CHECK report for SNPchip on malbec2
This page was generated on 2019-04-09 11:24:42 -0400 (Tue, 09 Apr 2019).
SNPchip 2.29.0
Robert Scharpf
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/SNPchip |
| Branch: master |
| Last Commit: effab19 |
| Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ ERROR ] | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
Summary
Command output
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### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SNPchip.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SNPchip_2.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SNPchip.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPchip/DESCRIPTION’ ... OK
* this is package ‘SNPchip’ version ‘2.29.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘VanillaICE’
* 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 ‘SNPchip’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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
* 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
centromereData: no visible global function definition for ‘read.delim’
dataFrameFromRange: no visible binding for global variable ‘data’
getCytoband: no visible global function definition for ‘read.table’
Undefined global functions or variables:
data read.delim read.table
Consider adding
importFrom("utils", "data", "read.delim", "read.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 ... ERROR
Running examples in ‘SNPchip-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xyplot
> ### Title: Plot copy number and physical position for a set of genomic
> ### intervals.
> ### Aliases: xyplot2 xyplot2,formula,gSet-method
> ### xyplot2,formula,SnpSet-method
> ### Keywords: dplot methods
>
> ### ** Examples
>
> ## simulated data
> library(oligoClasses)
Welcome to oligoClasses version 1.45.0
> library(IRanges)
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, colMeans, colSums, 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, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
> library(VanillaICE)
Error in library(VanillaICE) : there is no package called ‘VanillaICE’
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘doRUnit.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 ERROR, 3 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/SNPchip.Rcheck/00check.log’
for details.
Installation output
SNPchip.Rcheck/00install.out
Tests output
SNPchip.Rcheck/tests/doRUnit.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.
> ## from xmapcore package
> if( require( "RUnit", quietly=TRUE ) ) {
+ pkg <- "SNPchip"
+
+ if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) {
+ path <- file.path( getwd(), "..", "inst", "unitTests" )
+ } else {
+ path <- system.file( package=pkg, "unitTests" )
+ }
+
+ cat( "\nRunning unit tests\n" )
+ print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) )
+ library( package=pkg, character.only=TRUE )
+ ## fail on warnings (needed for SNPchip() test)
+ ##options(warn=2)
+ patt <- Sys.getenv( "RUNITFILEPATTERN" )
+ if( is.null( patt ) || nchar( patt ) == 0 ) {
+ testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+ dirs=path,
+ testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ))
+ } else {
+ ##testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=paste( "^runit\\.", patt, "\\.[rR]$", sep="" ), dirs=path )
+ testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+ testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ),
+ dirs=path )
+ }
+ tests <- runTestSuite( testSuite )
+
+ pathReport <- file.path( path, "report" )
+
+ cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" )
+ printTextProtocol( tests, showDetails=FALSE )
+ printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) )
+ printTextProtocol( tests, showDetails=TRUE, fileName=paste( pathReport, ".txt", sep="" ) )
+
+ printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) )
+
+ tmp <- getErrors( tests )
+ if( tmp$nFail > 0 | tmp$nErr > 0 ){
+ stop( paste( "\n\nunit testing failed (#test failures: ", tmp$nFail, ", #R errors: ", tmp$nErr, ")\n\n", sep=""))
+ }
+ } else {
+ warning( "cannot run unit tests -- package RUnit is not available" )
+ }
Running unit tests
$pkg
[1] "SNPchip"
$getwd
[1] "/home/biocbuild/bbs-3.9-bioc/meat/SNPchip.Rcheck/tests"
$pathToUnitTests
[1] "/home/biocbuild/bbs-3.9-bioc/R/library/SNPchip/unitTests"
Welcome to SNPchip version 2.29.0
------------------- UNIT TEST SUMMARY ---------------------
RUNIT TEST PROTOCOL -- Tue Apr 9 03:48:23 2019
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
SNPchip unit testing - 0 test functions, 0 errors, 0 failures
>
> proc.time()
user system elapsed
8.186 0.336 8.552
Example timings
SNPchip.Rcheck/SNPchip-Ex.timings