GenomicFiles 1.8.0
Bioconductor Package Maintainer
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/GenomicFiles | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings GenomicFiles_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/GenomicFiles.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicFiles/DESCRIPTION’ ... OK
* this is package ‘GenomicFiles’ version ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘BiocGenerics’ ‘GenomicRanges’ ‘SummarizedExperiment’ ‘BiocParallel’
‘Rsamtools’ ‘rtracklayer’
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 ‘GenomicFiles’ 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Biobase’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
REDUCEsampler : <anonymous>: no visible global function definition for
‘rbinom’
Undefined global functions or variables:
rbinom
Consider adding
importFrom("stats", "rbinom")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘RangedVcfStack’ ‘VcfStack’ ‘files’ ‘getVCFPath’ ‘paths1kg’
‘readVcfStack’
Undocumented S4 classes:
‘VcfStack’ ‘RangedVcfStack’
Undocumented S4 methods:
generic '[' and siglist 'RangedVcfStack,missing,character,missing'
generic '[' and siglist 'RangedVcfStack,missing,missing,missing'
generic '[' and siglist 'VcfStack,GenomicRanges,character,missing'
generic '[' and siglist 'VcfStack,GenomicRanges,missing,missing'
generic '[' and siglist 'VcfStack,missing,character,missing'
generic 'assay' and siglist 'RangedVcfStack,missing'
generic 'colData' and siglist 'VcfStack'
generic 'colData<-' and siglist 'VcfStack,DataFrame'
generic 'colnames' and siglist 'VcfStack'
generic 'dim' and siglist 'VcfStack'
generic 'files' and siglist 'VcfStack'
generic 'files<-' and siglist 'VcfStack,character'
generic 'rowRanges' and siglist 'RangedVcfStack'
generic 'rowRanges<-' and siglist 'RangedVcfStack,GRanges'
generic 'rownames' and siglist 'VcfStack'
generic 'seqinfo' and siglist 'VcfStack'
generic 'seqinfo<-' and siglist 'VcfStack'
generic 'show' and siglist 'VcfStack'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
GenomicFiles-class 0.584 0.091 6.757
reduceByYield 0.538 0.110 22.462
reduceByRange-methods 0.209 0.092 12.488
reduceByFile-methods 0.095 0.152 18.297
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘GenomicFiles_unit_tests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* 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: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/GenomicFiles.Rcheck/00check.log’
for details.