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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_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/qcmetrics.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qcmetrics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qcmetrics’ version ‘1.36.0’
* 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/RtmpWydazg/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")
Report written to /tmp/RtmpWydazg/testQCReport.html
> html
[1] "/tmp/RtmpWydazg/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-3.16-bioc/meat/qcmetrics.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL qcmetrics
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘qcmetrics’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (qcmetrics)