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This page was generated on 2021-11-26 15:05:41 -0500 (Fri, 26 Nov 2021).

CHECK results for a4Reporting on machv2

To the developers/maintainers of the a4Reporting package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/a4Reporting.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 6/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
a4Reporting 1.42.0  (landing page)
Laure Cougnaud
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/a4Reporting
git_branch: RELEASE_3_14
git_last_commit: b0d715b
git_last_commit_date: 2021-10-26 11:58:57 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: a4Reporting
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:a4Reporting.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings a4Reporting_1.42.0.tar.gz
StartedAt: 2021-11-25 13:37:00 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 13:37:31 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 30.9 seconds
RetCode: 0
Status:   OK  
CheckDir: a4Reporting.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:a4Reporting.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings a4Reporting_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/a4Reporting.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘a4Reporting/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Reporting’ version ‘1.42.0’
* 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 ‘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 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 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 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: OK


Installation output

a4Reporting.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL a4Reporting
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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)

Tests output

a4Reporting.Rcheck/tests/test.annotationTable.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 4.1.2 by xtable 1.8-4 package
% Thu Nov 25 13:37:24 2021
\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 
  0.418   0.088   0.480 

Example timings

a4Reporting.Rcheck/a4Reporting-Ex.timings

nameusersystemelapsed
annotationTable-class0.0020.0010.003
annotationTable0.0090.0010.009
generateEntrezIdLinks0.0000.0000.001
xtable-methods0.0210.0010.022