* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/htSeqTools.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘htSeqTools/DESCRIPTION’ ... OK
* this is package ‘htSeqTools’ version ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘multicore’
* 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 ‘htSeqTools’ can be installed ... [12s/12s] 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:
‘methods’
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 ... WARNING
‘library’ or ‘require’ call not declared from: ‘species’
‘library’ or ‘require’ call to ‘BSgenome’ which was already attached by Depends.
Please remove these calls from your code.
Package in Depends field not imported from: ‘Biobase’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
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
countHitsWindow,GRanges: possible error in countHitsWindow(x,
chrLengths = chrLengths, windowSize = windowSize): unused argument
(chrLengths = chrLengths)
countHitsWindow,GRanges: no visible binding for global variable
‘chrLengths’
extendRanges,GRanges: possible error in extendRanges(x, seqLen =
seqLen, chrLength = chrLength, mc.cores = mc.cores): unused argument
(chrLength = chrLength)
extendRanges,GRanges: no visible binding for global variable
‘chrLength’
extendRanges,GRangesList: possible error in extendRanges(x, seqLen =
seqLen, chrLength = chrLength, mc.cores = mc.cores): unused argument
(chrLength = chrLength)
extendRanges,GRangesList: no visible binding for global variable
‘chrLength’
tabDuplReads,GRangesList: possible error in tabDuplReads(x, ,
minRepeats = minRepeats, mc.cores = mc.cores): unused argument ()
* 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘htSeqTools.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [18s/18s] WARNING
Found the following significant warnings:
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Warning: seqselect() is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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
‘/home/biocbuild/bbs-2.13-bioc/meat/htSeqTools.Rcheck/00check.log’
for details.
* installing *source* package ‘htSeqTools’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘htSeqTools’
Creating a generic function for ‘lines’ from package ‘graphics’ in package ‘htSeqTools’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (htSeqTools)