Back to Long Tests report for BioC 3.15

This page was generated on 2022-10-15 21:00:02 -0400 (Sat, 15 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4383
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

CHECK results for GenomicFeatures on nebbiolo1


To the developers/maintainers of the GenomicFeatures package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 21/26HostnameOS / ArchCHECK
GenomicFeatures 1.48.4  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-10-15 06:55:01 -0400 (Sat, 15 Oct 2022)
git_url: https://git.bioconductor.org/packages/GenomicFeatures
git_branch: RELEASE_3_15
git_last_commit: 06e37dc
git_last_commit_date: 2022-09-19 10:06:15 -0400 (Mon, 19 Sep 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  WARNINGS  

Summary

Package: GenomicFeatures
Version: 1.48.4
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no GenomicFeatures_1.48.4.tar.gz
StartedAt: 2022-10-15 08:25:00 -0400 (Sat, 15 Oct 2022)
EndedAt: 2022-10-15 08:27:28 -0400 (Sat, 15 Oct 2022)
EllapsedTime: 147.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GenomicFeatures.Rcheck
Warnings: 1

Tests output


'R CMD check' output

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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no GenomicFeatures_1.48.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc-longtests/meat/GenomicFeatures.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.48.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
  'GenomicRanges', 'AnnotationDbi'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘GenomicFeatures’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 R 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 dependencies in R code ... NOTE
':::' call which should be '::': ‘rtracklayer:::tableNames’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘rtracklayer:::resourceDescription’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Unknown package ‘GenomicRange’ in Rd xrefs
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
 WARNING
directory ‘longtests’ not found
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc-longtests/meat/GenomicFeatures.Rcheck/00check.log’
for details.



Installation output

GenomicFeatures.Rcheck/00install.out

* installing *source* package ‘GenomicFeatures’ ...
** 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 (GenomicFeatures)