wateRmelon 1.4.0
Leo
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/wateRmelon | | Last Changed Rev: 88838 / Revision: 95116 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ WARNINGS ] | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch wateRmelon_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/wateRmelon.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wateRmelon/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wateRmelon’ version ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘IMA’
Depends: includes the non-default packages:
‘limma’ ‘matrixStats’ ‘methylumi’ ‘lumi’
‘IlluminaHumanMethylation450k.db’ ‘ROC’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [79s/79s] WARNING
Found the following significant warnings:
Warning: 'IlluminaHumanMethylation450k.db' is deprecated.
See ‘/Users/biocbuild/bbs-2.14-bioc/meat/wateRmelon.Rcheck/00install.out’ for details.
* 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:
‘methylumi’
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 ... NOTE
'library' or 'require' call to ‘methylumi’ which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
‘IlluminaHumanMethylation450k.db’ ‘limma’ ‘lumi’ ‘matrixStats’
‘methods’ ‘methylumi’ ‘ROC’
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
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’
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 ... WARNING
Undocumented code objects:
‘anSNP’ ‘dfort’ ‘genall’ ‘genme’ ‘genus’ ‘goodSNP’
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 ... WARNING
Codoc mismatches from documentation object 'dasen':
danes
Code: function(mn, un, onetwo, fudge = 100, ret2 = FALSE, ...)
Docs: function(mn, un, onetwo, fudge = 100, ...)
Argument names in code not in docs:
ret2
Mismatches in argument names:
Position: 5 Code: ret2 Docs: ...
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [93s/93s] 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 19.264 0.351 19.616
seabi 16.868 0.023 16.891
metrics 11.302 0.410 11.713
* 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 4 warnings.
NOTE: There were 4 notes.
See
‘/Users/biocbuild/bbs-2.14-bioc/meat/wateRmelon.Rcheck/00check.log’
for details.
* installing *source* package ‘wateRmelon’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graphics::image’ when loading ‘methylumi’
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 by ‘graphics::image’ when loading ‘methylumi’
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)