BioC 3.5: CHECK report for HelloRanges on malbec2

Package: HelloRanges

Version: 1.2.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings HelloRanges_1.2.0.tar.gz

StartedAt: 2017-10-17 23:57:56 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-18 00:02:40 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 283.8 seconds

RetCode: 0

Status:  OK

CheckDir: HelloRanges.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings HelloRanges_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/HelloRanges.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HelloRanges/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HelloRanges’ version ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘Biostrings’
  ‘BSgenome’ ‘GenomicFeatures’ ‘VariantAnnotation’ ‘Rsamtools’
  ‘GenomicAlignments’ ‘rtracklayer’ ‘GenomeInfoDb’
  ‘SummarizedExperiment’
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 ‘HelloRanges’ 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 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘BSgenome’ ‘GenomicAlignments’ ‘GenomicFeatures’ ‘VariantAnnotation’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::testPackage’ ‘IRanges:::subgrouping’
  ‘S4Vectors:::make_zero_col_DataFrame’
  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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘HelloRanges_unit_tests.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/HelloRanges.Rcheck/00check.log’
for details.

* installing *source* package ‘HelloRanges’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HelloRanges)

name	user	system	elapsed
bedtools_closest	0.704	0.000	0.737
bedtools_complement	0.016	0.000	0.015
bedtools_coverage	0.240	0.000	0.238
bedtools_flank	0.100	0.000	0.101
bedtools_genomecov	0.164	0.000	0.162
bedtools_getfasta	0.048	0.000	0.049
bedtools_groupby	0.108	0.000	0.110
bedtools_intersect	0.468	0.000	0.466
bedtools_jaccard	0.608	0.000	0.610
bedtools_makewindows	0.084	0.004	0.091
bedtools_map	0.184	0.000	0.180
bedtools_merge	0.176	0.004	0.182
bedtools_multiinter	0.084	0.000	0.084
bedtools_nuc	0.056	0.000	0.057
bedtools_shift	0.068	0.000	0.070
bedtools_slop	0.072	0.000	0.076
bedtools_subtract	0.144	0.000	0.144
bedtools_unionbedg	0.044	0.000	0.046
distmode	0.000	0.000	0.002