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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings genoset_1.23.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/genoset.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genoset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genoset’ version ‘1.23.5’
* 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 ‘genoset’ can be installed ... [14s/14s] WARNING
Found the following significant warnings:
Warning: subclass "GNCList" of class "GenomicRanges" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "GIntervalTree" of class "GenomicRanges" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: bad markup (extra space?) at GenoSet.Rd:15:56
Warning: bad markup (extra space?) at baf2mbaf.Rd:10:61
Warning: bad markup (extra space?) at calcGC.Rd:10:58
Warning: bad markup (extra space?) at calcGC.Rd:13:59
Warning: bad markup (extra space?) at do_rledf_views.Rd:17:56
Warning: bad markup (extra space?) at gcCorrect.Rd:12:60
Warning: bad markup (extra space?) at genoPlot-methods.Rd:23:56
Warning: bad markup (extra space?) at genoPlot-methods.Rd:56:56
Warning: bad markup (extra space?) at genomeAxis.Rd:13:59
Warning: bad markup (extra space?) at runCBS.Rd:17:63
Warning: bad markup (extra space?) at segs2Rle.Rd:11:56
See ‘/home/biocbuild/bbs-3.2-bioc/meat/genoset.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
.Call("RleViews_viewMaxs", ..., PACKAGE = "IRanges")
.Call("RleViews_viewMeans", ..., PACKAGE = "IRanges")
.Call("RleViews_viewMins", ..., PACKAGE = "IRanges")
.Call("RleViews_viewSums", ..., PACKAGE = "IRanges")
.Call("RleViews_viewWhichMaxs", ..., PACKAGE = "IRanges")
.Call("RleViews_viewWhichMins", ..., PACKAGE = "IRanges")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... WARNING
Found .Internal calls in methods for the following S4 generics:
‘rowMeans’ ‘rowSums’
Packages should not call .Internal(): it is not part of the API, for
use only by R itself and subject to change without notice.
In addition to the above warning(s), found the following notes:
calcGC : <anonymous>: no visible global function definition for ‘Views’
calcGC : <anonymous>: no visible global function definition for
‘alphabetFrequency’
calcGC2: no visible binding for global variable ‘gmapGenome’
calcGC2: no visible global function definition for ‘RleList’
calcGC2 : <anonymous>: no visible global function definition for
‘letterFrequencyInSlidingView’
initGenoSet: no visible global function definition for ‘universe<-’
initGenoSet: no visible global function definition for
‘assayDataValidMembers’
[<-,GenoSet-ANY-ANY-ANY : .local: no visible global function definition
for ‘assayDataElement<-’
colnames,GenoSet : .local: no visible global function definition for
‘pData’
colnames<-,GenoSet: no visible global function definition for ‘pData’
colnames<-,GenoSet: no visible global function definition for ‘pData<-’
colnames<-,GenoSet: no visible global function definition for
‘assayData’
colnames<-,GenoSet: no visible global function definition for
‘assayData<-’
dim,GenoSet: no visible global function definition for ‘featureData’
rownames,GenoSet : .local: no visible global function definition for
‘featureData’
rownames<-,GenoSet: no visible global function definition for ‘fData<-’
rownames<-,GenoSet: no visible global function definition for
‘assayData’
rownames<-,GenoSet: no visible global function definition for
‘assayData<-’
* checking Rd files ... WARNING
prepare_Rd: bad markup (extra space?) at GenoSet.Rd:15:56
prepare_Rd: bad markup (extra space?) at baf2mbaf.Rd:10:61
prepare_Rd: bad markup (extra space?) at calcGC.Rd:10:58
prepare_Rd: bad markup (extra space?) at calcGC.Rd:13:59
prepare_Rd: bad markup (extra space?) at do_rledf_views.Rd:17:56
prepare_Rd: bad markup (extra space?) at gcCorrect.Rd:12:60
prepare_Rd: bad markup (extra space?) at genoPlot-methods.Rd:23:56
prepare_Rd: bad markup (extra space?) at genoPlot-methods.Rd:56:56
prepare_Rd: bad markup (extra space?) at genomeAxis.Rd:13:59
prepare_Rd: bad markup (extra space?) at runCBS.Rd:17:63
prepare_Rd: bad markup (extra space?) at segs2Rle.Rd:11:56
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'bounds2Rle.Rd':
‘rangeSegMeanLength,GRanges,data.frame- ’
‘rangeSegMeanLength,GRanges,list- ’
‘segPairTable,DataFrame,DataFrame- ’ ‘segTable,DataFrame- ’
Missing link or links in documentation object 'chrOrder.Rd':
‘isGenomeOrder,GRanges- ’ ‘isGenomeOrder,GenoSet- ’
Missing link or links in documentation object 'genomeAxis.Rd':
‘genoPlot,GenoSetOrGenomicRanges,ANY- ’
Missing link or links in documentation object 'rangeSegMeanLength-methods.Rd':
‘segPairTable,DataFrame,DataFrame- ’ ‘segTable,DataFrame- ’
Missing link or links in documentation object 'runCBS.Rd':
‘rangeSegMeanLength,GRanges,data.frame- ’
‘rangeSegMeanLength,GRanges,list- ’
‘segPairTable,DataFrame,DataFrame- ’ ‘segTable,DataFrame- ’
Missing link or links in documentation object 'segPairTable-methods.Rd':
‘rangeSegMeanLength,GRanges,data.frame- ’
‘rangeSegMeanLength,GRanges,list- ’
Missing link or links in documentation object 'segTable-methods.Rd':
‘rangeSegMeanLength,GRanges,data.frame- ’
‘rangeSegMeanLength,GRanges,list- ’
‘segPairTable,DataFrame,DataFrame- ’
Missing link or links in documentation object 'segs2Granges.Rd':
‘rangeSegMeanLength,GRanges,data.frame- ’
‘rangeSegMeanLength,GRanges,list- ’
‘segPairTable,DataFrame,DataFrame- ’ ‘segTable,DataFrame- ’
Missing link or links in documentation object 'segs2Rle.Rd':
‘rangeSegMeanLength,GRanges,data.frame- ’
‘rangeSegMeanLength,GRanges,list- ’
‘segPairTable,DataFrame,DataFrame- ’ ‘segTable,DataFrame- ’
Missing link or links in documentation object 'segs2RleDataFrame.Rd':
‘rangeSegMeanLength,GRanges,data.frame- ’
‘rangeSegMeanLength,GRanges,list- ’
‘segPairTable,DataFrame,DataFrame- ’ ‘segTable,DataFrame- ’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'calcGC2':
‘window’
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘prove.R’ [15s/13s]
Comparing ‘prove.Rout’ to ‘prove.Rout.save’ ...13c13
< The following objects are masked from 'package:stats':
---
> The following object is masked from 'package:stats':
15c15
< IQR, mad, xtabs
---
> xtabs
21,24c21,24
< eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
< mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
< rank, rbind, rep.int, rownames, sapply, setdiff, sort, table,
< tapply, union, unique, unlist, unsplit
---
> eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
> mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
> rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
> unique, unlist, unsplit
51c51
< RUNIT TEST PROTOCOL -- Mon Aug 24 00:15:56 2015
---
> RUNIT TEST PROTOCOL -- Tue Mar 17 12:16:04 2015
53c53
< Number of test functions: 36
---
> Number of test functions: 33
59,60c59,60
< genoset RUnit Tests - 36 test functions, 0 errors, 0 failures
< Number of test functions: 36
---
> genoset RUnit Tests - 33 test functions, 0 errors, 0 failures
> Number of test functions: 33
[15s/13s] OK
* checking PDF version of manual ... OK
* DONE
Status: 5 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/genoset.Rcheck/00check.log’
for details.
