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(v0.7.1.9086) small fix

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dr. M.S. (Matthijs) Berends 2019-09-23 23:00:18 +02:00
parent ad5f211a8f
commit 38336d7408
10 changed files with 17 additions and 15 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 0.7.1.9085 Version: 0.7.1.9086
Date: 2019-09-23 Date: 2019-09-23
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.1.9085 # AMR 0.7.1.9086
<small>Last updated: 23-Sep-2019</small> <small>Last updated: 23-Sep-2019</small>
### Breaking ### Breaking

2
R/mo.R
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@ -241,7 +241,7 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
pull(mo) pull(mo)
# save them to history # save them to history
set_mo_history(x, y, 0, force = isTRUE(list(...)$force_mo_history)) set_mo_history(x, y, 0, force = isTRUE(list(...)$force_mo_history), disable = isTRUE(list(...)$disable_mo_history))
} else { } else {
# will be checked for mo class in validation and uses exec_as.mo internally if necessary # will be checked for mo class in validation and uses exec_as.mo internally if necessary

8
R/mo_history.R
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@ -60,8 +60,7 @@ set_mo_history <- function(x, mo, uncertainty_level, force = FALSE, disable = FA
# if (tryCatch(nrow(getOption("mo_remembered_results")), error = function(e) 1001) > 1000) { # if (tryCatch(nrow(getOption("mo_remembered_results")), error = function(e) 1001) > 1000) {
# return(base::invisible()) # return(base::invisible())
# } # }
if (is.null(mo_hist) & interactive() & warning_new_write == FALSE) { if (is.null(mo_hist) & interactive()) {
message(blue(paste0("NOTE: results are saved to ", mo_history_file(), ".")))
warning_new_write <- TRUE warning_new_write <- TRUE
} }
tryCatch(write.csv(rbind(mo_hist, tryCatch(write.csv(rbind(mo_hist,
@ -73,10 +72,13 @@ set_mo_history <- function(x, mo, uncertainty_level, force = FALSE, disable = FA
stringsAsFactors = FALSE)), stringsAsFactors = FALSE)),
row.names = FALSE, row.names = FALSE,
file = mo_history_file()), file = mo_history_file()),
error = function(e) base::invisible()) error = function(e) { warning_new_write <- FALSE; base::invisible()})
} }
} }
} }
if (warning_new_write == TRUE) {
message(blue(paste0("NOTE: results are saved to ", mo_history_file(), ".")))
}
return(base::invisible()) return(base::invisible())
} }

2
docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9085</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9086</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9085</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9086</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9085</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9086</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -42,7 +42,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9085</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9086</span>
</span> </span>
</div> </div>

8
docs/news/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9085</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9086</span>
</span> </span>
</div> </div>
@ -225,9 +225,9 @@
</div> </div>
<div id="amr-0-7-1-9085" class="section level1"> <div id="amr-0-7-1-9086" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-7-1-9085" class="anchor"></a>AMR 0.7.1.9085<small> Unreleased </small> <a href="#amr-0-7-1-9086" class="anchor"></a>AMR 0.7.1.9086<small> Unreleased </small>
</h1> </h1>
<p><small>Last updated: 23-Sep-2019</small></p> <p><small>Last updated: 23-Sep-2019</small></p>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
@ -1280,7 +1280,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9085">0.7.1.9085</a></li> <li><a href="#amr-0-7-1-9086">0.7.1.9086</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li> <li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li> <li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li> <li><a href="#amr-0-6-1">0.6.1</a></li>

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docs/reference/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9085</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9086</span>
</span> </span>
</div> </div>