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This page was generated on 2016-10-13 12:58:46 -0700 (Thu, 13 Oct 2016).
| Package 138/1210 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| bumphunter 1.12.0 Rafael A. Irizarry
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | ERROR | ||||||
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |  | |||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ ERROR ] | OK |
| Package: bumphunter |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bumphunter_1.12.0.tar.gz |
| StartedAt: 2016-10-12 23:47:34 -0700 (Wed, 12 Oct 2016) |
| EndedAt: 2016-10-12 23:51:16 -0700 (Wed, 12 Oct 2016) |
| EllapsedTime: 222.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: bumphunter.Rcheck |
| Warnings: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bumphunter_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/bumphunter.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bumphunter/DESCRIPTION’ ... OK
* this is package ‘bumphunter’ version ‘1.12.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’ ‘foreach’
‘iterators’ ‘parallel’ ‘locfit’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘bumphunter’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘doParallel:::.options’
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 ... NOTE
bumphunterEngine: no visible binding for global variable ‘bootstraps’
Undefined global functions or variables:
bootstraps
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
Running ‘test-all.R’
ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Error in normArgTable(value, x) : unknown table name 'chromInfo'
Calls: test_check ... tableName<- -> tableName<- -> .local -> normArgTable
Timing stopped at: 0.714 0.01 3.594
testthat results ================================================================
OK: 10 SKIPPED: 0 FAILED: 0
Execution halted
* 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, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/bumphunter.Rcheck/00check.log’
for details.
test-all.Rout.fail:
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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.
> library('testthat')
> test_check('bumphunter')
Loading required package: bumphunter
Loading required package: S4Vectors
Loading required package: stats4
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Attaching package: 'S4Vectors'
The following object is masked from 'package:testthat':
compare
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Error in normArgTable(value, x) : unknown table name 'chromInfo'
Calls: test_check ... tableName<- -> tableName<- -> .local -> normArgTable
Timing stopped at: 0.714 0.01 3.594
testthat results ================================================================
OK: 10 SKIPPED: 0 FAILED: 0
Execution halted
bumphunter.Rcheck/00install.out:
* installing *source* package ‘bumphunter’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (bumphunter)
bumphunter.Rcheck/bumphunter-Ex.timings:
| name | user | system | elapsed | |
| annotateNearest | 0.576 | 0.024 | 0.601 | |
| annotateTranscripts | 0.000 | 0.001 | 0.001 | |
| bumphunter | 3.567 | 1.354 | 2.704 | |
| clusterMaker | 0.014 | 0.002 | 0.016 | |
| dummyData | 0.004 | 0.000 | 0.005 | |
| getSegments | 0.007 | 0.001 | 0.009 | |
| locfitByCluster | 0.040 | 0.007 | 0.048 | |
| loessByCluster | 0.294 | 0.023 | 0.318 | |
| matchGenes | 0.001 | 0.000 | 0.001 | |
| regionFinder | 0.027 | 0.000 | 0.027 | |
| runmedByCluster | 0.004 | 0.000 | 0.004 | |
| smoother | 0.134 | 0.065 | 0.163 | |