Merge pull request #21 from jasenfinch/devel

v1.0.7
jasenfinch · Jun 11, 2021 · 98813f7 · 98813f7
2 parents fd87eb7 + d6e4b44
commit 98813f7
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -63,12 +63,14 @@ jobs:
           do
             eval sudo $cmd
           done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+          sudo apt install mono-xbuild
 
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran(c("rcmdcheck","goodpractice"))
-          install.packages('http://fgcz-ms.uzh.ch/~cpanse/rawrr_0.1.8.tar.gz',repos = NULL)
+          rawrr::installRawFileReaderDLLs()
+          rawrr::buildRawrrExe()
           msconverteR::get_pwiz_container()
         shell: Rscript {0}
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,17 +1,17 @@
 Package: grover
 Title: Web API Framework for Mass Spectrometry Data Transfer
-Version: 1.0.6
+Version: 1.0.7
 Authors@R: 
     person(given = "Jasen",
            family = "Finch",
            role = c("aut", "cre"),
            email = "jsf9@aber.ac.uk")
 Description: A web based API framework for hosting and interfacing a mass spectrometry raw data data repository. Transfer files, retrieve file information, convert raw mass spectromery data to .mzML format and retrieve sample information from .raw file headers.
+biocViews: MassSpectrometry, Metabolomics
 URL: https://jasenfinch.github.io/grover/
 BugReports: https://github.com/jasenfinch/grover/issues
 License: GPL-3
 Encoding: UTF-8
-LazyData: true
 Imports: callr,
         cli,
         crayon,

diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,14 @@
+# grover 1.0.7
+
+* Added `biocViews` field to the DESCRIPTION to ensure the [`rawrr](https://bioconductor.org/packages/release/bioc/html/rawrr.html) Bioconductor dependency is installed automatically.
+
+* Fixed [`grover::converFile`](https://jasenfinch.github.io/grover/reference/convert.html) error when more than two options are supplied to the `args` parameter.
+
 # grover 1.0.6
 
 * [`grover::converFile`](https://jasenfinch.github.io/grover/reference/convert.html) creates the output directory if it doesn't already exist.
 
-* converted files now correctly zipped by [`grover::converFile`](https://jasenfinch.github.io/grover/reference/convert.html) to ensure they are readable by the [`mzR`](https://www.bioconductor.org/packages/release/bioc/html/mzR.html) package.
+* Converted files now correctly zipped by [`grover::converFile`](https://jasenfinch.github.io/grover/reference/convert.html) to ensure they are readable by the [`mzR`](https://www.bioconductor.org/packages/release/bioc/html/mzR.html) package.
 
 # grover 1.0.5
 

diff --git a/R/client-conversion.R b/R/client-conversion.R
@@ -48,6 +48,12 @@ setMethod('convertFile',signature = 'GroverClient',
               args <- ''
             }
 
+            if (length(args) > 1) {
+              args <- args %>% 
+                .[. != ''] %>% 
+                str_c(collapse = ' ')
+            }
+
             cmd <- str_c(cmd,args)
 
             fileName <- str_split(file,'[.]')[[1]][1]

diff --git a/R/host-conversion.R b/R/host-conversion.R
@@ -20,20 +20,20 @@ hostConvertFile <- function(auth,instrument,directory,file,args = NULL){
   }
 
   msconverteR::convert_files(files = stringr::str_c(host_repository,
-                              instrument,
-                              directory,
-                              file,
-                              sep = '/'),
-                outpath = host_temp,
-                msconvert_args = args,
-                docker_args = '--privileged')
+                                                    instrument,
+                                                    directory,
+                                                    file,
+                                                    sep = '/'),
+                             outpath = host_temp,
+                             msconvert_args = args,
+                             docker_args = '--privileged')
 
   out_file <- stringr::str_c(host_temp,
-                    stringr::str_c(tools::file_path_sans_ext(file),
-                          '.mzML'),
-                    sep = '/')
+                             stringr::str_c(tools::file_path_sans_ext(file),
+                                            '.mzML'),
+                             sep = '/')
 
-out_file <- readr::read_file(out_file)
+  out_file <- readr::read_file(out_file)
 
   return(out_file)
 

diff --git a/README.md b/README.md
@@ -21,9 +21,6 @@ The package functionality is platform independent with file conversion and sampl
 
 ### Installation
 
-This package requires the `rawrr` package.
-Details of how to install the latest version can be found [here](https://github.com/fgcz/rawrr/releases).
-
 The `grover` package can be installed from GitHub using the following:
 
 ```

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/client-usage.html b/docs/articles/client-usage.html
diff --git a/docs/articles/hosting.html b/docs/articles/hosting.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/introduction.html b/docs/articles/introduction.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -5,5 +5,5 @@ articles:
   client-usage: client-usage.html
   hosting: hosting.html
   introduction: introduction.html
-last_built: 2021-05-09T11:32Z
+last_built: 2021-06-11T15:22Z
 
diff --git a/docs/reference/GroverClient-accessors.html b/docs/reference/GroverClient-accessors.html
diff --git a/docs/reference/GroverClient-class.html b/docs/reference/GroverClient-class.html
diff --git a/docs/reference/GroverHost-accessors.html b/docs/reference/GroverHost-accessors.html
diff --git a/docs/reference/GroverHost-class.html b/docs/reference/GroverHost-class.html