MinimumDistance 1.6.0
Robert B Scharpf
| 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/MinimumDistance | | 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 ‘/Users/biocbuild/bbs-2.13-bioc/meat/MinimumDistance.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MinimumDistance/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MinimumDistance’ version ‘1.6.0’
* 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 ‘MinimumDistance’ can be installed ... [38s/39s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘BiocGenerics’
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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘IRanges’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
‘:::’ call which should be ‘::’: ‘VanillaICE:::rescale’
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ‘:::’ calls:
‘Biobase:::annotatedDataFrameFromMatrix’ ‘Biobase:::assayDataDim’
‘Biobase:::assayDataEnvLock’ ‘oligoClasses:::.checkOrder’
‘oligoClasses:::.getArm’ ‘oligoClasses:::setSequenceLengths’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘initializeLrrAndBafArrays’ ‘narrowRangeForChromosome’
‘originalNames’ ‘read.bsfiles2’ ‘stackListByColIndex’
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 ... NOTE
.map_trioSet: no visible global function definition for ‘ocSamples’
.map_trioSet: no visible binding for global variable ‘i’
.map_trioSetList: no visible global function definition for ‘ocSamples’
.map_trioSetList: no visible binding for global variable ‘i’
computeBayesFactorTrioSet: no visible global function definition for
‘joint4’
close,TrioSet: no visible global function definition for ‘isFF’
open,TrioSet: no visible global function definition for ‘isFF’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'ff_array,ANY,ANY,ANY'
generic '[' and siglist 'Pedigree,ANY,ANY,ANY'
generic '[' and siglist 'TrioSet,ANY,ANY,ANY'
generic '[' and siglist 'TrioSetList,ANY,ANY,ANY'
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 ... 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 ... [157s/159s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
computeBayesFactor 55.657 7.448 63.882
callDenovoSegments 36.022 0.534 37.014
TrioSetListLD 9.127 0.199 9.406
narrow 6.528 0.160 6.831
TrioSet-class 5.280 0.220 5.563
TrioSet 4.945 0.148 5.224
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘doRUnit.R’ [245s/382s]
[245s/383s] 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 was 1 warning.
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-2.13-bioc/meat/MinimumDistance.Rcheck/00check.log’
for details.
* installing *source* package ‘MinimumDistance’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘xyplot’ from package ‘lattice’ in package ‘MinimumDistance’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MinimumDistance)