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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qcmetrics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qcmetrics_1.38.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/qcmetrics.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qcmetrics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qcmetrics’ version ‘1.38.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘qcmetrics’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘qcmetrics-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: qcReport-methods
> ### Title: Automatic report generation
> ### Aliases: qcReport-methods qcReport,QcMetrics-method qcReport reporting
> ### reporting_pdf reporting_tex reporting_rmd reporting_html
> ### example_reports
> ### Keywords: methods report
>
> ### ** Examples
>
> example(QcMetrics)
QcMtrc> example(QcMetric)
QcMtrc> (qc <- QcMetric())
Object of class "QcMetric"
Name: A QcMetric prototype
Status: NA
Data: empty
QcMtrc> qcdata(qc)
character(0)
QcMtrc> try(qcdata(qc, "x"))
Error in qcdata(qc, "x") : No qcdata 'x' in object.
QcMtrc> x <- rnorm(10)
QcMtrc> qcdata(qc, "qc1") <- x
QcMtrc> qcdata(qc, "qc2") <- 1:10
QcMtrc> qcdata(qc)
[1] "qc1" "qc2"
QcMtrc> all.equal(qcdata(qc, "qc1"), x)
[1] TRUE
QcMtrc> all.equal(qcdata(qc, "qc2"), 1:10)
[1] TRUE
QcMtrc> name(qc) <- "My test QcMetric"
QcMtrc> description(qc) <- "This qc metric describes bla bla bla, indicating possible issues in the third step of protocol bla bla bla."
QcMtrc> status(qc) <- FALSE
QcMtrc> qc
Object of class "QcMetric"
Name: My test QcMetric
Description:
This qc metric describes bla bla bla, indicating possible issues in the
third step of protocol bla bla bla.
Status: FALSE
Data: qc1 qc2
QcMtrc> ## or
QcMtrc> e <- new.env()
QcMtrc> e$qc1 <- rnorm(100)
QcMtrc> e$qc2 <- 1:100
QcMtrc> qcdata(qc) <- e
QcMtrc> length(qcdata(qc, "qc1"))
[1] 100
QcMtrc> head(qcdata(qc, "qc2"))
[1] 1 2 3 4 5 6
QcMtrc> show(qc)
Object of class "QcMetric"
Name: My test QcMetric
Description:
This qc metric describes bla bla bla, indicating possible issues in the
third step of protocol bla bla bla.
Status: FALSE
Data: qc1 qc2
QcMtrc> show(qc) <- function(object) cat("Updated show method\n")
QcMtrc> show(qc)
Updated show method
QcMtrc> show(qc) <- qcshow
QcMtrc> qc
Object of class "QcMetric"
Name: My test QcMetric
Description:
This qc metric describes bla bla bla, indicating possible issues in the
third step of protocol bla bla bla.
Status: FALSE
Data: qc1 qc2
QcMtrc> plot(qc)
Warning in x@plot(x, ...) : No specific plot function defined
QcMtrc> plot(qc) <-
QcMtrc+ function(object, ...)
QcMtrc+ plot(qcdata(object, "qc2"),
QcMtrc+ qcdata(object, "qc1"),
QcMtrc+ xlab = "qc1",
QcMtrc+ ylab = "qc2",
QcMtrc+ ...)
QcMtrc> plot(qc)
QcMtrc> plot(qc, col = "red", pch = 19)
QcMtrc> ## Not run:
QcMtrc> ##D ## generate a report
QcMtrc> ##D qcReport(qcm)
QcMtrc> ## End(Not run)
QcMtrc>
QcMtrc>
QcMtrc>
QcMtrc> show(qc)
Object of class "QcMetric"
Name: My test QcMetric
Description:
This qc metric describes bla bla bla, indicating possible issues in the
third step of protocol bla bla bla.
Status: FALSE
Data: qc1 qc2
QcMtrc> qc2 <- QcMetric(name = "My other metric", status = TRUE)
QcMtrc> qcdata(qc2, "x") <- rnorm(100)
QcMtrc> qcdata(qc2, "k") <- rep(LETTERS[1:2], 50)
QcMtrc> plot(qc2) <- function(object, ...) {
QcMtrc+ require("lattice")
QcMtrc+ d <- data.frame(x = qcdata(object, "x"),
QcMtrc+ k = qcdata(object, "k"))
QcMtrc+ bwplot(x ~ k, data = d)
QcMtrc+ }
QcMtrc> qcm <- QcMetrics(qcdata = list(qc, qc2))
QcMtrc> qcm
Object of class "QcMetrics"
containing 2 QC metrics.
and no metadata variables.
QcMtrc> qcm[1] ## a QcMetrics instance
Object of class "QcMetrics"
containing 1 QC metrics.
and no metadata variables.
QcMtrc> qcm[[1]] ## a single QcMetric
Object of class "QcMetric"
Name: My test QcMetric
Description:
This qc metric describes bla bla bla, indicating possible issues in the
third step of protocol bla bla bla.
Status: FALSE
Data: qc1 qc2
QcMtrc> metadata(qcm)
list()
QcMtrc> metadata(qcm) <- QcMetadata(list(name = "Prof. Who",
QcMtrc+ lab = "Cabin University"))
QcMtrc> ## or, shorter but equivalent
QcMtrc> metadata(qcm) <- list(name = "Prof. Who",
QcMtrc+ lab = "Cabin University")
QcMtrc> metadata(qcm) ## or mdata(qcm)
$name
[1] "Prof. Who"
$lab
[1] "Cabin University"
QcMtrc> ## update metadata
QcMtrc> metadata(qcm) <- list(lab = "Big lab", ## updated
QcMtrc+ uni = "Cabin University") ## added
QcMtrc> mdata(qcm)
$name
[1] "Prof. Who"
$lab
[1] "Big lab"
$uni
[1] "Cabin University"
> show(qcm)
Object of class "QcMetrics"
containing 2 QC metrics.
and 3 metadata variables.
>
> destdir <- tempdir()
> (report <- file.path(destdir, "testQCReport"))
[1] "/tmp/RtmprzZLjc/testQCReport"
>
>
> ## Not run:
> ##D ## pdf report
> ##D qcReport(qcm, reportname = report)
> ##D ## use pdflatex to generate the pdf file
> ##D qcReport(qcm, reportname = report, texi2dvi = "pdflatex")
> ## End(Not run)
>
> ## default html report
> html <- qcReport(qcm, reportname = report, type = "html")
Warning in file.info(x, extra_cols = FALSE) :
expanded path length 1663 would be too long for
<style type="text/css">
body {
font-family: sans-serif;
max-width: 800px;
margin: auto;
padding: 1em;
line-height: 1.5;
box-sizing: border-box;
}
body, .footnotes, code { font-size: .9em; }
li li { font-size: .95em; }
*, *:before, *:after {
box-sizing: inherit;
}
pre, img { max-width: 100%; }
pre, pre:hover {
white-space: pre-wrap;
word-break: break-all;
}
pre code {
display: block;
overflow-x: auto;
}
code { font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Monaco, monospace; }
:not(pre) > code, code[class] { background-color: #F8F8F8; }
code.language-undefined, pre > code:not([class]) {
background-color: inherit;
border: 1px solid #eee;
}
table {
margin: auto;
border-top: 1px solid #666;
}
table thead th { border-bottom: 1px solid #ddd; }
th, td { padding: 5px; }
thead, tfoot, tr:nth-child(even) { background: #eee; }
blockquote {
color: #666;
margin: 0;
padding-left: 1em; [... truncated]
Warning in file.info(x, extra_cols = FALSE) :
expanded path length 4012 would be too long for
<h1 id="quality-control-report-generated-with-qcmetrics">Quality control report generated with <code>qcmetrics</code></h1>
<p>Author: biocbuild</p>
<p>Date: Wed Oct 18 16:39:26 2023</p>
<h2 id="metadata">Metadata</h2>
<ul>
<li><strong>name</strong> Prof. Who</li>
<li><strong>lab</strong> Big lab</li>
<li><strong>uni</strong> Cabin University</li>
</ul>
<h2 id="my-test-qcmetric">My test QcMetric</h2>
<pre><code>## Object of class "QcMetric"
## Name: My test QcMetric
## Description:
## This qc metric describes bla bla bla, indicating possible issues in the
## third step of protocol bla bla bla.
## Status: FALSE
## Data: qc1 qc2
</code></pre>
<div class="figure" style="text-align: left">
<img src="figure/unnamed-chunk-1-1.png" alt="plot of chunk unnamed-chunk-1" />
<p class="caption">plot of chunk unnamed-chunk-1</p>
</div>
My other metric
-------------------------
<pre><code>## Object of class "QcMetric"
## Name: [... truncated]
Report written to /tmp/RtmprzZLjc/testQCReport.html
> html
[1] "/tmp/RtmprzZLjc/testQCReport.html"
> if (interactive())
+ browseURL(html)
>
> ## using a custom css templates
> writeLines("
+ body {
+ font-size: 14pt;
+ width: 650px;
+ background: #789855;
+ margin-left: auto;
+ margin-right: auto;
+ margin-top: 20px;
+ margin-bottom: 20;
+ text-align:justify;
+ }", con = "style.css")
>
> html2 <- qcReport(qcm, reportname = "customreport", template = "style.css", type = "html")
Error in mark(..., format = "html", template = template) :
unused argument (stylesheet = "style.css")
Calls: qcReport ... reporting_html -> knit2html -> mark_html -> <Anonymous>
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/qcmetrics.Rcheck/00check.log’
for details.