ggtut 0.0.21
VJ Carey
| Snapshot Date: 2011-07-06 11:15:18 -0700 (Wed, 06 Jul 2011) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/ggtut | | Last Changed Rev: 1678 / Revision: 1678 | | Last Changed Date: 2011-07-06 03:59:00 -0700 (Wed, 06 Jul 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ WARNINGS ] | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory 'E:/biocbld/bbs-2.9-data-experiment/meat/ggtut.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ggtut/DESCRIPTION' ... OK
* this is package 'ggtut' version '0.0.21'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ggtut' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'space' when loading 'IRanges'
Warning: replacing previous import 'getSeq' when loading 'BSgenome'
See 'E:/biocbld/bbs-2.9-data-experiment/meat/ggtut.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 236.1Mb
sub-directories of 1Mb or more:
bam 15.1Mb
data 31.3Mb
doc 7.0Mb
ffarchives 129.9Mb
ffobjects 1.6Mb
images 12.9Mb
sqlite 38.0Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* 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 data sets:
'permsb1' 'rsb2_list' 'rsb2_perm_list' 'sb1'
All user-level objects in a package 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 examples ... OK
* checking PDF version of manual ... OK
WARNING: There were 2 warnings, see
'E:/biocbld/bbs-2.9-data-experiment/meat/ggtut.Rcheck/00check.log'
for details
* installing *source* package 'ggtut' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.
Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: splines
Loading required package: Matrix
Loading required package: lattice
Attaching package: 'Matrix'
The following object(s) are masked from 'package:base':
det
Loading required package: RSQLite
Loading required package: DBI
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: IRanges
Attaching package: 'IRanges'
The following object(s) are masked from 'package:Biobase':
updateObject
The following object(s) are masked from 'package:base':
Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union
Loading required package: rtracklayer
Loading required package: RCurl
Loading required package: bitops
Loading required package: org.Hs.eg.db
Loading required package: GenomicRanges
Loading package bit1.1-7
package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit
Loading package ff2.2-2
- getOption("fftempdir")=="E:/biocbld/bbs-2.9-data-experiment/tmpdir/Rtmpc5GAR0"
- getOption("ffextension")=="ff"
- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==16095641.6 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==804782080 -- consider a different value for tuning your system
Attaching package: 'GGtools'
The following object(s) are masked from 'package:Biobase':
geneNames
Loading required package: tools
Loading required package: bit
Attaching package: 'bit'
The following object(s) are masked from 'package:base':
xor
Attaching package ff
Attaching package: 'ff'
The following object(s) are masked from 'package:utils':
write.csv, write.csv2
The following object(s) are masked from 'package:base':
is.factor, is.ordered
Loading required package: illuminaHumanv1.db
To get a tailored smlSet, use getSS("GGdata", [chrvec])
available chromosomes are named 1 10 ... X Y
Loading required package: biomaRt
Attaching package: 'biomaRt'
The following object(s) are masked from 'package:annotate':
getGO
Loading required package: multtest
Loading required package: Biostrings
Attaching package: 'Biostrings'
The following object(s) are masked from 'package:ff':
mismatch, pattern
Loading required package: BSgenome
Attaching package: 'BSgenome'
The following object(s) are masked from 'package:annotate':
organism
Loading required package: BSgenome.Ecoli.NCBI.20080805
Loading required package: GO.db
Loading required package: limma
Loading required package: gplots
Loading required package: gtools
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
Attaching package: 'gdata'
The following object(s) are masked from 'package:IRanges':
trim
The following object(s) are masked from 'package:Biobase':
combine
The following object(s) are masked from 'package:stats':
nobs
The following object(s) are masked from 'package:utils':
object.size
Loading required package: caTools
Attaching package: 'caTools'
The following object(s) are masked from 'package:IRanges':
runmean
Loading required package: grid
Attaching package: 'gplots'
The following object(s) are masked from 'package:multtest':
wapply
The following object(s) are masked from 'package:rtracklayer':
space
The following object(s) are masked from 'package:IRanges':
space
The following object(s) are masked from 'package:stats':
lowess
Warning: replacing previous import 'space' when loading 'IRanges'
Warning: replacing previous import 'getSeq' when loading 'BSgenome'
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
To get a tailored smlSet, use getSS("GGdata", [chrvec])
available chromosomes are named 1 10 ... X Y
Warning messages:
1: replacing previous import 'space' when loading 'IRanges'
2: replacing previous import 'getSeq' when loading 'BSgenome'
* DONE (ggtut)