| 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).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (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 | ||||
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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. |
| Package 6/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| a4Reporting 1.42.0 (landing page) Laure Cougnaud
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| 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 |
############################################################################## ############################################################################## ### ### 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
a4Reporting.Rcheck/00install.out
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### Running command:
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### 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
###
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Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
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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
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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
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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
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a4Reporting.Rcheck/examples_i386/a4Reporting-Ex.timings
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a4Reporting.Rcheck/examples_x64/a4Reporting-Ex.timings
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