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This page was generated on 2024-03-28 11:36:11 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 88/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
appreci8R 1.21.6  (landing page)
Sarah Sandmann
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/appreci8R
git_branch: devel
git_last_commit: dd97042
git_last_commit_date: 2024-02-14 07:22:16 -0400 (Wed, 14 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for appreci8R on nebbiolo1


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.

raw results


Summary

Package: appreci8R
Version: 1.21.6
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:appreci8R.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings appreci8R_1.21.6.tar.gz
StartedAt: 2024-03-27 20:15:55 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 20:23:22 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 447.5 seconds
RetCode: 0
Status:   OK  
CheckDir: appreci8R.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:appreci8R.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings appreci8R_1.21.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/appreci8R.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘appreci8R/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘appreci8R’ version ‘1.21.6’
* 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 re-building of vignette outputs ... OK
* 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/bbs-3.19-bioc/R/bin/R CMD INSTALL appreci8R
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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
annotate0.0900.0080.098
appreci8R-package000
appreci8Rshiny0.0000.0000.001
combineOutput0.2960.0240.320
determineCharacteristics0.1010.0080.110
evaluateCovAndBQ0.0750.0220.096
filterTarget0.0010.0000.002
finalFiltration0.1240.0280.152
normalize0.0010.0000.001