Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:07 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for a4Reporting on tokay2


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? 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: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
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 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:a4Reporting.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings a4Reporting_1.42.0.tar.gz
StartedAt: 2022-04-12 15:22:53 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 15:23:57 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 64.3 seconds
RetCode: 0
Status:   OK  
CheckDir: a4Reporting.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:a4Reporting.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings a4Reporting_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/a4Reporting.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.annotationTable.R'
 OK
** running tests for arch 'x64' ...
  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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/a4Reporting_1.42.0.tar.gz && rm -rf a4Reporting.buildbin-libdir && mkdir a4Reporting.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=a4Reporting.buildbin-libdir a4Reporting_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL a4Reporting_1.42.0.zip && rm a4Reporting_1.42.0.tar.gz a4Reporting_1.42.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 85  7671   85  6542    0     0  81701      0 --:--:-- --:--:-- --:--:-- 81775
100  7671  100  7671    0     0  21380      0 --:--:-- --:--:-- --:--:-- 21367

install for i386

* installing *source* package 'a4Reporting' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'a4Reporting'
    finding HTML links ... done
    annotationTable-class                   html  
    annotationTable                         html  
    generateEntrezIdLinks                   html  
    generateGOIdLinks                       html  
    print.xtableAnnotationTable             html  
    xtable-methods                          html  
** 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

install for x64

* installing *source* package 'a4Reporting' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'a4Reporting' as a4Reporting_1.42.0.zip
* DONE (a4Reporting)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'a4Reporting' successfully unpacked and MD5 sums checked

Tests output

a4Reporting.Rcheck/tests_i386/test.annotationTable.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 4.1.3 by xtable 1.8-4 package
% Tue Apr 12 15:23:46 2022
\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 
   0.43    0.03    0.48 

a4Reporting.Rcheck/tests_x64/test.annotationTable.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 4.1.3 by xtable 1.8-4 package
% Tue Apr 12 15:23:47 2022
\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 
   0.37    0.04    0.39 

Example timings

a4Reporting.Rcheck/examples_i386/a4Reporting-Ex.timings

nameusersystemelapsed
annotationTable-class0.000.000.05
annotationTable000
generateEntrezIdLinks000
xtable-methods0.140.000.15

a4Reporting.Rcheck/examples_x64/a4Reporting-Ex.timings

nameusersystemelapsed
annotationTable-class0.020.000.01
annotationTable000
generateEntrezIdLinks000
xtable-methods0.100.000.09