PADOG 1.8.0
Adi Laurentiu Tarca
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/PADOG | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings PADOG_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/PADOG.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PADOG/DESCRIPTION’ ... OK
* this is package ‘PADOG’ version ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘KEGGdzPathwaysGEO’ ‘limma’ ‘AnnotationDbi’ ‘Biobase’ ‘nlme’ ‘GSA’
‘KEGG.db’
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 ‘PADOG’ can be installed ... [10s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘graphics’ ‘limma’ ‘KEGG.db’ ‘AnnotationDbi’ ‘Biobase’ ‘methods’ ‘nlme’
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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
‘GSA’ ‘KEGG.db’ ‘limma’ ‘nlme’
Please remove these calls from your code.
'library' or 'require' call to ‘parallel’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
‘Biobase’ ‘KEGG.db’ ‘hgu133a.db’ ‘hgu133plus2.db’ ‘limma’ ‘methods’
All declared Imports should be used.
Packages in Depends field not imported from:
‘Biobase’ ‘GSA’ ‘KEGG.db’ ‘KEGGdzPathwaysGEO’ ‘limma’ ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compPADOG : getdataaslist: no visible global function definition for
‘experimentData’
compPADOG : getdataaslist: no visible global function definition for
‘notes’
compPADOG : getdataaslist: no visible global function definition for
‘exprs’
compPADOG : getdataaslist: no visible global function definition for
‘pData’
compPADOG : gsaF: no visible global function definition for ‘GSA’
compPADOG: no visible binding for global variable ‘KEGGPATHID2EXTID’
compPADOG: no visible binding for global variable ‘KEGGPATHID2NAME’
compPADOG: no visible global function definition for ‘mclapply’
filteranot: no visible global function definition for ‘lmFit’
filteranot: no visible global function definition for ‘makeContrasts’
filteranot: no visible global function definition for ‘contrasts.fit’
filteranot: no visible global function definition for ‘eBayes’
filteranot: no visible global function definition for ‘topTable’
filteranot: no visible global function definition for ‘keys’
padog: no visible binding for global variable ‘KEGGPATHID2EXTID’
padog: no visible binding for global variable ‘KEGGPATHID2NAME’
padog: no visible global function definition for ‘mappedkeys’
padog: no visible global function definition for ‘lmFit’
padog: no visible global function definition for ‘makeContrasts’
padog: no visible global function definition for ‘contrasts.fit’
padog: no visible global function definition for ‘eBayes’
padog: no visible global function definition for ‘topTable’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [125s/105s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
compPADOG 91.337 1.18 72.022
padog 22.958 0.40 23.769
* 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
* DONE
NOTE: There were 4 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/PADOG.Rcheck/00check.log’
for details.