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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### rm -rf GenomicFiles.buildbin-libdir GenomicFiles.Rcheck && mkdir GenomicFiles.buildbin-libdir GenomicFiles.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicFiles.buildbin-libdir GenomicFiles_1.8.0.tar.gz >GenomicFiles.Rcheck\00install.out 2>&1 && cp GenomicFiles.Rcheck\00install.out GenomicFiles-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=GenomicFiles.buildbin-libdir --install="check:GenomicFiles-install.out" --force-multiarch --no-vignettes --timings GenomicFiles_1.8.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/GenomicFiles.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
reduceByYield 1.16 0.08 32.65
GenomicFiles-class 0.68 0.06 49.89
reduceByRange-methods 0.43 0.01 54.19
reduceByFile-methods 0.27 0.02 83.98
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
reduceByYield 0.87 0.13 32.41
GenomicFiles-class 0.88 0.03 62.18
reduceByRange-methods 0.38 0.04 59.70
reduceByFile-methods 0.18 0.04 72.23
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'GenomicFiles_unit_tests.R'
OK
** running tests for arch 'x64' ...
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
'E:/biocbld/bbs-3.3-bioc/meat/GenomicFiles.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'GenomicFiles' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'GenomicFiles' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicFiles' as GenomicFiles_1.8.0.zip
* DONE (GenomicFiles)