Jitao David Zhang
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ddCt |
| Branch: RELEASE_3_8 |
| Last Commit: e42a7c5 |
| Last Changed Date: 2018-10-30 11:41:45 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:21:01 -0400 (Sat, 13 Apr 2019).
| Package 374/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ddCt 1.38.0 Jitao David Zhang
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ddCt |
| Version: 1.38.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ddCt.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ddCt_1.38.0.tar.gz |
| StartedAt: 2019-04-13 01:39:00 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 01:40:46 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 106.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ddCt.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ddCt.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ddCt_1.38.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/ddCt.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ddCt/DESCRIPTION' ... OK
* this is package 'ddCt' version '1.38.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'ddCt' 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 ... NOTE
barploterrbar: no visible global function definition for 'par'
barploterrbar: no visible global function definition for 'layout'
barploterrbar: no visible global function definition for 'barplot'
barploterrbar: no visible global function definition for 'segments'
barploterrbar: no visible global function definition for 'plot'
ddCtErrBarchart: no visible global function definition for 'as.formula'
ddCtReport: no visible global function definition for 'write.table'
na.mad: no visible global function definition for 'mad'
na.median: no visible global function definition for 'median'
na.sd: no visible global function definition for 'sd'
replaceNames: no visible global function definition for 'na.omit'
ddCtWithEExec,InputFrame: no visible global function definition for
'deriv'
ddCtWithEExec,InputFrame: no visible global function definition for
'as.formula'
elistWrite,ddCtExpression-character: no visible global function
definition for 'write.table'
readRawData,QuantStudioReader-character: no visible global function
definition for 'read.table'
readRawData,SDMReader-character: no visible global function definition
for 'read.table'
readRawData,TSVReader-character: no visible global function definition
for 'read.table'
Undefined global functions or variables:
as.formula barplot deriv layout mad median na.omit par plot
read.table sd segments write.table
Consider adding
importFrom("graphics", "barplot", "layout", "par", "plot", "segments")
importFrom("stats", "as.formula", "deriv", "mad", "median", "na.omit",
"sd")
importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... 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 'unit.R'
OK
** running tests for arch 'x64' ...
Running 'unit.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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/ddCt.Rcheck/00check.log'
for details.
ddCt.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/ddCt_1.38.0.tar.gz && rm -rf ddCt.buildbin-libdir && mkdir ddCt.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ddCt.buildbin-libdir ddCt_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL ddCt_1.38.0.zip && rm ddCt_1.38.0.tar.gz ddCt_1.38.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 193k 100 193k 0 0 3129k 0 --:--:-- --:--:-- --:--:-- 3328k
install for i386
* installing *source* package 'ddCt' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ddCt'
finding HTML links ... done
InputFrame html
InputReader-class html
QuantStudioFrame html
SDMFrame-class html
SDMFrame html
barploterrbar html
ddCtAbsolute html
finding level-2 HTML links ... done
ddCtExpression-class html
ddCtExpression-methods html
elistWrite-methods html
errBarchart-methods html
errBarchartParameter-class html
getDir html
removeNTC-methods html
replaceVectorByEquality html
write.htmltable html
writeSimpleTabCsv html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'ddCt' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ddCt' as ddCt_1.38.0.zip
* DONE (ddCt)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'ddCt' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
ddCt.Rcheck/tests_i386/unit.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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.
> ################################################################################
> ##
> ## This software is created by Molecular Genom Analysis Group
> ## Department of German Cancer Research Center in Heidelberg
> ##
> ##
> ## unit.R
> ## Created on: Oct 23, 2008
> ## Author: Rudolf Biczok <r.biczok@dkfz-heidelberg.de>
> ## Description: RUnit test suit for ddCt classes
> ##
> ################################################################################
>
> pkg <- "ddCt"
> unit.path <- file.path(getwd(), "units")
>
> unitMode <- function() {
+ if(Sys.getenv("R_DEVELOP_MODE") == "TRUE")
+ return("unit")
+ else
+ return("normal")
+ }
>
> normalTest <- function() {
+ testFile <- system.file("./extdata/Experiment2.txt", package=pkg)
+
+ ## Basic SDMFrame
+ sdm <- SDMFrame(testFile)
+
+ ## ddCt
+ x <- ddCtExpression(sdm,
+ calibrationSample="Sample3",
+ housekeepingGenes="Gene2")
+
+ ## coerece as data frame
+ y1 <- as(x, "data.frame")
+ y2 <- elist(x)
+ stopifnot(all.equal(y1,y2))
+
+ ## visualization
+ errBarchart(x)
+ }
>
>
> ## --- Setup ---
>
> library(package=pkg, character.only=TRUE)
>
> # put this in an enclosure so we can return early
> (function() {
+ if(unitMode() != "unit") {
+ normalTest()
+ return()
+ }
+
+ if(!require("RUnit", quietly=TRUE)) {
+ stop("cannot run unit tests -- package RUnit is not available")
+ }
+
+ ## --- Testing ---
+ cat("------------------- BEGIN UNIT TESTS ----------------------\n\n")
+
+ ## --- Setup test suit ---
+ testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), dirs=unit.path)
+ tests <- runTestSuite(testSuite)
+
+ ## --- Setup report directory ---
+ pathReport <- file.path(getwd(),"report")
+ if (!file.exists(pathReport)) {
+ dir.create(pathReport)
+ }
+
+ ## --- Reporting ---
+ cat("------------------- UNIT TEST SUMMARY ---------------------\n\n")
+
+ printTextProtocol(tests, showDetails=FALSE)
+ printTextProtocol(tests, showDetails=FALSE,
+ fileName=file.path(pathReport, "summary.txt"))
+ printTextProtocol(tests, showDetails=TRUE,
+ fileName=file.path(pathReport, "summary-detail.txt"))
+ printHTMLProtocol(tests,
+ fileName=file.path(pathReport, "summary.html"))
+
+ errors <- getErrors(tests)
+ if(errors$nFail > 0 | errors$nErr > 0) {
+ warning(paste("\n\nunit testing failed (#unit failures: ", errors$nFail,
+ ", #R errors: ", errors$nErr, ")\n\n", sep=""))
+ }
+
+ cat("------------------- END OF UNIT TESTING -------------------\n\n")
+ })()
NULL
>
> proc.time()
user system elapsed
0.98 0.03 1.00
|
ddCt.Rcheck/tests_x64/unit.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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.
> ################################################################################
> ##
> ## This software is created by Molecular Genom Analysis Group
> ## Department of German Cancer Research Center in Heidelberg
> ##
> ##
> ## unit.R
> ## Created on: Oct 23, 2008
> ## Author: Rudolf Biczok <r.biczok@dkfz-heidelberg.de>
> ## Description: RUnit test suit for ddCt classes
> ##
> ################################################################################
>
> pkg <- "ddCt"
> unit.path <- file.path(getwd(), "units")
>
> unitMode <- function() {
+ if(Sys.getenv("R_DEVELOP_MODE") == "TRUE")
+ return("unit")
+ else
+ return("normal")
+ }
>
> normalTest <- function() {
+ testFile <- system.file("./extdata/Experiment2.txt", package=pkg)
+
+ ## Basic SDMFrame
+ sdm <- SDMFrame(testFile)
+
+ ## ddCt
+ x <- ddCtExpression(sdm,
+ calibrationSample="Sample3",
+ housekeepingGenes="Gene2")
+
+ ## coerece as data frame
+ y1 <- as(x, "data.frame")
+ y2 <- elist(x)
+ stopifnot(all.equal(y1,y2))
+
+ ## visualization
+ errBarchart(x)
+ }
>
>
> ## --- Setup ---
>
> library(package=pkg, character.only=TRUE)
>
> # put this in an enclosure so we can return early
> (function() {
+ if(unitMode() != "unit") {
+ normalTest()
+ return()
+ }
+
+ if(!require("RUnit", quietly=TRUE)) {
+ stop("cannot run unit tests -- package RUnit is not available")
+ }
+
+ ## --- Testing ---
+ cat("------------------- BEGIN UNIT TESTS ----------------------\n\n")
+
+ ## --- Setup test suit ---
+ testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), dirs=unit.path)
+ tests <- runTestSuite(testSuite)
+
+ ## --- Setup report directory ---
+ pathReport <- file.path(getwd(),"report")
+ if (!file.exists(pathReport)) {
+ dir.create(pathReport)
+ }
+
+ ## --- Reporting ---
+ cat("------------------- UNIT TEST SUMMARY ---------------------\n\n")
+
+ printTextProtocol(tests, showDetails=FALSE)
+ printTextProtocol(tests, showDetails=FALSE,
+ fileName=file.path(pathReport, "summary.txt"))
+ printTextProtocol(tests, showDetails=TRUE,
+ fileName=file.path(pathReport, "summary-detail.txt"))
+ printHTMLProtocol(tests,
+ fileName=file.path(pathReport, "summary.html"))
+
+ errors <- getErrors(tests)
+ if(errors$nFail > 0 | errors$nErr > 0) {
+ warning(paste("\n\nunit testing failed (#unit failures: ", errors$nFail,
+ ", #R errors: ", errors$nErr, ")\n\n", sep=""))
+ }
+
+ cat("------------------- END OF UNIT TESTING -------------------\n\n")
+ })()
NULL
>
> proc.time()
user system elapsed
0.82 0.12 0.93
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ddCt.Rcheck/examples_i386/ddCt-Ex.timings
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ddCt.Rcheck/examples_x64/ddCt-Ex.timings
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