AGDEX 1.22.0
Cuilan lani Gao
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/AGDEX | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | 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 AGDEX_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/AGDEX.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AGDEX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AGDEX’ version ‘1.22.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘AGDEX’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
GPL Version 2 or later
Standardizable: TRUE
Standardized license specification:
GPL (>= 2)
* 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
Packages in Depends field not imported from:
‘Biobase’ ‘GSEABase’
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
agdex: no visible global function definition for ‘exprs’
agdex: no visible global function definition for ‘qnorm’
agdex: no visible global function definition for ‘pnorm’
agdex: no visible global function definition for ‘sampleNames’
agdex: no visible global function definition for ‘pData’
agdex.scatterplot: no visible global function definition for ‘plot’
agdex.scatterplot: no visible global function definition for ‘points’
agdex.scatterplot: no visible global function definition for ‘lines’
agdex.scatterplot: no visible global function definition for ‘prcomp’
agdex.scatterplot: no visible global function definition for ‘abline’
gsc.to.index.list: no visible global function definition for ‘geneIds’
prep.dex.set: no visible global function definition for ‘exprs’
prep.dex.set: no visible global function definition for ‘pData’
read.agdex.gset.details: no visible global function definition for
‘read.table’
read.agdex.gset.list: no visible global function definition for
‘read.table’
read.agdex.result: no visible global function definition for
‘read.table’
read.enrich.gset.list: no visible global function definition for
‘read.table’
read.gset.collection: no visible global function definition for
‘read.table’
read.gset.collection: no visible global function definition for
‘GeneSet’
read.gset.collection: no visible global function definition for
‘geneIds<-’
read.gset.collection: no visible global function definition for
‘GeneSetCollection’
write.agdex.gset.details: no visible global function definition for
‘write.table’
write.agdex.result: no visible global function definition for
‘write.table’
write.gset.list.result: no visible global function definition for
‘write.table’
Undefined global functions or variables:
GeneSet GeneSetCollection abline exprs geneIds geneIds<- lines pData
plot pnorm points prcomp qnorm read.table sampleNames write.table
Consider adding
importFrom("graphics", "abline", "lines", "plot", "points")
importFrom("stats", "pnorm", "prcomp", "qnorm")
importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/AGDEX.Rcheck/00check.log’
for details.