Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 6/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
a4Reporting 1.52.0  (landing page)
Laure Cougnaud
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/a4Reporting
git_branch: RELEASE_3_19
git_last_commit: ce1eea6
git_last_commit_date: 2024-04-30 10:24:18 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for a4Reporting on kjohnson3

To the developers/maintainers of the a4Reporting package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: a4Reporting
Version: 1.52.0
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_1.52.0.tar.gz
StartedAt: 2024-06-10 06:50:16 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 06:51:02 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 45.7 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_1.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/a4Reporting.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘a4Reporting/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Reporting’ version ‘1.52.0’
* 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 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 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 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 4.4.0 by xtable 1.8-4 package
% Mon Jun 10 06:50:47 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 
  0.268   0.067   0.620 

Example timings

a4Reporting.Rcheck/a4Reporting-Ex.timings

nameusersystemelapsed
annotationTable-class0.0010.0000.001
annotationTable0.0050.0010.011
generateEntrezIdLinks000
xtable-methods0.0190.0010.033