Merge pull request #161 from MoTrPAC/develop

v0.7.2: update package dependency
MoTrPAC · Sep 22, 2022 · 401c135 · 401c135
2 parents fa98a3b + 9879a3e
commit 401c135
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: MotrpacBicQC
 Type: Package
 Title: QC/QA functions for the MoTrPAC community
-Version: 0.7.1
-Date: 2022-09-17
+Version: 0.7.2
+Date: 2022-09-22
 Author: MoTrPAC Bioinformatics Center
 Maintainer: David Jimenez-Morales <davidjm@stanford.edu>
 Description: R Package for the analysis of MoTrPAC datasets. 
@@ -33,6 +33,7 @@ Imports:
     naniar,
     progress,
     purrr,
+    readr,
     scales,
     stats,
     stringr,

diff --git a/NAMESPACE b/NAMESPACE
@@ -54,6 +54,7 @@ importFrom(gridExtra,arrangeGrob)
 importFrom(gridExtra,grid.arrange)
 importFrom(inspectdf,inspect_na)
 importFrom(jsonlite,fromJSON)
+importFrom(readr,read_lines)
 importFrom(scales,percent)
 importFrom(stats,median)
 importFrom(stats,reorder)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# MotrpacBicQC 0.7.2 (2022-09-22)
+
+* Update a package's dependendy
+
 # MotrpacBicQC 0.7.1 (2022-09-17)
 
 Updates affecting the proteomics validation:

diff --git a/R/misc.R b/R/misc.R
@@ -12,6 +12,7 @@
 #' @import naniar
 #' @import progress
 #' @import purrr
+#' @importFrom readr read_lines
 #' @importFrom scales percent
 #' @importFrom stats median reorder
 #' @import stringr

diff --git a/R/validations.R b/R/validations.R
@@ -98,9 +98,7 @@ set_phase <- function(input_results_folder,
   # To be adjusted if two different batches are provided:
   phase_check <- phase
   if ( !(purrr::is_empty(file_phase)) ){
-    con <- file(file_phase,"r")
-    batch_info <- readLines(con, n=1)
-    close(con)
+    batch_info <- readr::read_lines(file_phase, n_max = 1)
     if ( !(is.na(batch_info) || batch_info == '') ){
       if(verbose) message("+ Motrpac phase reported: ", batch_info, " (info from metadata_phase.txt available)")
       if( is.null(dmaqc_phase2validate) ){

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/other_functions.html b/docs/articles/other_functions.html
@@ -4,7 +4,7 @@
 <meta charset="utf-8">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="generator" content="pandoc">
-<meta name="date" content="2022-09-17">
+<meta name="date" content="2022-09-22">
 <title>MotrpacBicQC: Other Functions</title>
 <script src="other_functions_files/header-attrs-2.16/header-attrs.js"></script><script src="other_functions_files/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1">
 <link href="other_functions_files/bootstrap-3.3.7/css/bootstrap.min.css" rel="stylesheet">
@@ -123,7 +123,7 @@ <h1 class="title">MotrpacBicQC: Other Functions</h1>
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2022-09-17</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2022-09-22</p>
 
 
 

diff --git a/docs/articles/qc_metabolomics.html b/docs/articles/qc_metabolomics.html
@@ -4,7 +4,7 @@
 <meta charset="utf-8">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="generator" content="pandoc">
-<meta name="date" content="2022-09-17">
+<meta name="date" content="2022-09-22">
 <title>MotrpacBicQC: Metabolomics QC</title>
 <script src="qc_metabolomics_files/header-attrs-2.16/header-attrs.js"></script><script src="qc_metabolomics_files/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1">
 <link href="qc_metabolomics_files/bootstrap-3.3.7/css/bootstrap.min.css" rel="stylesheet">
@@ -125,7 +125,7 @@ <h1 class="title">MotrpacBicQC: Metabolomics QC</h1>
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2022-09-17</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2022-09-22</p>
 
 
 

diff --git a/docs/articles/qc_proteomics.html b/docs/articles/qc_proteomics.html
@@ -4,7 +4,7 @@
 <meta charset="utf-8">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 <meta name="generator" content="pandoc">
-<meta name="date" content="2022-09-17">
+<meta name="date" content="2022-09-22">
 <title>MotrpacBicQC: Proteomics QC</title>
 <script src="qc_proteomics_files/header-attrs-2.16/header-attrs.js"></script><script src="qc_proteomics_files/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1">
 <link href="qc_proteomics_files/bootstrap-3.3.7/css/bootstrap.min.css" rel="stylesheet">
@@ -125,7 +125,7 @@ <h1 class="title">MotrpacBicQC: Proteomics QC</h1>
 
       <p class="authors">
          </p>
-<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2022-09-17</p>
+<p class="date"><span class="glyphicon glyphicon-calendar"></span> 2022-09-22</p>
 
 
 

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/notes_developers.html b/docs/notes_developers.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -5,5 +5,5 @@ articles:
   other_functions: other_functions.html
   qc_metabolomics: qc_metabolomics.html
   qc_proteomics: qc_proteomics.html
-last_built: 2022-09-18T01:10Z
+last_built: 2022-09-22T16:24Z
 
diff --git a/docs/reference/assay_abbr.html b/docs/reference/assay_abbr.html
diff --git a/docs/reference/assay_codes.html b/docs/reference/assay_codes.html
diff --git a/docs/reference/assay_order.html b/docs/reference/assay_order.html
diff --git a/docs/reference/bic_animal_tissue_code.html b/docs/reference/bic_animal_tissue_code.html
diff --git a/docs/reference/check_failedsamples.html b/docs/reference/check_failedsamples.html
diff --git a/docs/reference/check_manifest_rawdata.html b/docs/reference/check_manifest_rawdata.html
diff --git a/docs/reference/check_metadata_metabolites.html b/docs/reference/check_metadata_metabolites.html
diff --git a/docs/reference/check_metadata_samples.html b/docs/reference/check_metadata_samples.html
diff --git a/docs/reference/check_ratio_proteomics.html b/docs/reference/check_ratio_proteomics.html
diff --git a/docs/reference/check_results.html b/docs/reference/check_results.html
diff --git a/docs/reference/check_rii_proteomics.html b/docs/reference/check_rii_proteomics.html
diff --git a/docs/reference/check_vial_metadata_proteomics.html b/docs/reference/check_vial_metadata_proteomics.html
diff --git a/docs/reference/check_viallabel_dmaqc.html b/docs/reference/check_viallabel_dmaqc.html
diff --git a/docs/reference/combine_metabolomics_batch.html b/docs/reference/combine_metabolomics_batch.html
diff --git a/docs/reference/create_folder.html b/docs/reference/create_folder.html
diff --git a/docs/reference/filter_required_columns.html b/docs/reference/filter_required_columns.html
diff --git a/docs/reference/get_and_validate_mdd.html b/docs/reference/get_and_validate_mdd.html
diff --git a/docs/reference/group_abbr.html b/docs/reference/group_abbr.html
diff --git a/docs/reference/group_cols.html b/docs/reference/group_cols.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/load_metabolomics_batch.html b/docs/reference/load_metabolomics_batch.html