Pbase 0.14.0
Sebastian Gibb
| Snapshot Date: 2017-03-30 17:16:31 -0400 (Thu, 30 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/Pbase | | Last Changed Rev: 122710 / Revision: 127890 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | 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 Pbase_0.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/Pbase.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pbase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pbase’ version ‘0.14.0’
* 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 ‘Pbase’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives more than one person with maintainer role:
Laurent Gatto <lg390@cam.ac.uk> [aut, cre]
Sebastian Gibb <mail@sebastiangibb.de> [aut, cre]
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': 'Gviz:::.chrName'
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
.calculateMolecularWeight: no visible global function definition for
'setNames'
.peptidePosition: no visible global function definition for 'setNames'
mapplot: no visible global function definition for 'par'
mapplot: no visible global function definition for 'rect'
mapplot: no visible global function definition for 'abline'
mapplot: no visible global function definition for 'text'
mapplot: no visible global function definition for 'segments'
plotRanges: no visible global function definition for 'plot.new'
plotRanges: no visible global function definition for 'plot.window'
plotRanges: no visible global function definition for 'rect'
plotRanges: no visible global function definition for 'title'
plotRanges: no visible global function definition for 'axis'
pplot : darrow: no visible global function definition for 'points'
pplot : darrow: no visible global function definition for 'arrows'
pplot : addpeps: no visible global function definition for 'rect'
pplot : addpeps: no visible global function definition for 'segments'
pplot : addpeps: no visible global function definition for 'text'
pplot: no visible global function definition for 'par'
pplot: no visible global function definition for 'rect'
pplot: no visible global function definition for 'text'
pplot: no visible global function definition for 'segments'
Undefined global functions or variables:
abline arrows axis par plot.new plot.window points rect segments
setNames text title
Consider adding
importFrom("graphics", "abline", "arrows", "axis", "par", "plot.new",
"plot.window", "points", "rect", "segments", "text",
"title")
importFrom("stats", "setNames")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Pbase-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: etrid2grl
> ### Title: From a transcript identifier to 'GRanges' object
> ### Aliases: etrid2grl
>
> ### ** Examples
>
> id <- c("ENST00000612959", "ENST00000317091")
> grl1 <- etrid2grl(id[1])
> grl1
GRangesList object of length 1:
$ENST00000612959
GRanges object with 8 ranges and 7 metadata columns:
seqnames ranges strand | feature gene
<Rle> <IRanges> <Rle> | <character> <character>
[1] chr17 [30116807, 30116863] + | utr5 ENSG00000126653
[2] chr17 [30172542, 30172589] + | utr5 ENSG00000126653
[3] chr17 [30172590, 30172598] + | protein_coding ENSG00000126653
[4] chr17 [30178071, 30178199] + | protein_coding ENSG00000126653
[5] chr17 [30179090, 30179297] + | protein_coding ENSG00000126653
[6] chr17 [30180908, 30181016] + | protein_coding ENSG00000126653
[7] chr17 [30184615, 30185674] + | protein_coding ENSG00000126653
[8] chr17 [30185675, 30186474] + | utr3 ENSG00000126653
exon transcript symbol rank phase
<character> <character> <character> <numeric> <integer>
[1] ENSE00003738663 ENST00000612959 NSRP1 1 -1
[2] ENSE00003689679 ENST00000612959 NSRP1 2 -1
[3] ENSE00003689679 ENST00000612959 NSRP1 2 -1
[4] ENSE00003519306 ENST00000612959 NSRP1 3 0
[5] ENSE00003659893 ENST00000612959 NSRP1 4 0
[6] ENSE00003562538 ENST00000612959 NSRP1 5 1
[7] ENSE00003744594 ENST00000612959 NSRP1 6 0
[8] ENSE00003744594 ENST00000612959 NSRP1 6 -1
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
> grl <- etrid2grl(id)
Error in getBM(attributes = columns, filters = keytype, values = keys, :
Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_87: DBI connect('database=ensembl_mart_87;host=martdb.local.cloud.local;port=3306','ensro',...) failed: Unknown MySQL server host 'martdb.local.cloud.local' (45) at /ensemblweb/www/www_87/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
Calls: etrid2grl -> select -> select -> getBM
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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
‘/Users/biocbuild/bbs-3.4-bioc/meat/Pbase.Rcheck/00check.log’
for details.