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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:a4Reporting.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings a4Reporting_1.54.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/a4Reporting.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘a4Reporting/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Reporting’ version ‘1.54.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘a4Reporting’ 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 code 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.annotationTable.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL a4Reporting
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘a4Reporting’ ...
** using staged installation
** R
** 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 (a4Reporting)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # test annotationTable functionality
> 
> library(a4Reporting)
> 
> ## some dummy data
> set.seed(123)
> dData <- data.frame(someSymbol = LETTERS[1:5], 
+     accessionNumber = 
+         c("X83928", "V00540", "U21090", "L38487", "M34057"),
+     floats = rnorm(5))
> 
> at <- annotationTable(displayData = dData, 
+     displayCols = list(accessionNumber = "EntrezId"))
> 
> at
annotationTable with hyperlink annotation for columns:
someSymbol, accessionNumber, floats 

  someSymbol accessionNumber      floats
1          A          X83928 -0.56047565
2          B          V00540 -0.23017749
3          C          U21090  1.55870831
4          D          L38487  0.07050839
5          E          M34057  0.12928774
> 
> xat <- xtable(at, caption = "Example LaTeX table with Hyperlinks", digits = 3)
> 
> print(xat, include.rownames = FALSE) # OK
% latex table generated in R 4.4.2 by xtable 1.8-4 package
% Thu Dec 19 19:42:33 2024
\begin{table}[ht]
\centering
\begin{tabular}{llr}
  \hline
someSymbol & accessionNumber & floats \\ 
  \hline
A & \href{http://www.ncbi.nlm.nih.gov/gene/X83928}{X83928} & -0.560 \\ 
  B & \href{http://www.ncbi.nlm.nih.gov/gene/V00540}{V00540} & -0.230 \\ 
  C & \href{http://www.ncbi.nlm.nih.gov/gene/U21090}{U21090} & 1.559 \\ 
  D & \href{http://www.ncbi.nlm.nih.gov/gene/L38487}{L38487} & 0.071 \\ 
  E & \href{http://www.ncbi.nlm.nih.gov/gene/M34057}{M34057} & 0.129 \\ 
   \hline
\end{tabular}
\caption{Example LaTeX table with Hyperlinks} 
\end{table}
> 
> 
> proc.time()
   user  system elapsed 
  0.205   0.041   0.236