SplicingGraphs 1.2.0
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| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/SplicingGraphs | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ WARNINGS ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | WARNINGS | OK |
* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/SplicingGraphs.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SplicingGraphs/DESCRIPTION' ... OK
* this is package 'SplicingGraphs' version '1.2.0'
* 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 whether package 'SplicingGraphs' can be installed ... OK
* checking installed package size ... NOTE
installed size is 19.8Mb
sub-directories of 1Mb or more:
doc 15.7Mb
extdata 3.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'BiocGenerics' 'IRanges' 'GenomicRanges' 'GenomicFeatures' '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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 objects imported by ':::' calls:
'BiocGenerics:::testPackage' 'GenomicRanges:::fillGaps'
'IRanges:::decodeRle' 'IRanges:::matchIntegerPairs'
'IRanges:::newCompressedList0' 'IRanges:::orderIntegerPairs'
'IRanges:::selfmatchIntegerPairs' 'IRanges:::setPrototypeFromObject'
See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
'SplicingGraphs.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [186s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotTranscripts-methods 40.92 0.33 41.25
toy_data 21.31 0.25 21.55
countReads-methods 11.38 0.22 11.61
sgedges-methods 8.78 0.14 10.43
txpath-methods 6.12 0.33 7.74
rsgedgesByGene-methods 6.05 0.19 8.32
sgedgesByGene-methods 5.43 0.39 5.82
bubbles-methods 5.39 0.00 5.38
assignReads 4.99 0.01 5.63
** running examples for arch 'x64' ... [234s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotTranscripts-methods 44.96 0.31 49.84
toy_data 22.98 0.03 23.01
countReads-methods 12.21 0.43 12.97
assignReads 9.15 0.41 11.68
sgedges-methods 8.84 0.25 14.09
bubbles-methods 6.65 0.29 8.30
rsgedgesByGene-methods 5.70 0.00 6.19
txpath-methods 5.29 0.00 11.26
sgedgesByGene-methods 5.12 0.01 6.47
SplicingGraphs-class 4.33 0.33 5.26
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
Running 'run_unitTests.R' [17s]
[19s] OK
** running tests for arch 'x64'
Running 'run_unitTests.R' [27s]
[27s] 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
WARNING: There were 2 warnings.
NOTE: There were 4 notes.
See
'D:/biocbld/bbs-2.13-bioc/meat/SplicingGraphs.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'SplicingGraphs' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'SplicingGraphs' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SplicingGraphs' as SplicingGraphs_1.2.0.zip
* DONE (SplicingGraphs)