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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 88/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
appreci8R 1.23.0  (landing page)
Sarah Sandmann
Snapshot Date: 2024-05-13 14:05:07 -0400 (Mon, 13 May 2024)
git_url: https://git.bioconductor.org/packages/appreci8R
git_branch: devel
git_last_commit: d9c0f80
git_last_commit_date: 2024-04-30 11:07:43 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for appreci8R on kunpeng2


To the developers/maintainers of the appreci8R package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/appreci8R.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: appreci8R
Version: 1.22.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:appreci8R.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings appreci8R_1.22.0.tar.gz
StartedAt: 2024-05-09 04:47:09 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 04:54:55 -0000 (Thu, 09 May 2024)
EllapsedTime: 466.9 seconds
RetCode: 0
Status:   OK  
CheckDir: appreci8R.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:appreci8R.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings appreci8R_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/appreci8R.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 ‘appreci8R/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘appreci8R’ version ‘1.22.0’
* 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 ‘appreci8R’ 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 ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotate: no visible global function definition for ‘write.table’
appreci8Rshiny : <anonymous>: no visible global function definition for
  ‘read.table’
appreci8Rshiny : <anonymous>: no visible global function definition for
  ‘write.table’
appreci8Rshiny : <anonymous>: no visible global function definition for
  ‘data’
appreci8Rshiny : <anonymous>: no visible global function definition for
  ‘ncbi_snp_query’
combineOutput: no visible global function definition for ‘write.table’
determineCharacteristics: no visible global function definition for
  ‘data’
determineCharacteristics: no visible global function definition for
  ‘ncbi_snp_query’
determineCharacteristics: no visible global function definition for
  ‘write.table’
evaluateCovAndBQ: no visible global function definition for
  ‘write.table’
filterTarget: no visible global function definition for ‘write.table’
finalFiltration: no visible global function definition for
  ‘write.table’
normalize: no visible global function definition for ‘write.table’
readInput : <anonymous>: no visible global function definition for
  ‘read.table’
readInput: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  data ncbi_snp_query read.table write.table
Consider adding
  importFrom("utils", "data", "read.table", "write.table")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/appreci8R.Rcheck/00check.log’
for details.


Installation output

appreci8R.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL appreci8R
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘appreci8R’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh37’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘XtraSNPlocs.Hsapiens.dbSNP144.GRCh37’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.1Kgenomes.phase3.hs37d5’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.ExAC.r1.0.hs37d5’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.gnomADex.r2.1.hs37d5’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh37’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘XtraSNPlocs.Hsapiens.dbSNP144.GRCh37’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.1Kgenomes.phase3.hs37d5’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.ExAC.r1.0.hs37d5’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.gnomADex.r2.1.hs37d5’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh37’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘XtraSNPlocs.Hsapiens.dbSNP144.GRCh37’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.1Kgenomes.phase3.hs37d5’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.ExAC.r1.0.hs37d5’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.gnomADex.r2.1.hs37d5’
** testing if installed package keeps a record of temporary installation path
* DONE (appreci8R)

Tests output


Example timings

appreci8R.Rcheck/appreci8R-Ex.timings

nameusersystemelapsed
annotate0.1790.0040.183
appreci8R-package000
appreci8Rshiny0.0000.0000.001
combineOutput0.4890.0040.494
determineCharacteristics0.1800.0090.190
evaluateCovAndBQ0.1560.0040.160
filterTarget0.0020.0000.002
finalFiltration0.2240.0080.232
normalize0.0020.0000.001