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This page was generated on 2024-05-15 13:46:27 -0400 (Wed, 15 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4663
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 84/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
APAlyzer 1.19.0  (landing page)
Ruijia Wang
Snapshot Date: 2024-05-13 14:05:07 -0400 (Mon, 13 May 2024)
git_url: https://git.bioconductor.org/packages/APAlyzer
git_branch: devel
git_last_commit: efcd08d
git_last_commit_date: 2024-04-30 11:16:25 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for APAlyzer on kunpeng2


To the developers/maintainers of the APAlyzer package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/APAlyzer.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: APAlyzer
Version: 1.18.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:APAlyzer.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings APAlyzer_1.18.0.tar.gz
StartedAt: 2024-05-09 04:46:56 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 05:18:54 -0000 (Thu, 09 May 2024)
EllapsedTime: 1918.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: APAlyzer.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:APAlyzer.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings APAlyzer_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/APAlyzer.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 ‘APAlyzer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘APAlyzer’ version ‘1.18.0’
* 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)
=================
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’/home/biocbuild/R/R-beta-2024-04-15_r86425/bin/BATCH: line 60: 1271809 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Complete output:
  > require("APAlyzer") || stop("unable to load Package:APAlyzer")
  Loading required package: APAlyzer
* 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, 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/APAlyzer.Rcheck/00check.log’
for details.


Installation output

APAlyzer.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL APAlyzer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘APAlyzer’ ...
** 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)

Tests output

APAlyzer.Rcheck/tests/runTests.Rout.fail


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 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

Example timings

APAlyzer.Rcheck/APAlyzer-Ex.timings

nameusersystemelapsed
APABox0.5190.0120.534
APAVolcano0.5380.0080.547
APAdiff2.2620.0402.308
GENEXP_CDS14.792 2.24316.719
PAS2GEF 0.017 0.14378.211
PASEXP_3UTR16.482 3.54823.526
PASEXP_IPA16.591 1.34018.796
REF3UTR0.1660.0191.105
REF4PAS0.1720.0080.512
REFCDS0.6840.0760.762
ThreeMostPairBam1.5030.0641.570