SplicingGraphs 1.0.4 H. Pages
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/SplicingGraphs | Last Changed Rev: 77220 / Revision: 81334 | Last Changed Date: 2013-06-05 13:08:16 -0700 (Wed, 05 Jun 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | [ WARNINGS ] | |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | WARNINGS | OK |
* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/SplicingGraphs.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SplicingGraphs/DESCRIPTION’ ... OK
* this is package ‘SplicingGraphs’ version ‘1.0.4’
* 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 ... [37s/47s] OK
* checking installed package size ... NOTE
installed size is 19.6Mb
sub-directories of 1Mb or more:
doc 15.5Mb
extdata 3.7Mb
* checking package 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 for unstated 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 ... 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 'reportReads' and siglist 'SplicingGraphs'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the 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 the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [541s/566s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotTranscripts-methods 59.708 0.096 62.882
toy_data 30.350 0.028 31.455
countReads-methods 17.553 0.028 18.508
sgedges-methods 11.229 0.012 11.449
rsgedgesByGene-methods 8.800 0.012 8.980
bubbles-methods 8.636 0.004 9.327
assignReads 7.973 0.004 8.129
txpath-methods 6.816 0.028 6.929
sgedgesByGene-methods 6.737 0.020 7.059
SplicingGraphs-class 5.288 0.084 6.011
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘run_unitTests.R’ [25s/25s]
[25s/26s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There were 2 warnings.
NOTE: There was 1 note.
See
‘/home/biocbuild/bbs-2.12-bioc/meat/SplicingGraphs.Rcheck/00check.log’
for details.