674
PASEXP_IPA  14.874  0.895  26.800
GENEXP_CDS  12.678  1.971  17.153
PAS2GEF      0.235  0.257 130.063
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL APAlyzer
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘APAlyzer’ ...
** this is package ‘APAlyzer’ version ‘1.24.0’
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (APAlyzer)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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("APAlyzer") || stop("unable to load Package:APAlyzer")
Loading required package: APAlyzer