20660: Add devtools::check to run_test.R

[arvados.git] / sdk / R / man / Collection.Rd

diff --git a/sdk/R/man/Collection.Rd b/sdk/R/man/Collection.Rd
index bb72cc1b3fe75e192f81c9c091c1a4d6f7a259df..8ac6fcce14ac4320e6d45b6b7e7faef39db9d687 100644 (file)
--- a/sdk/R/man/Collection.Rd
+++ b/sdk/R/man/Collection.Rd
@@ -13,24 +13,29 @@ for exaplme actions like creating, updating, moving or removing are possible.
 ## Method `Collection$new`\r
 ## ------------------------------------------------\r
 \r
+\dontrun{\r
 collection <- Collection$new(arv, CollectionUUID)\r
+}\r
 \r
 ## ------------------------------------------------\r
 ## Method `Collection$readArvFile`\r
 ## ------------------------------------------------\r
 \r
+\dontrun{\r
 collection <- Collection$new(arv, collectionUUID)\r
 readFile <- collection$readArvFile(arvadosFile, istable = 'yes')                    # table\r
 readFile <- collection$readArvFile(arvadosFile, istable = 'no')                     # text\r
 readFile <- collection$readArvFile(arvadosFile)                                     # xlsx, csv, tsv, rds, rdata\r
-readFile <- collection$readArvFile(arvadosFile, fileclass = 'lala')                 # fasta\r
+readFile <- collection$readArvFile(arvadosFile, fileclass = 'fasta')                # fasta\r
 readFile <- collection$readArvFile(arvadosFile, Ncol= 4, Nrow = 32)                 # binary, only numbers\r
 readFile <- collection$readArvFile(arvadosFile, Ncol = 5, Nrow = 150, istable = "factor") # binary with factor or text\r
+}\r
 \r
 ## ------------------------------------------------\r
 ## Method `Collection$writeFile`\r
 ## ------------------------------------------------\r
 \r
+\dontrun{\r
 collection <- Collection$new(arv, collectionUUID)\r
 writeFile <- collection$writeFile(name = "myoutput.csv", file = file, fileFormat = "csv", istable = NULL, collectionUUID = collectionUUID)             # csv\r
 writeFile <- collection$writeFile(name = "myoutput.tsv", file = file, fileFormat = "tsv", istable = NULL, collectionUUID = collectionUUID)             # tsv\r
@@ -39,49 +44,64 @@ writeFile <- collection$writeFile(name = "myoutputtable.txt", file = file, fileF
 writeFile <- collection$writeFile(name = "myoutputtext.txt", file = file, fileFormat = "txt", istable = "no", collectionUUID = collectionUUID)         # txt text\r
 writeFile <- collection$writeFile(name = "myoutputbinary.dat", file = file, fileFormat = "dat", collectionUUID = collectionUUID)                       # binary\r
 writeFile <- collection$writeFile(name = "myoutputxlsx.xlsx", file = file, fileFormat = "xlsx", collectionUUID = collectionUUID)                       # xlsx\r
+}\r
 \r
 ## ------------------------------------------------\r
 ## Method `Collection$create`\r
 ## ------------------------------------------------\r
 \r
+\dontrun{\r
 collection <- arv$collections_create(name = collectionTitle, description = collectionDescription, owner_uuid = collectionOwner, properties = list("ROX37196928443768648" = "ROX37742976443830153"))\r
+}\r
 \r
 ## ------------------------------------------------\r
 ## Method `Collection$remove`\r
 ## ------------------------------------------------\r
 \r
+\dontrun{\r
 collection$remove(fileName.format)\r
+}\r
 \r
 ## ------------------------------------------------\r
 ## Method `Collection$move`\r
 ## ------------------------------------------------\r
 \r
+\dontrun{\r
 collection$move("fileName.format", path)\r
+}\r
 \r
 ## ------------------------------------------------\r
 ## Method `Collection$copy`\r
 ## ------------------------------------------------\r
 \r
+\dontrun{\r
 copied <- collection$copy("oldName.format", "newName.format")\r
+}\r
 \r
 ## ------------------------------------------------\r
 ## Method `Collection$refresh`\r
 ## ------------------------------------------------\r
 \r
+\dontrun{\r
 collection$refresh()\r
+}\r
 \r
 ## ------------------------------------------------\r
 ## Method `Collection$getFileListing`\r
 ## ------------------------------------------------\r
 \r
+\dontrun{\r
 list <- collection$getFileListing()\r
+}\r
 \r
 ## ------------------------------------------------\r
 ## Method `Collection$get`\r
 ## ------------------------------------------------\r
 \r
+\dontrun{\r
 arvadosFile <- collection$get(fileName)\r
 }\r
+}\r
 \seealso{\r
 \code{\link{https://github.com/arvados/arvados/tree/main/sdk/R}}\r
 }\r
@@ -95,24 +115,24 @@ arvadosFile <- collection$get(fileName)
 \section{Methods}{\r
 \subsection{Public methods}{\r
 \itemize{\r
-\item \href{#method-new}{\code{Collection$new()}}\r
-\item \href{#method-add}{\code{Collection$add()}}\r
-\item \href{#method-readArvFile}{\code{Collection$readArvFile()}}\r
-\item \href{#method-writeFile}{\code{Collection$writeFile()}}\r
-\item \href{#method-create}{\code{Collection$create()}}\r
-\item \href{#method-remove}{\code{Collection$remove()}}\r
-\item \href{#method-move}{\code{Collection$move()}}\r
-\item \href{#method-copy}{\code{Collection$copy()}}\r
-\item \href{#method-refresh}{\code{Collection$refresh()}}\r
-\item \href{#method-getFileListing}{\code{Collection$getFileListing()}}\r
-\item \href{#method-get}{\code{Collection$get()}}\r
-\item \href{#method-getRESTService}{\code{Collection$getRESTService()}}\r
-\item \href{#method-setRESTService}{\code{Collection$setRESTService()}}\r
+\item \href{#method-Collection-new}{\code{Collection$new()}}\r
+\item \href{#method-Collection-add}{\code{Collection$add()}}\r
+\item \href{#method-Collection-readArvFile}{\code{Collection$readArvFile()}}\r
+\item \href{#method-Collection-writeFile}{\code{Collection$writeFile()}}\r
+\item \href{#method-Collection-create}{\code{Collection$create()}}\r
+\item \href{#method-Collection-remove}{\code{Collection$remove()}}\r
+\item \href{#method-Collection-move}{\code{Collection$move()}}\r
+\item \href{#method-Collection-copy}{\code{Collection$copy()}}\r
+\item \href{#method-Collection-refresh}{\code{Collection$refresh()}}\r
+\item \href{#method-Collection-getFileListing}{\code{Collection$getFileListing()}}\r
+\item \href{#method-Collection-get}{\code{Collection$get()}}\r
+\item \href{#method-Collection-getRESTService}{\code{Collection$getRESTService()}}\r
+\item \href{#method-Collection-setRESTService}{\code{Collection$setRESTService()}}\r
 }\r
 }\r
 \if{html}{\out{<hr>}}\r
-\if{html}{\out{<a id="method-new"></a>}}\r
-\if{latex}{\out{\hypertarget{method-new}{}}}\r
+\if{html}{\out{<a id="method-Collection-new"></a>}}\r
+\if{latex}{\out{\hypertarget{method-Collection-new}{}}}\r
 \subsection{Method \code{new()}}{\r
 Initialize new enviroment.\r
 \subsection{Usage}{\r
@@ -133,7 +153,9 @@ A new `Collection` object.
 }\r
 \subsection{Examples}{\r
 \if{html}{\out{<div class="r example copy">}}\r
-\preformatted{collection <- Collection$new(arv, CollectionUUID)\r
+\preformatted{\dontrun{\r
+collection <- Collection$new(arv, CollectionUUID)\r
+}\r
 }\r
 \if{html}{\out{</div>}}\r
 \r
@@ -141,8 +163,8 @@ A new `Collection` object.
 \r
 }\r
 \if{html}{\out{<hr>}}\r
-\if{html}{\out{<a id="method-add"></a>}}\r
-\if{latex}{\out{\hypertarget{method-add}{}}}\r
+\if{html}{\out{<a id="method-Collection-add"></a>}}\r
+\if{latex}{\out{\hypertarget{method-Collection-add}{}}}\r
 \subsection{Method \code{add()}}{\r
 Adds ArvadosFile or Subcollection specified by content to the collection. Used only with ArvadosFile or Subcollection.\r
 \subsection{Usage}{\r
@@ -160,8 +182,8 @@ Adds ArvadosFile or Subcollection specified by content to the collection. Used o
 }\r
 }\r
 \if{html}{\out{<hr>}}\r
-\if{html}{\out{<a id="method-readArvFile"></a>}}\r
-\if{latex}{\out{\hypertarget{method-readArvFile}{}}}\r
+\if{html}{\out{<a id="method-Collection-readArvFile"></a>}}\r
+\if{latex}{\out{\hypertarget{method-Collection-readArvFile}{}}}\r
 \subsection{Method \code{readArvFile()}}{\r
 Read file content.\r
 \subsection{Usage}{\r
@@ -198,22 +220,24 @@ Read file content.
 }\r
 \subsection{Examples}{\r
 \if{html}{\out{<div class="r example copy">}}\r
-\preformatted{collection <- Collection$new(arv, collectionUUID)\r
+\preformatted{\dontrun{\r
+collection <- Collection$new(arv, collectionUUID)\r
 readFile <- collection$readArvFile(arvadosFile, istable = 'yes')                    # table\r
 readFile <- collection$readArvFile(arvadosFile, istable = 'no')                     # text\r
 readFile <- collection$readArvFile(arvadosFile)                                     # xlsx, csv, tsv, rds, rdata\r
-readFile <- collection$readArvFile(arvadosFile, fileclass = 'lala')                 # fasta\r
+readFile <- collection$readArvFile(arvadosFile, fileclass = 'fasta')                # fasta\r
 readFile <- collection$readArvFile(arvadosFile, Ncol= 4, Nrow = 32)                 # binary, only numbers\r
 readFile <- collection$readArvFile(arvadosFile, Ncol = 5, Nrow = 150, istable = "factor") # binary with factor or text\r
 }\r
+}\r
 \if{html}{\out{</div>}}\r
 \r
 }\r
 \r
 }\r
 \if{html}{\out{<hr>}}\r
-\if{html}{\out{<a id="method-writeFile"></a>}}\r
-\if{latex}{\out{\hypertarget{method-writeFile}{}}}\r
+\if{html}{\out{<a id="method-Collection-writeFile"></a>}}\r
+\if{latex}{\out{\hypertarget{method-Collection-writeFile}{}}}\r
 \subsection{Method \code{writeFile()}}{\r
 Write file content\r
 \subsection{Usage}{\r
@@ -240,7 +264,8 @@ Write file content
 }\r
 \subsection{Examples}{\r
 \if{html}{\out{<div class="r example copy">}}\r
-\preformatted{collection <- Collection$new(arv, collectionUUID)\r
+\preformatted{\dontrun{\r
+collection <- Collection$new(arv, collectionUUID)\r
 writeFile <- collection$writeFile(name = "myoutput.csv", file = file, fileFormat = "csv", istable = NULL, collectionUUID = collectionUUID)             # csv\r
 writeFile <- collection$writeFile(name = "myoutput.tsv", file = file, fileFormat = "tsv", istable = NULL, collectionUUID = collectionUUID)             # tsv\r
 writeFile <- collection$writeFile(name = "myoutput.fasta", file = file, fileFormat = "fasta", istable = NULL, collectionUUID = collectionUUID)         # fasta\r
@@ -249,14 +274,15 @@ writeFile <- collection$writeFile(name = "myoutputtext.txt", file = file, fileFo
 writeFile <- collection$writeFile(name = "myoutputbinary.dat", file = file, fileFormat = "dat", collectionUUID = collectionUUID)                       # binary\r
 writeFile <- collection$writeFile(name = "myoutputxlsx.xlsx", file = file, fileFormat = "xlsx", collectionUUID = collectionUUID)                       # xlsx\r
 }\r
+}\r
 \if{html}{\out{</div>}}\r
 \r
 }\r
 \r
 }\r
 \if{html}{\out{<hr>}}\r
-\if{html}{\out{<a id="method-create"></a>}}\r
-\if{latex}{\out{\hypertarget{method-create}{}}}\r
+\if{html}{\out{<a id="method-Collection-create"></a>}}\r
+\if{latex}{\out{\hypertarget{method-Collection-create}{}}}\r
 \subsection{Method \code{create()}}{\r
 Creates one or more ArvadosFiles and adds them to the collection at specified path.\r
 \subsection{Usage}{\r
@@ -272,7 +298,9 @@ Creates one or more ArvadosFiles and adds them to the collection at specified pa
 }\r
 \subsection{Examples}{\r
 \if{html}{\out{<div class="r example copy">}}\r
-\preformatted{collection <- arv$collections_create(name = collectionTitle, description = collectionDescription, owner_uuid = collectionOwner, properties = list("ROX37196928443768648" = "ROX37742976443830153"))\r
+\preformatted{\dontrun{\r
+collection <- arv$collections_create(name = collectionTitle, description = collectionDescription, owner_uuid = collectionOwner, properties = list("ROX37196928443768648" = "ROX37742976443830153"))\r
+}\r
 }\r
 \if{html}{\out{</div>}}\r
 \r
@@ -280,8 +308,8 @@ Creates one or more ArvadosFiles and adds them to the collection at specified pa
 \r
 }\r
 \if{html}{\out{<hr>}}\r
-\if{html}{\out{<a id="method-remove"></a>}}\r
-\if{latex}{\out{\hypertarget{method-remove}{}}}\r
+\if{html}{\out{<a id="method-Collection-remove"></a>}}\r
+\if{latex}{\out{\hypertarget{method-Collection-remove}{}}}\r
 \subsection{Method \code{remove()}}{\r
 Remove one or more files from the collection.\r
 \subsection{Usage}{\r
@@ -297,7 +325,9 @@ Remove one or more files from the collection.
 }\r
 \subsection{Examples}{\r
 \if{html}{\out{<div class="r example copy">}}\r
-\preformatted{collection$remove(fileName.format)\r
+\preformatted{\dontrun{\r
+collection$remove(fileName.format)\r
+}\r
 }\r
 \if{html}{\out{</div>}}\r
 \r
@@ -305,8 +335,8 @@ Remove one or more files from the collection.
 \r
 }\r
 \if{html}{\out{<hr>}}\r
-\if{html}{\out{<a id="method-move"></a>}}\r
-\if{latex}{\out{\hypertarget{method-move}{}}}\r
+\if{html}{\out{<a id="method-Collection-move"></a>}}\r
+\if{latex}{\out{\hypertarget{method-Collection-move}{}}}\r
 \subsection{Method \code{move()}}{\r
 Moves ArvadosFile or Subcollection to another location in the collection.\r
 \subsection{Usage}{\r
@@ -324,7 +354,9 @@ Moves ArvadosFile or Subcollection to another location in the collection.
 }\r
 \subsection{Examples}{\r
 \if{html}{\out{<div class="r example copy">}}\r
-\preformatted{collection$move("fileName.format", path)\r
+\preformatted{\dontrun{\r
+collection$move("fileName.format", path)\r
+}\r
 }\r
 \if{html}{\out{</div>}}\r
 \r
@@ -332,8 +364,8 @@ Moves ArvadosFile or Subcollection to another location in the collection.
 \r
 }\r
 \if{html}{\out{<hr>}}\r
-\if{html}{\out{<a id="method-copy"></a>}}\r
-\if{latex}{\out{\hypertarget{method-copy}{}}}\r
+\if{html}{\out{<a id="method-Collection-copy"></a>}}\r
+\if{latex}{\out{\hypertarget{method-Collection-copy}{}}}\r
 \subsection{Method \code{copy()}}{\r
 Copies ArvadosFile or Subcollection to another location in the collection.\r
 \subsection{Usage}{\r
@@ -351,7 +383,9 @@ Copies ArvadosFile or Subcollection to another location in the collection.
 }\r
 \subsection{Examples}{\r
 \if{html}{\out{<div class="r example copy">}}\r
-\preformatted{copied <- collection$copy("oldName.format", "newName.format")\r
+\preformatted{\dontrun{\r
+copied <- collection$copy("oldName.format", "newName.format")\r
+}\r
 }\r
 \if{html}{\out{</div>}}\r
 \r
@@ -359,8 +393,8 @@ Copies ArvadosFile or Subcollection to another location in the collection.
 \r
 }\r
 \if{html}{\out{<hr>}}\r
-\if{html}{\out{<a id="method-refresh"></a>}}\r
-\if{latex}{\out{\hypertarget{method-refresh}{}}}\r
+\if{html}{\out{<a id="method-Collection-refresh"></a>}}\r
+\if{latex}{\out{\hypertarget{method-Collection-refresh}{}}}\r
 \subsection{Method \code{refresh()}}{\r
 Refreshes the environment.\r
 \subsection{Usage}{\r
@@ -369,7 +403,9 @@ Refreshes the environment.
 \r
 \subsection{Examples}{\r
 \if{html}{\out{<div class="r example copy">}}\r
-\preformatted{collection$refresh()\r
+\preformatted{\dontrun{\r
+collection$refresh()\r
+}\r
 }\r
 \if{html}{\out{</div>}}\r
 \r
@@ -377,8 +413,8 @@ Refreshes the environment.
 \r
 }\r
 \if{html}{\out{<hr>}}\r
-\if{html}{\out{<a id="method-getFileListing"></a>}}\r
-\if{latex}{\out{\hypertarget{method-getFileListing}{}}}\r
+\if{html}{\out{<a id="method-Collection-getFileListing"></a>}}\r
+\if{latex}{\out{\hypertarget{method-Collection-getFileListing}{}}}\r
 \subsection{Method \code{getFileListing()}}{\r
 Returns collections file content as character vector.\r
 \subsection{Usage}{\r
@@ -387,7 +423,9 @@ Returns collections file content as character vector.
 \r
 \subsection{Examples}{\r
 \if{html}{\out{<div class="r example copy">}}\r
-\preformatted{list <- collection$getFileListing()\r
+\preformatted{\dontrun{\r
+list <- collection$getFileListing()\r
+}\r
 }\r
 \if{html}{\out{</div>}}\r
 \r
@@ -395,8 +433,8 @@ Returns collections file content as character vector.
 \r
 }\r
 \if{html}{\out{<hr>}}\r
-\if{html}{\out{<a id="method-get"></a>}}\r
-\if{latex}{\out{\hypertarget{method-get}{}}}\r
+\if{html}{\out{<a id="method-Collection-get"></a>}}\r
+\if{latex}{\out{\hypertarget{method-Collection-get}{}}}\r
 \subsection{Method \code{get()}}{\r
 If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.\r
 \subsection{Usage}{\r
@@ -412,7 +450,9 @@ If relativePath is valid, returns ArvadosFile or Subcollection specified by rela
 }\r
 \subsection{Examples}{\r
 \if{html}{\out{<div class="r example copy">}}\r
-\preformatted{arvadosFile <- collection$get(fileName)\r
+\preformatted{\dontrun{\r
+arvadosFile <- collection$get(fileName)\r
+}\r
 }\r
 \if{html}{\out{</div>}}\r
 \r
@@ -420,8 +460,8 @@ If relativePath is valid, returns ArvadosFile or Subcollection specified by rela
 \r
 }\r
 \if{html}{\out{<hr>}}\r
-\if{html}{\out{<a id="method-getRESTService"></a>}}\r
-\if{latex}{\out{\hypertarget{method-getRESTService}{}}}\r
+\if{html}{\out{<a id="method-Collection-getRESTService"></a>}}\r
+\if{latex}{\out{\hypertarget{method-Collection-getRESTService}{}}}\r
 \subsection{Method \code{getRESTService()}}{\r
 \subsection{Usage}{\r
 \if{html}{\out{<div class="r">}}\preformatted{Collection$getRESTService()}\if{html}{\out{</div>}}\r
@@ -429,8 +469,8 @@ If relativePath is valid, returns ArvadosFile or Subcollection specified by rela
 \r
 }\r
 \if{html}{\out{<hr>}}\r
-\if{html}{\out{<a id="method-setRESTService"></a>}}\r
-\if{latex}{\out{\hypertarget{method-setRESTService}{}}}\r
+\if{html}{\out{<a id="method-Collection-setRESTService"></a>}}\r
+\if{latex}{\out{\hypertarget{method-Collection-setRESTService}{}}}\r
 \subsection{Method \code{setRESTService()}}{\r
 \subsection{Usage}{\r
 \if{html}{\out{<div class="r">}}\preformatted{Collection$setRESTService(newRESTService)}\if{html}{\out{</div>}}\r