SplicingGraphs 1.13.1
H. Pagès
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs | | Last Changed Rev: 119308 / Revision: 121152 | | Last Changed Date: 2016-07-12 02:29:28 -0700 (Tue, 12 Jul 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | | |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | ERROR | 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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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SplicingGraphs_1.13.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/SplicingGraphs.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SplicingGraphs/DESCRIPTION’ ... OK
* this is package ‘SplicingGraphs’ version ‘1.13.1’
* package encoding: UTF-8
* 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 ‘SplicingGraphs’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘IRanges::from’ by ‘Rgraphviz::from’ when loading ‘SplicingGraphs’
Warning: replacing previous import ‘IRanges::to’ by ‘Rgraphviz::to’ when loading ‘SplicingGraphs’
See ‘/home/biocbuild/bbs-3.4-bioc/meat/SplicingGraphs.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘GenomicFeatures’ ‘GenomicAlignments’ ‘Rgraphviz’ ‘igraph’
A package should be listed in only one of these fields.
* 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
'library' or 'require' call to 'igraph' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' calls which should be '::':
'S4Vectors:::matchIntegerPairs' 'S4Vectors:::orderIntegerPairs'
'S4Vectors:::selfmatchIntegerPairs'
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
'BiocGenerics:::testPackage' 'GenomicAlignments:::fillJunctionGaps'
'GenomicFeatures:::.collapse_df' 'IRanges:::newCompressedList0'
'IRanges:::regroupBySupergroup' 'S4Vectors:::setPrototypeFromObject'
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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘reportReads’
Undocumented S4 methods:
generic '[' and siglist 'SplicingGraphs,ANY,ANY,ANY'
generic 'reportReads' and siglist 'SplicingGraphs'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'countReads-methods':
‘reportReads’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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 ‘SplicingGraphs-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TSPCsg
> ### Title: TSPC splicing graphs
> ### Aliases: TSPCsg TSPC
>
> ### ** Examples
>
> ## Load SplicingGraphs object 'TSPCsg':
> filepath <- system.file("extdata", "TSPCsg.rda", package="SplicingGraphs")
> load(filepath)
> TSPCsg
SplicingGraphs object with 9 gene(s) and 33 transcript(s)
>
> ## 'TSPCsg' has 1 element per gene and 'names(sg)' gives the gene ids.
> names(TSPCsg)
[1] "BAI1" "CYB561" "DAPL1" "ITGB8" "KIAA0319L" "LGSN"
[7] "MKRN3" "ST14" "TREM2"
>
> ## 1 splicing graph per gene. (Note that gene MUC16 was dropped
> ## because transcripts T-4 and T-5 in this gene both have their
> ## 2nd exon *inside* their 3rd exon. Splicing graph theory doesn't
> ## apply in that case.)
>
> ## Extract the edges of a given graph:
> TSPCsgedges <- sgedges(TSPCsg["LGSN"])
> TSPCsgedges
DataFrame with 19 rows and 5 columns
from to sgedge_id ex_or_in tx_id
<character> <character> <character> <factor> <CharacterList>
1 R 1 LGSN:R,1 T-1,T-2,T-3,...
2 1 5 LGSN:1,5 ex T-1,T-4n
3 5 6 LGSN:5,6 in T-1,T-2,T-4n,...
4 6 8 LGSN:6,8 ex T-1,T-2,T-4n,...
5 8 11 LGSN:8,11 in T-1,T-2
... ... ... ... ... ...
15 6 7 LGSN:6,7 ex T-3
16 7 9 LGSN:7,9 in T-3
17 9 10 LGSN:9,10 ex T-3,T-4n,T-5n
18 10 11 LGSN:10,11 in T-3,T-4n,T-5n
19 8 9 LGSN:8,9 in T-4n,T-5n
>
> ## Plot the graph for a given gene:
> plot(TSPCsg["LGSN"]) # or 'plot(sgraph(TSPCsgedges))'
Error in as.double(y) :
cannot coerce type 'S4' to vector of type 'double'
Calls: plot -> plot -> plot -> plot.default -> xy.coords
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run_unitTests.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 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/SplicingGraphs.Rcheck/00check.log’
for details.
* installing *source* package ‘SplicingGraphs’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘IRanges::from’ by ‘Rgraphviz::from’ when loading ‘SplicingGraphs’
Warning: replacing previous import ‘IRanges::to’ by ‘Rgraphviz::to’ when loading ‘SplicingGraphs’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘IRanges::from’ by ‘Rgraphviz::from’ when loading ‘SplicingGraphs’
Warning: replacing previous import ‘IRanges::to’ by ‘Rgraphviz::to’ when loading ‘SplicingGraphs’
* DONE (SplicingGraphs)