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BioC 3.4: CHECK report for HelloRanges on malbec1

This page was generated on 2017-04-15 16:14:10 -0400 (Sat, 15 Apr 2017).

Package 586/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HelloRanges 1.0.1
Michael Lawrence
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/HelloRanges
Last Changed Rev: 125974 / Revision: 128728
Last Changed Date: 2017-01-17 10:22:52 -0500 (Tue, 17 Jan 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: HelloRanges
Version: 1.0.1
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings HelloRanges_1.0.1.tar.gz
StartedAt: 2017-04-14 23:10:41 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:14:56 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 254.5 seconds
RetCode: 0
Status:  OK 
CheckDir: HelloRanges.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings HelloRanges_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/HelloRanges.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.0.1’
* 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-3.4-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_closest0.6800.0000.679
bedtools_complement0.0200.0000.019
bedtools_coverage0.1320.0080.138
bedtools_flank0.1000.0080.108
bedtools_genomecov0.1160.0000.116
bedtools_getfasta0.0480.0000.045
bedtools_groupby0.0560.0000.057
bedtools_intersect0.4160.0000.417
bedtools_jaccard0.1040.0000.104
bedtools_makewindows0.0960.0000.095
bedtools_map0.1760.0000.177
bedtools_merge0.1880.0000.190
bedtools_multiinter0.0720.0000.070
bedtools_nuc0.0480.0000.047
bedtools_shift0.0560.0000.055
bedtools_slop0.0560.0040.060
bedtools_subtract0.1080.0000.108
bedtools_unionbedg0.0480.0000.052
distmode0.0000.0000.003