Merge pull request #26 from wkumler/version_1.3.2

Version 1.3.4 now on CRAN

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: RaMS
 Type: Package
 Title: R Access to Mass-Spec Data
-Version: 1.3.3
+Version: 1.3.4
 Authors@R: c(
   person(given = "William", family = "Kumler", email = "[email protected]",
          role = c("aut", "cre", "cph")),

cran-comments.md

@@ -1,6 +1,12 @@
 
 ## Resubmission
 
+This is a resubmission. In this version I have set data.table to use only two
+threads to avoid CPU time > 2.5 times elapsed time in the vignettes
+
+
+## Resubmission (prior)
+
 This is a resubmission. In this version I have reduced the example runtimes to
 below 5s (I hope) for tests and examples and set data.table to use only two
 threads to avoid CPU time > 2.5 times elapsed time

doc/Intro-to-RaMS.R

@@ -1,6 +1,7 @@
-## ---- include = FALSE---------------------------------------------------------
+## ----include = FALSE----------------------------------------------------------
 options(rmarkdown.html_vignette.check_title = FALSE)
 options(tidyverse.quiet = TRUE)
+data.table::setDTthreads(2)
 
 knitr::opts_chunk$set(
   collapse = TRUE,
@@ -142,7 +143,7 @@ msdata$MS2 <- mutate(msdata$MS2, neutral_loss=premz-fragmz) %>%
 msdata$MS2[neutral_loss%between%pmppm(homarine_neutral_loss, ppm = 5)] %>%
   arrange(desc(int)) %>% head() %>% knitr::kable()
 
-## ---- fig.height=3------------------------------------------------------------
+## ----fig.height=3-------------------------------------------------------------
 chrom_file <- system.file("extdata", "wk_chrom.mzML.gz", package = "RaMS")
 msdata_chroms <- grabMSdata(chrom_file, verbosity = 0, grab_what = "chroms")
 given_chrom <- msdata_chroms$chroms[chrom_type=="SRM iletter1"]
@@ -192,7 +193,7 @@ as.numeric(object.size(all_data)/object.size(small_data))
 ## ----verbosedemo--------------------------------------------------------------
 all_data <- grabMSdata(data_files, grab_what = c("MS1", "MS2"), verbosity = 2)
 
-## ---- eval=FALSE--------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #  ## Not run:
 #  library(parallel)
 #  cl <- makeCluster(getOption("cl.cores", detectCores()-1))
@@ -206,12 +207,12 @@ all_data <- grabMSdata(data_files, grab_what = c("MS1", "MS2"), verbosity = 2)
 #  }
 #  stopImplicitCluster()
 
-## ---- eval=FALSE--------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #  ## Not run:
 #  data_nodes <- xml2::xml_find_all(mzML_nodes, xpath="//d1:precursorMz")
 #  raw_data <- xml2::xml_attr(data_nodes, "value")
 
-## ---- eval=FALSE--------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #  ## Not run:
 #  decoded_binary <- base64enc::base64decode(binary)
 #  raw_binary <- as.raw(decoded_binary)

doc/Intro-to-RaMS.Rmd

@@ -12,6 +12,7 @@ vignette: >
 ```{r, include = FALSE}
 options(rmarkdown.html_vignette.check_title = FALSE)
 options(tidyverse.quiet = TRUE)
+data.table::setDTthreads(2)
 
 knitr::opts_chunk$set(
   collapse = TRUE,

doc/Intro-to-tmzML.R

@@ -1,6 +1,7 @@
 ## ----setup, include = FALSE---------------------------------------------------
 options(rmarkdown.html_vignette.check_title = FALSE)
 options(tidyverse.quiet = TRUE)
+data.table::setDTthreads(2)
 
 knitr::opts_chunk$set(
   collapse = TRUE,

doc/Intro-to-tmzML.Rmd

@@ -12,6 +12,7 @@ vignette: >
 ```{r setup, include = FALSE}
 options(rmarkdown.html_vignette.check_title = FALSE)
 options(tidyverse.quiet = TRUE)
+data.table::setDTthreads(2)
 
 knitr::opts_chunk$set(
   collapse = TRUE,

doc/Intro-to-tmzML.html

@@ -462,27 +462,16 @@ <h2>Getting started with tmzML documents</h2>
 <span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a><span class="fu">ggplot</span>(ms_data_table) <span class="sc">+</span> <span class="fu">geom_line</span>(<span class="fu">aes</span>(<span class="at">x=</span>rt, <span class="at">y=</span>int, <span class="at">color=</span>filename)) <span class="sc">+</span> <span class="fu">xlim</span>(<span class="dv">8</span>, <span class="fl">9.5</span>)</span></code></pre></div>
 <p><img src="data:image/png;base64,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" width="80%" style="display: block; margin: auto;" /></p>
 <div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="fu">library</span>(dplyr)</span>
-<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="co">#&gt; </span></span>
-<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a><span class="co">#&gt; Attaching package: &#39;dplyr&#39;</span></span>
-<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="co">#&gt; The following object is masked from &#39;package:RaMS&#39;:</span></span>
-<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a><span class="co">#&gt; </span></span>
-<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="co">#&gt;     between</span></span>
-<span id="cb6-7"><a href="#cb6-7" tabindex="-1"></a><span class="co">#&gt; The following objects are masked from &#39;package:stats&#39;:</span></span>
-<span id="cb6-8"><a href="#cb6-8" tabindex="-1"></a><span class="co">#&gt; </span></span>
-<span id="cb6-9"><a href="#cb6-9" tabindex="-1"></a><span class="co">#&gt;     filter, lag</span></span>
-<span id="cb6-10"><a href="#cb6-10" tabindex="-1"></a><span class="co">#&gt; The following objects are masked from &#39;package:base&#39;:</span></span>
-<span id="cb6-11"><a href="#cb6-11" tabindex="-1"></a><span class="co">#&gt; </span></span>
-<span id="cb6-12"><a href="#cb6-12" tabindex="-1"></a><span class="co">#&gt;     intersect, setdiff, setequal, union</span></span>
-<span id="cb6-13"><a href="#cb6-13" tabindex="-1"></a>ms_data_table <span class="sc">%&gt;%</span></span>
-<span id="cb6-14"><a href="#cb6-14" tabindex="-1"></a>  <span class="fu">filter</span>(rt<span class="sc">%between%</span><span class="fu">c</span>(<span class="fl">8.4</span>, <span class="fl">8.9</span>)) <span class="sc">%&gt;%</span></span>
-<span id="cb6-15"><a href="#cb6-15" tabindex="-1"></a>  <span class="fu">group_by</span>(filename) <span class="sc">%&gt;%</span></span>
-<span id="cb6-16"><a href="#cb6-16" tabindex="-1"></a>  <span class="fu">summarise</span>(<span class="at">area=</span><span class="fu">sum</span>(int))</span>
-<span id="cb6-17"><a href="#cb6-17" tabindex="-1"></a><span class="co">#&gt; # A tibble: 3 × 2</span></span>
-<span id="cb6-18"><a href="#cb6-18" tabindex="-1"></a><span class="co">#&gt;   filename             area</span></span>
-<span id="cb6-19"><a href="#cb6-19" tabindex="-1"></a><span class="co">#&gt;   &lt;chr&gt;               &lt;dbl&gt;</span></span>
-<span id="cb6-20"><a href="#cb6-20" tabindex="-1"></a><span class="co">#&gt; 1 LB12HL_AB.tmzML 13057831.</span></span>
-<span id="cb6-21"><a href="#cb6-21" tabindex="-1"></a><span class="co">#&gt; 2 LB12HL_CD.tmzML 24925878.</span></span>
-<span id="cb6-22"><a href="#cb6-22" tabindex="-1"></a><span class="co">#&gt; 3 LB12HL_EF.tmzML 21913457.</span></span></code></pre></div>
+<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a>ms_data_table <span class="sc">%&gt;%</span></span>
+<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a>  <span class="fu">filter</span>(rt<span class="sc">%between%</span><span class="fu">c</span>(<span class="fl">8.4</span>, <span class="fl">8.9</span>)) <span class="sc">%&gt;%</span></span>
+<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a>  <span class="fu">group_by</span>(filename) <span class="sc">%&gt;%</span></span>
+<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a>  <span class="fu">summarise</span>(<span class="at">area=</span><span class="fu">sum</span>(int))</span>
+<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="co">#&gt; # A tibble: 3 × 2</span></span>
+<span id="cb6-7"><a href="#cb6-7" tabindex="-1"></a><span class="co">#&gt;   filename             area</span></span>
+<span id="cb6-8"><a href="#cb6-8" tabindex="-1"></a><span class="co">#&gt;   &lt;chr&gt;               &lt;dbl&gt;</span></span>
+<span id="cb6-9"><a href="#cb6-9" tabindex="-1"></a><span class="co">#&gt; 1 LB12HL_AB.tmzML 13057831.</span></span>
+<span id="cb6-10"><a href="#cb6-10" tabindex="-1"></a><span class="co">#&gt; 2 LB12HL_CD.tmzML 24925878.</span></span>
+<span id="cb6-11"><a href="#cb6-11" tabindex="-1"></a><span class="co">#&gt; 3 LB12HL_EF.tmzML 21913457.</span></span></code></pre></div>
 </div>
 <div id="why-not-tmzml" class="section level2">
 <h2>Why not tmzML?</h2>
@@ -509,7 +498,7 @@ <h2>Why not tmzML?</h2>
 <span id="cb8-4"><a href="#cb8-4" tabindex="-1"></a><span class="co">#&gt;  $ MS2       : NULL</span></span>
 <span id="cb8-5"><a href="#cb8-5" tabindex="-1"></a><span class="co">#&gt;  $ connection:List of 3</span></span>
 <span id="cb8-6"><a href="#cb8-6" tabindex="-1"></a><span class="co">#&gt;   ..$ files    : Named chr [1:3] &quot;tmzMLs/LB12HL_AB.tmzML&quot; &quot;tmzMLs/LB12HL_CD.tmzML&quot; &quot;tmzMLs/LB12HL_EF.tmzML&quot;</span></span>
-<span id="cb8-7"><a href="#cb8-7" tabindex="-1"></a><span class="co">#&gt;   .. ..- attr(*, &quot;names&quot;)= chr [1:3] &quot;C:/Users/willi/AppData/Local/R/win-library/4.3/RaMS/extdata/LB12HL_AB.mzML.gz&quot; &quot;C:/Users/willi/AppData/Local/R/win-library/4.3/RaMS/extdata/LB12HL_CD.mzML.gz&quot; &quot;C:/Users/willi/AppData/Local/R/win-library/4.3/RaMS/extdata/LB12HL_EF.mzML.gz&quot;</span></span>
+<span id="cb8-7"><a href="#cb8-7" tabindex="-1"></a><span class="co">#&gt;   .. ..- attr(*, &quot;names&quot;)= chr [1:3] &quot;C:/Users/willi/AppData/Local/Temp/RtmpQ9wT8y/temp_libpath49a055ab1e9b/RaMS/extdata/LB12HL_AB.mzML.gz&quot; &quot;C:/Users/willi/AppData/Local/Temp/RtmpQ9wT8y/temp_libpath49a055ab1e9b/RaMS/extdata/LB12HL_CD.mzML.gz&quot; &quot;C:/Users/willi/AppData/Local/Temp/RtmpQ9wT8y/temp_libpath49a055ab1e9b/RaMS/extdata/LB12HL_EF.mzML.gz&quot;</span></span>
 <span id="cb8-8"><a href="#cb8-8" tabindex="-1"></a><span class="co">#&gt;   ..$ grab_what: chr [1:2] &quot;MS1&quot; &quot;MS2&quot;</span></span>
 <span id="cb8-9"><a href="#cb8-9" tabindex="-1"></a><span class="co">#&gt;   ..$ verbosity: num 0</span></span>
 <span id="cb8-10"><a href="#cb8-10" tabindex="-1"></a><span class="co">#&gt;  - attr(*, &quot;class&quot;)= chr &quot;msdata_connection&quot;</span></span></code></pre></div>
@@ -573,7 +562,7 @@ <h2>tmzML internals</h2>
 fast so we may be approaching diminishing returns.</p>
 <div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a><span class="fu">unlink</span>(<span class="st">&quot;tmzMLs&quot;</span>, <span class="at">recursive =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
 <hr />
-<p>Vignette last built on 2023-11-29</p>
+<p>Vignette last built on 2023-12-13</p>
 </div>
 
 

doc/Minifying-files-with-RaMS.R

@@ -1,6 +1,7 @@
 ## ----setup, include = FALSE---------------------------------------------------
 options(rmarkdown.html_vignette.check_title = FALSE)
 options(tidyverse.quiet = TRUE)
+data.table::setDTthreads(2)
 
 knitr::opts_chunk$set(
   collapse = TRUE,

doc/Minifying-files-with-RaMS.Rmd

@@ -12,6 +12,7 @@ vignette: >
 ```{r setup, include = FALSE}
 options(rmarkdown.html_vignette.check_title = FALSE)
 options(tidyverse.quiet = TRUE)
+data.table::setDTthreads(2)
 
 knitr::opts_chunk$set(
   collapse = TRUE,