Tobias Verbeke
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/a4Reporting |
| Branch: RELEASE_3_9 |
| Last Commit: 8d78189 |
| Last Changed Date: 2019-05-02 11:53:25 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:25:05 -0400 (Wed, 16 Oct 2019).
| Package 6/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| a4Reporting 1.32.0 Tobias Verbeke
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: a4Reporting |
| Version: 1.32.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:a4Reporting.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings a4Reporting_1.32.0.tar.gz |
| StartedAt: 2019-10-16 01:49:17 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:51:05 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 108.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: a4Reporting.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:a4Reporting.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings a4Reporting_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/a4Reporting.Rcheck' * using R version 3.6.1 (2019-07-05) * 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 '1.32.0' * 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 DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 ... NOTE Packages in Depends field not imported from: 'annaffy' 'methods' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported objects imported by ':::' calls: 'xtable:::xtable.data.frame' 'xtable:::xtable.matrix' See the note in ?`:::` about the use of this operator. * 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 ... NOTE S3 methods shown with full name in documentation object 'print.xtableAnnotationTable': 'print.xtableAnnotationTable' The \usage entries for S3 methods should use the \method markup and not their full name. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... 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 PDF version of manual ... OK * DONE Status: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/a4Reporting.Rcheck/00check.log' for details.
a4Reporting.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/a4Reporting_1.32.0.tar.gz && rm -rf a4Reporting.buildbin-libdir && mkdir a4Reporting.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=a4Reporting.buildbin-libdir a4Reporting_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL a4Reporting_1.32.0.zip && rm a4Reporting_1.32.0.tar.gz a4Reporting_1.32.0.zip
###
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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
** 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_1.32.0.zip
* DONE (a4Reporting)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'a4Reporting' successfully unpacked and MD5 sums checked
|
a4Reporting.Rcheck/tests_i386/test.annotationTable.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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)
Loading required package: annaffy
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: KEGG.db
KEGG.db contains mappings based on older data because the original
resource was removed from the the public domain before the most
recent update was produced. This package should now be considered
deprecated and future versions of Bioconductor may not have it
available. Users who want more current data are encouraged to look
at the KEGGREST or reactome.db packages
>
> ## 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 3.6.1 by xtable 1.8-4 package
% Wed Oct 16 01:50:57 2019
\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
3.53 0.17 3.68
|
a4Reporting.Rcheck/tests_x64/test.annotationTable.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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)
Loading required package: annaffy
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: KEGG.db
KEGG.db contains mappings based on older data because the original
resource was removed from the the public domain before the most
recent update was produced. This package should now be considered
deprecated and future versions of Bioconductor may not have it
available. Users who want more current data are encouraged to look
at the KEGGREST or reactome.db packages
>
> ## 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 3.6.1 by xtable 1.8-4 package
% Wed Oct 16 01:51:01 2019
\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
3.35 0.12 3.48
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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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