R.filesets

Package: R.filesets
Version: 2.10.0
Depends: R (>= 3.1.2), R.oo (>= 1.19.0)
Imports: digest (>= 0.6.8), future (>= 0.10.0), listenv (>= 0.6.0),
R.methodsS3 (>= 1.7.0), R.utils (>= 2.2.0), R.cache (>=
0.12.0), stats
Suggests: BatchJobs (>= 1.6), BiocParallel (>= 1.0.3), gtools (>=
3.5.0)
SuggestsNote: BioC (>= 3.0), Recommended: gtools
Date: 2016-01-04
Title: Easy Handling of and Access to Files Organized in Structured
Directories
Authors@R: c(person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"),
email = "henrikb@braju.com"))
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Description: A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
License: LGPL (>= 2.1)
URL: https://github.com/HenrikBengtsson/R.filesets,
http://www.aroma-project.org/
BugReports: https://github.com/HenrikBengtsson/R.filesets/issues
LazyLoad: TRUE
biocViews: Infrastructure, DataImport, DataRepresentation
NeedsCompilation: no
Packaged: 2016-01-04 23:36:06 UTC; hb
Repository: CRAN
Date/Publication: 2016-01-05 07:03:05

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'R.filesets' ...
** package 'R.filesets' successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'R.filesets'
    finding HTML links ... done
    ChecksumFile                            html  
    ChecksumFileSet                         html  
    ColumnNamesInterface                    html  
    Deprecated_and_defunct_objects          html  
    FullNameInterface                       html  
    GenericDataFile                         html  
    GenericDataFileSet                      html  
    GenericDataFileSetList                  html  
    GenericTabularFile                      html  
    GenericTabularFileSet                   html  
    Non-documented_objects                  html  
    R.filesets-package                      html  
    RDataFile                               html  
    RDataFileSet                            html  
    RdsFile                                 html  
Rd warning: /tmp/RtmpYAgZCy/R.INSTALL1d243af287d8/R.filesets/man/RdsFile.Rd:38: missing file link 'saveRDS'
    RdsFileSet                              html  
    TabularTextFile                         html  
    TabularTextFileSet                      html  
    anyNA.GenericDataFileSet                html  
Rd warning: /tmp/RtmpYAgZCy/R.INSTALL1d243af287d8/R.filesets/man/anyNA.GenericDataFileSet.Rd:38: missing file link 'na.omit'
    append.GenericDataFileSet               html  
    appendFiles.GenericDataFileSet          html  
Rd warning: /tmp/RtmpYAgZCy/R.INSTALL1d243af287d8/R.filesets/man/appendFiles.GenericDataFileSet.Rd:32: missing file link 'getFileClass.GenericDataFileSet'
    as.character.GenericDataFile            html  
    as.character.GenericDataFileSet         html  
    as.list.GenericDataFileSet              html  
Rd warning: /tmp/RtmpYAgZCy/R.INSTALL1d243af287d8/R.filesets/man/as.list.GenericDataFileSet.Rd:25: missing file link 'getFiles.GenericDataFileSet'
    byName.GenericDataFileSet               html  
    byPath.GenericDataFileSet               html  
    compareChecksum.GenericDataFile         html  
    copyTo.GenericDataFile                  html  
    copyTo.GenericDataFileSet               html  
    dim.GenericTabularFile                  html  
    dsApply.GenericDataFileSet              html  
    equals.GenericDataFile                  html  
    extract.GenericDataFileSet              html  
Rd warning: /tmp/RtmpYAgZCy/R.INSTALL1d243af287d8/R.filesets/man/extract.GenericDataFileSet.Rd:51: missing file link 'na.omit'
    extractMatrix.GenericTabularFile        html  
    findByName.GenericDataFileSet           html  
    fromFile.GenericDataFile                html  
    getChecksum.GenericDataFile             html  
    getChecksum.GenericDataFileSet          html  
    getChecksumObjects.GenericDataFileSet   html  
    getColumnNames.ColumnNamesInterface     html  
    getCreatedOn.GenericDataFile            html  
    getDefaultColumnNames.ColumnNamesInterface
                                            html  
    getDefaultColumnNames.TabularTextFile   html  
    getDefaultFullName.FullNameInterface    html  
    getDefaultFullName.GenericDataFile      html  
    getDefaultFullName.GenericDataFileSet   html  
    getExtension.GenericDataFile            html  
    getFile.GenericDataFileSet              html  
    getFileSize.GenericDataFile             html  
    getFileType.GenericDataFile             html  
    getFilename.GenericDataFile             html  
    getFullName.FullNameInterface           html  
    getHeader.TabularTextFile               html  
Rd warning: /tmp/RtmpYAgZCy/R.INSTALL1d243af287d8/R.filesets/man/getHeader.TabularTextFile.Rd:25: missing file link 'readRawHeader.TabularTextFile'
    getLastAccessedOn.GenericDataFile       html  
    getLastModifiedOn.GenericDataFile       html  
    getName.FullNameInterface               html  
    getNames.GenericDataFileSet             html  
    getPath.GenericDataFile                 html  
    getPath.GenericDataFileSet              html  
    getPathname.GenericDataFile             html  
    getPathnames.GenericDataFileSet         html  
    getTags.Arguments                       html  
    getTags.FullNameInterface               html  
    gzip.GenericDataFile                    html  
Rd warning: /tmp/RtmpYAgZCy/R.INSTALL1d243af287d8/R.filesets/man/gzip.GenericDataFile.Rd:56: missing file link 'gzip'
    gzip.GenericDataFileSet                 html  
Rd warning: /tmp/RtmpYAgZCy/R.INSTALL1d243af287d8/R.filesets/man/gzip.GenericDataFileSet.Rd:43: missing file link 'gzip'
Rd warning: /tmp/RtmpYAgZCy/R.INSTALL1d243af287d8/R.filesets/man/gzip.GenericDataFileSet.Rd:43: missing file link 'gunzip'
    hasBeenModified.GenericDataFile         html  
    hasColumnHeader.TabularTextFile         html  
    hasTags.FullNameInterface               html  
    indexOf.GenericDataFileSet              html  
Rd warning: /tmp/RtmpYAgZCy/R.INSTALL1d243af287d8/R.filesets/man/indexOf.GenericDataFileSet.Rd:40: missing file link 'getFullNames.GenericDataFileSet'
    isFile.GenericDataFile                  html  
    length.GenericDataFileSet               html  
    linkTo.GenericDataFile                  html  
    loadRDS                                 html  
    loadToEnv                               html  
    nbrOfColumns.ColumnNamesInterface       html  
    nbrOfLines.TabularTextFile              html  
    nbrOfRows.GenericTabularFile            html  
    nbrOfRows.TabularTextFile               html  
    readChecksum.ChecksumFile               html  
    readChecksum.GenericDataFile            html  
    readColumns.GenericTabularFile          html  
    readDataFrame.GenericTabularFile        html  
    readDataFrame                           html  
Rd warning: /tmp/RtmpYAgZCy/R.INSTALL1d243af287d8/R.filesets/man/readDataFrame.Rd:42: missing file link 'rbind'
    readDataFrame.TabularTextFile           html  
Rd warning: /tmp/RtmpYAgZCy/R.INSTALL1d243af287d8/R.filesets/man/readDataFrame.TabularTextFile.Rd:35: missing file link 'getReadArguments.TabularTextFile'
    readDataFrame.TabularTextFileSet        html  
    readLines.TabularTextFile               html  
    renameTo.GenericDataFile                html  
    setColumnNames.ColumnNamesInterface     html  
    setFullName.FullNameInterface           html  
    setName.FullNameInterface               html  
    setTags.FullNameInterface               html  
    sortBy.GenericDataFileSet               html  
    validate.ChecksumFile                   html  
    validate.GenericDataFile                html  
    validate.GenericDataFileSet             html  
    validateChecksum.GenericDataFile        html  
    writeChecksum.GenericDataFile           html  
    writeColumnsToFiles.GenericTabularFile
                                            html  
** building package indices
** testing if installed package can be loaded
* DONE (R.filesets)
Making 'packages.html' ... done