wateRmelon 1.0.1
Leo
| Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/wateRmelon | | Last Changed Rev: 75816 / Revision: 76155 | | Last Changed Date: 2013-04-19 14:06:51 -0700 (Fri, 19 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | WARNINGS | OK |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/wateRmelon.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'wateRmelon/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'wateRmelon' version '1.0.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'IMA'
* 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 'wateRmelon' can be installed ... [48s/49s] WARNING
Found the following significant warnings:
Warning: 'IlluminaHumanMethylation450k.db' is deprecated.
Warning: 'IlluminaHumanMethylation450k.db' is deprecated.
See '/Users/biocbuild/bbs-2.12-bioc/meat/wateRmelon.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 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 ... NOTE
beadcount: no visible global function definition for 'getProbeInfo'
beadcount: no visible global function definition for 'getManifestInfo'
got: no visible global function definition for 'getProbeInfo'
pipelineIlluminaMethylation.batch: possible error in
preprocessIlluminaMethylation(path2data = path2data, path2controlData
= path2controlData, projectName = projectName, nbBeads.threshold =
nbBeads.threshold, detectionPval.threshold = detectionPval.threshold,
detectionPval.perc.threshold = detectionPval.perc.threshold,
sample2keep = path2sampleList, probeSNP_LIST, XY.filtering =
XY.filtering, colorBias.corr = colorBias.corr, bg.adjust = bg.adjust,
PATH = PATH_RES): unused arguments (path2data = path2data,
path2controlData = path2controlData, projectName = projectName)
pipelineIlluminaMethylation.batch: no visible binding for global
variable 'PATH_RES'
pipelineIlluminaMethylation.batch: no visible binding for global
variable 'probeAnnotationsCategory'
preprocessIlluminaMethylation: no visible binding for global variable
'projectName'
betaqn,MethylSet: no visible global function definition for 'getBeta'
betaqn,RGChannelSet: no visible global function definition for
'getBeta'
danen,MethylSet: no visible global function definition for 'getMeth'
danen,MethylSet: no visible global function definition for 'getUnmeth'
danen,RGChannelSet: no visible global function definition for
'preprocessRaw'
daten1,MethylSet: no visible global function definition for 'getMeth'
daten1,MethylSet: no visible global function definition for 'getUnmeth'
daten1,RGChannelSet: no visible global function definition for
'preprocessRaw'
daten2,MethylSet: no visible global function definition for 'getMeth'
daten2,MethylSet: no visible global function definition for 'getUnmeth'
dmrse,MethylSet: no visible global function definition for 'getBeta'
dmrse,RGChannelSet: no visible global function definition for 'getBeta'
dmrse_col,MethylSet: no visible global function definition for
'getBeta'
dmrse_col,RGChannelSet: no visible global function definition for
'getBeta'
dmrse_row,MethylSet: no visible global function definition for
'getBeta'
dmrse_row,RGChannelSet: no visible global function definition for
'getBeta'
seabi,MethylSet: no visible global function definition for 'getBeta'
seabi,RGChannelSet: no visible global function definition for 'getBeta'
seabi,exprmethy450: no visible binding for global variable 'object'
* 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 examples ... [110s/111s] WARNING
Found the following significant warnings:
Warning: 'IlluminaHumanMethylation450k.db' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
sextest 21.608 0.907 22.615
seabi 15.623 0.061 15.733
metrics 13.775 1.032 15.053
dmrse 6.967 0.967 7.943
dasen 6.633 0.855 7.490
genki 6.324 0.962 7.289
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There were 2 warnings.
NOTE: There were 2 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/wateRmelon.Rcheck/00check.log'
for details.
* installing *source* package 'wateRmelon' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'image' when loading 'graphics'
Warning: replacing previous import 'nleqslv' when loading 'nleqslv'
Warning: 'IlluminaHumanMethylation450k.db' is deprecated.
Use 'FDb.InfiniumMethylation.hg19' instead.
Use 'FDb.InfiniumMethylation.hg18' instead.
Use 'mapToGenome() function in minfi or methylumi' instead.
See help("Deprecated")
in method for 'betaqn' with signature 'bn="exprmethy450"': no definition for class "exprmethy450"
in method for 'fuks' with signature 'data="exprmethy450"': no definition for class "exprmethy450"
in method for 'genki' with signature 'bn="exprmethy450"': no definition for class "exprmethy450"
in method for 'dmrse' with signature 'betas="exprmethy450"': no definition for class "exprmethy450"
in method for 'dmrse_row' with signature 'betas="exprmethy450"': no definition for class "exprmethy450"
in method for 'dmrse_col' with signature 'betas="exprmethy450"': no definition for class "exprmethy450"
in method for 'seabi' with signature 'bn="exprmethy450"': no definition for class "exprmethy450"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'image' when loading 'graphics'
Warning: replacing previous import 'nleqslv' when loading 'nleqslv'
Warning: 'IlluminaHumanMethylation450k.db' is deprecated.
Use 'FDb.InfiniumMethylation.hg19' instead.
Use 'FDb.InfiniumMethylation.hg18' instead.
Use 'mapToGenome() function in minfi or methylumi' instead.
See help("Deprecated")
* DONE (wateRmelon)