Back to Long Tests report for BioC 3.10

CHECK report for GenomicFeatures on malbec1

This page was generated on 2019-12-14 19:30:02 -0500 (Sat, 14 Dec 2019).

Package 3/4HostnameOS / ArchCHECK
GenomicFeatures 1.38.0
Bioconductor Package Maintainer
Snapshot Date: 2019-12-14 10:00:01 -0500 (Sat, 14 Dec 2019)
URL: https://git.bioconductor.org/packages/GenomicFeatures
Branch: RELEASE_3_10
Last Commit: cd3bfc3
Last Changed Date: 2019-11-27 02:06:53 -0500 (Wed, 27 Nov 2019)
malbec1 Linux (Ubuntu 18.04.3 LTS) / x86_64 [ WARNINGS ]

Summary

Package: GenomicFeatures
Version: 1.38.0
Command: /home/biocbuild/bbs-3.10-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_1.38.0.tar.gz
StartedAt: 2019-12-14 11:00:21 -0500 (Sat, 14 Dec 2019)
EndedAt: 2019-12-14 11:02:32 -0500 (Sat, 14 Dec 2019)
EllapsedTime: 130.8 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-3.10-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_1.38.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc-longtests/meat/GenomicFeatures.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.38.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
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 ‘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
':::' calls which should be '::':
  ‘S4Vectors:::duplicatedIntegerPairs’ ‘S4Vectors:::matchIntegerPairs’
  ‘S4Vectors:::orderIntegerPairs’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘rtracklayer:::resourceDescription’ ‘rtracklayer:::ucscTableOutputs’
  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 ... OK
* 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-3.10-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)