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BioC 3.5: CHECK report for HelloRanges on veracruz2

This page was generated on 2017-08-16 13:35:10 -0400 (Wed, 16 Aug 2017).

Package 621/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HelloRanges 1.2.0
Michael Lawrence
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/HelloRanges
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: HelloRanges
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HelloRanges_1.2.0.tar.gz
StartedAt: 2017-08-16 04:03:14 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 04:08:07 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 293.8 seconds
RetCode: 0
Status:  OK 
CheckDir: HelloRanges.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HelloRanges_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/HelloRanges.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 sizes of PDF files under ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/HelloRanges.Rcheck/00check.log’
for details.


HelloRanges.Rcheck/00install.out:

* 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)

HelloRanges.Rcheck/HelloRanges-Ex.timings:

nameusersystemelapsed
bedtools_closest0.9140.0060.929
bedtools_complement0.0220.0000.022
bedtools_coverage0.2970.0010.306
bedtools_flank0.1500.0010.152
bedtools_genomecov0.7550.0010.773
bedtools_getfasta0.0610.0000.064
bedtools_groupby0.1000.0000.101
bedtools_intersect0.5670.0360.626
bedtools_jaccard0.2080.0010.209
bedtools_makewindows0.1300.0010.143
bedtools_map0.2440.0020.258
bedtools_merge0.2250.0010.233
bedtools_multiinter0.1380.0010.145
bedtools_nuc0.0870.0000.095
bedtools_shift0.1090.0000.111
bedtools_slop0.1010.0010.102
bedtools_subtract0.1790.0010.185
bedtools_unionbedg0.0510.0000.053
distmode0.0030.0000.002