MinimumDistance 1.16.0
Robert B Scharpf
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/MinimumDistance | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MinimumDistance_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/MinimumDistance.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 ‘MinimumDistance/DESCRIPTION’ ... OK
* this is package ‘MinimumDistance’ version ‘1.16.0’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘GenomicRanges’ ‘SummarizedExperiment’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.compute_trio_posterior: no visible global function definition for
‘rowRanges’
.constructMDE: no visible global function definition for
‘SummarizedExperiment’
.dnacopy2granges: no visible global function definition for ‘GRanges’
.filter_mdexperiment: no visible global function definition for
‘rowRanges’
.pedigreeId: no visible global function definition for ‘colData’
MDRanges: no visible global function definition for ‘GRanges’
MinDistGRanges: no visible global function definition for ‘GRangesList’
MinDistGRanges: no visible global function definition for ‘GRanges’
MinDistPosterior: no visible global function definition for
‘GRangesList’
computeEmissionProbs: no visible global function definition for
‘SummarizedExperiment’
computeEmissionProbs: no visible global function definition for
‘rowRanges’
dataFrameFromRange2: no visible binding for global variable ‘data’
generatorTransitionProbs : toGRanges: no visible global function
definition for ‘GRanges’
generatorTransitionProbs : toGRanges: no visible global function
definition for ‘GRangesList’
generatorTransitionProbs: no visible global function definition for
‘GRanges’
logEmissionArray: no visible global function definition for ‘assays’
narrow2: no visible global function definition for ‘GRangesList’
narrowRangeForChromosome: no visible global function definition for
‘GRangesList’
narrowRanges: no visible global function definition for ‘GRangesList’
overlapsCentromere: no visible global function definition for ‘data’
pruneByFactor: no visible global function definition for ‘GRangesList’
segmentArray: no visible global function definition for ‘GRangesList’
segmentList: no visible global function definition for ‘GRangesList’
segmentMatrix: no visible global function definition for ‘GRanges’
segmentff_matrix: no visible global function definition for
‘GRangesList’
segmentff_matrix2: no visible global function definition for
‘GRangesList’
stackRangedDataList: no visible global function definition for
‘GRangesList’
trioSetListExample: no visible global function definition for ‘data’
MAP2,MinDistExperiment-GRanges: no visible global function definition
for ‘GRangesList’
MAP2,MinDistExperiment-GRangesList: no visible global function
definition for ‘GRangesList’
MAP2,MinDistExperiment-MinDistGRanges: no visible global function
definition for ‘GRangesList’
MinDistExperiment,ArrayViews-ParentOffspring: no visible global
function definition for ‘assays’
MinDistExperiment,ArrayViews-ParentOffspring: no visible global
function definition for ‘rowRanges’
MinDistExperiment,ArrayViews-ParentOffspring: no visible global
function definition for ‘colData’
calculateMindist,list: no visible binding for global variable ‘elt’
coerce,TrioSet-MinDistExperiment: no visible global function definition
for ‘GRanges’
coerce,TrioSetList-RangedSummarizedExperiment: no visible global
function definition for ‘GRanges’
coerce,TrioSetList-RangedSummarizedExperiment: no visible global
function definition for ‘SummarizedExperiment’
father,RangedSummarizedExperiment: no visible global function
definition for ‘assays’
mother,RangedSummarizedExperiment: no visible global function
definition for ‘assays’
offspring,RangedSummarizedExperiment: no visible global function
definition for ‘assays’
segment2,MinDistExperiment: no visible global function definition for
‘rowRanges’
segment2,MinDistExperiment: no visible global function definition for
‘GRangesList’
segs,MinDistPosterior: no visible global function definition for
‘granges’
show,MinDistPosterior: no visible global function definition for
‘granges’
subsetAndSort,MinDistExperiment: no visible global function definition
for ‘rowRanges’
subsetAndSort,MinDistExperiment: no visible global function definition
for ‘rowRanges<-’
Undefined global functions or variables:
GRanges GRangesList SummarizedExperiment assays colData data elt
granges rowRanges rowRanges<-
Consider adding
importFrom("utils", "data")
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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘doRUnit.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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/MinimumDistance.Rcheck/00check.log’
for details.
* installing *source* package ‘MinimumDistance’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘allNames’ in package ‘MinimumDistance’
Creating a generic function for ‘colMads’ from package ‘matrixStats’ in package ‘MinimumDistance’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MinimumDistance)