genomeIntervals 1.31.0
Julien Gagneur
| Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genomeIntervals | | Last Changed Rev: 122712 / Revision: 127142 | | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | ERROR | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | ERROR | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ ERROR ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomeIntervals_1.31.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/genomeIntervals.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genomeIntervals/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomeIntervals’ version ‘1.31.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘genomeIntervals’ 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
* 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
interval_complement,Genome_intervals: warning in
factor(rep(as.character(fac.comb[, 2]), times = nrows), level =
levels(seqnames(x))): partial argument match of 'level' to 'levels'
interval_complement,Genome_intervals_stranded: warning in
factor(rep(names(s), times = sapply(gi.list, nrow)), level =
levels(strand(x))): partial argument match of 'level' to 'levels'
coerce,Genome_intervals-RangedData: no visible global function
definition for ‘na.omit’
writeGff3,data.frame: no visible global function definition for
‘write.table’
Undefined global functions or variables:
na.omit write.table
Consider adding
importFrom("stats", "na.omit")
importFrom("utils", "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 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 ... ERROR
Running examples in ‘genomeIntervals-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Genome_intervals-ordering
> ### Title: Ordering methods for Genome intervals
> ### Aliases: Genome_intervals-ordering order rank sort xtfrm
> ### order,Genome_intervals-method order,Genome_intervals_stranded-method
> ### rank,Genome_intervals-method rank,Genome_intervals_stranded-method
> ### sort,Genome_intervals-method sort,Genome_intervals_stranded-method
> ### xtfrm,Genome_intervals-method xtfrm,Genome_intervals_stranded-method
>
> ### ** Examples
>
> ## an example with ties
> gi = GenomeIntervals(c("chr2", "chr2", "chr1", "chr1"), c(1,1,10,10), c(5,3,12,12) )
>
> sort(gi)
Object of class Genome_intervals
4 base intervals and 0 inter-base intervals(*):
chr1 [10, 12]
chr1 [10, 12]
chr2 [1, 3]
chr2 [1, 5]
annotation:
seq_name inter_base
3 chr1 FALSE
4 chr1 FALSE
2 chr2 FALSE
1 chr2 FALSE
> rank(gi)
Error in .local(x, na.last, ties.method, ...) :
only 'ties.method="first"' is supported when ranking GenomeIntervals
Calls: rank -> rank -> .local
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘benchmarking-tests.R’
Comparing ‘benchmarking-tests.Rout’ to ‘benchmarking-tests.Rout.save’ ...13,35d12
<
< 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
<
Running ‘consistency-tests.R’
Running ‘fullShow.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, 1 NOTE
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/genomeIntervals.Rcheck/00check.log’
for details.