BioC 3.5: CHECK report for bumphunter on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings bumphunter_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/bumphunter.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bumphunter/DESCRIPTION’ ... OK
* this is package ‘bumphunter’ version ‘1.16.0’
* 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 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:
  testthat results ================================================================
  OK: 24 SKIPPED: 0 FAILED: 5
  1. Failure: Annotate Nearest (@test_annotation.R#13) 
  2. Failure: Annotate Nearest (@test_annotation.R#14) 
  3. Failure: Annotate Nearest (@test_annotation.R#15) 
  4. Failure: Annotate Nearest (@test_annotation.R#17) 
  5. Failure: Annotate Nearest (@test_annotation.R#19) 
  
  Error: testthat unit tests failed
  In addition: Warning messages:
  1: In .set_group_names(grl, use.names, txdb, by) :
    some group names are NAs or duplicated
  2: In .set_group_names(grl, use.names, txdb, by) :
    some group names are NAs or duplicated
  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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/bumphunter.Rcheck/00check.log’
for details.


R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 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.

> 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, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

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
1. Failure: Annotate Nearest (@test_annotation.R#13) ---------------------------
annotateNearest(x, subject)$distance not equal to rep(c(0, -2, 1, 0), c(5, 1, 1, 2)).
4/9 mismatches (average diff: 1)
[2] -1 - 0 == -1
[3] -1 - 0 == -1
[4] -1 - 0 == -1
[5] -1 - 0 == -1


2. Failure: Annotate Nearest (@test_annotation.R#14) ---------------------------
annotateNearest(x, subject)$subjectHits not equal to c(1:5, 5:6, 6:7).
4/9 mismatches (average diff: 1)
[2] 1 - 2 == -1
[3] 2 - 3 == -1
[4] 3 - 4 == -1
[5] 4 - 5 == -1


3. Failure: Annotate Nearest (@test_annotation.R#15) ---------------------------
annotateNearest(x, subject)$type not equal to rep(c("inside", "cover", "disjoint", "overlap"), c(2, 3, 2, 2)).
4/9 mismatches
x[2]: "disjoint"
y[2]: "inside"

x[3]: "disjoint"
y[3]: "cover"

x[4]: "disjoint"
y[4]: "cover"

x[5]: "disjoint"
y[5]: "cover"


4. Failure: Annotate Nearest (@test_annotation.R#17) ---------------------------
annotateNearest(x, subject)$insideDist not equal to rep(c(0, NA), c(2, 7)).
1/9 mismatches
[2] NA - 0 == NA


5. Failure: Annotate Nearest (@test_annotation.R#19) ---------------------------
annotateNearest(x, subject)$size2 not equal to rep(c(3, 2, 3), c(3, 5, 1)).
1/9 mismatches
[4] 3 - 2 == 1


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")'.

Download the refGene table ... OK
Download the hgFixed.refLink table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
No annotationPackage supplied. Trying org.Cf.eg.db.
Loading required package: org.Cf.eg.db

org.Cf.eg contains GO mappings based on older data because the Blast2GO
  data resource was removed from the public domain just before the most
  recent update was produced. We are working on an alternative means to
  get this kind of data before the next release.

Getting TSS and TSE.
Getting CSS and CSE.
Getting exons.
Annotating genes.
Loading required package: NA
Failed with error:  'invalid package name'
In addition: Warning messages:
1: In .extractCdsLocsFromUCSCTxTable(ucsc_txtable, exon_locs) :
  UCSC data anomaly in 113 transcript(s): the cds cumulative length is
  not a multiple of 3 for transcripts 'NM_001286967' 'NM_001002949'
  'NM_001003268' 'NM_001003372' 'NM_001012395' 'NM_001003021'
  'NM_001097552' 'NM_001197156' 'NM_001003011' 'NM_001097552'
  'NM_001003148' 'NM_001003195' 'NM_001003184' 'NM_001247976'
  'NM_001003321' 'NM_001284483' 'NM_001003140' 'NM_001003300'
  'NM_001197035' 'NM_001314111' 'NM_001252229' 'NM_001284472'
  'NM_001003125' 'NM_001003083' 'NM_001251942' 'NM_001003207'
  'NM_001002958' 'NM_001006646' 'NM_001161713' 'NM_001252035'
  'NM_001006650' 'NM_001197118' 'NM_001003077' 'NM_001003341'
  'NM_001002995' 'NM_001006123' 'NM_001002939' 'NM_001002960'
  'NM_001130437' 'NM_001113711' 'NM_001003356' 'NM_001008717'
  'NM_001003114' 'NM_001003082' 'NM_001252581' 'NM_001097559'
  'NM_001002978' 'NM_001284440' 'NM_001110179' 'NM_001003966'
  'NM_001005252' 'NM_001197187' 'NM_001131049' 'NM_001003343'
  'NM_001002979' 'NM_001003103' 'NM_001048084' 'NM_001005 [... truncated]
2: In .set_group_names(grl, use.names, txdb, by) :
  some group names are NAs or duplicated
3: In .set_group_names(grl, use.names, txdb, by) :
  some group names are NAs or duplicated
Could not load NA. Will continue without annotation
Getting TSS and TSE.
Getting CSS and CSE.
Getting exons.
No annotationPackage supplied. Trying org.Hs.eg.db.
Loading required package: org.Hs.eg.db

Getting TSS and TSE.
Getting CSS and CSE.
Getting exons.
Annotating genes.
testthat results ================================================================
OK: 24 SKIPPED: 0 FAILED: 5
1. Failure: Annotate Nearest (@test_annotation.R#13) 
2. Failure: Annotate Nearest (@test_annotation.R#14) 
3. Failure: Annotate Nearest (@test_annotation.R#15) 
4. Failure: Annotate Nearest (@test_annotation.R#17) 
5. Failure: Annotate Nearest (@test_annotation.R#19) 

Error: testthat unit tests failed
In addition: Warning messages:
1: In .set_group_names(grl, use.names, txdb, by) :
  some group names are NAs or duplicated
2: In .set_group_names(grl, use.names, txdb, by) :
  some group names are NAs or duplicated
Execution halted

name	user	system	elapsed
annotateNearest	1.332	0.012	1.347
annotateTranscripts	0.000	0.000	0.001
bumphunter	2.564	0.832	2.234
clusterMaker	0.016	0.000	0.017
dummyData	0.036	0.000	0.039
getSegments	0.084	0.000	0.084
locfitByCluster	0.292	0.012	0.306
loessByCluster	0.212	0.000	0.214
matchGenes	0	0	0
regionFinder	0.092	0.000	0.093
runmedByCluster	0.004	0.000	0.004
smoother	0.108	0.100	0.147

BioC 3.5: CHECK report for bumphunter on malbec2

Summary

Command output