Mulder2012 0.12.0
Xin Wang
| Snapshot Date: 2016-10-08 07:15:25 -0700 (Sat, 08 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_3/experiment/pkgs/Mulder2012 | | Last Changed Rev: 3760 / Revision: 3935 | | Last Changed Date: 2016-05-03 14:35:06 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Mulder2012_0.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-data-experiment/meat/Mulder2012.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Mulder2012/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Mulder2012’ version ‘0.12.0’
* 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 ‘Mulder2012’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 22.5Mb
sub-directories of 1Mb or more:
data 19.9Mb
doc 2.4Mb
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘snow’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘MASS’
All declared Imports should be used.
Packages in Depends field not imported from:
‘KEGG.db’ ‘org.Hs.eg.db’
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
Arora2010.fig: no visible global function definition for ‘data’
Arora2010.fig: no visible global function definition for ‘pdf’
Arora2010.fig: no visible binding for global variable ‘bm_Arora2010’
Arora2010.fig: no visible global function definition for ‘graphics.off’
Arora2010.fig: no visible binding for global variable ‘pan_Arora2010’
Arora2010.fig: no visible global function definition for ‘par’
Arora2010.fig: no visible global function definition for ‘barplot’
Arora2010.hypergeo : Arora2010.pathway: no visible global function
definition for ‘p.adjust’
Arora2010.hypergeo : Arora2010.pathway: no visible binding for global
variable ‘KEGGPATHID2NAME’
Arora2010.pipeline: no visible global function definition for ‘data’
Arora2010.pipeline: no visible binding for global variable ‘Arora2010’
GSEARandomWalkFig: no visible global function definition for ‘par’
Mulder2012.PPIPre: no visible global function definition for ‘data’
Mulder2012.PPIPre: no visible binding for global variable
‘PINdbProteins’
Mulder2012.PPIPre : <anonymous>: no visible binding for global variable
‘PINdbProteins’
Mulder2012.RNAiPre: no visible global function definition for ‘sd’
Mulder2012.fig: no visible global function definition for ‘data’
Mulder2012.fig: no visible global function definition for ‘pdf’
Mulder2012.fig: no visible binding for global variable ‘bm_Mulder2012’
Mulder2012.fig: no visible global function definition for
‘graphics.off’
Mulder2012.fig: no visible binding for global variable ‘Mulder2012’
Mulder2012.fig: no visible binding for global variable ‘PPI’
Mulder2012.fig: no visible binding for global variable
‘bm_ext_Mulder2012’
Mulder2012.fig: no visible binding for global variable
‘pan_ext_Mulder2012’
dist.pvclust4PAN: no visible global function definition for ‘as.dist’
dist.pvclust4PAN: no visible global function definition for ‘cor’
dist.pvclust4PAN: no visible global function definition for ‘na.omit’
dist.pvclust4PAN: no visible global function definition for ‘dist’
parPvclust4PAN: no visible global function definition for ‘parLapply’
parPvclust4PAN: no visible global function definition for
‘getFromNamespace’
parPvclust4PAN: no visible global function definition for ‘hclust’
Undefined global functions or variables:
Arora2010 KEGGPATHID2NAME Mulder2012 PINdbProteins PPI as.dist
barplot bm_Arora2010 bm_Mulder2012 bm_ext_Mulder2012 cor data dist
getFromNamespace graphics.off hclust na.omit p.adjust pan_Arora2010
pan_ext_Mulder2012 par parLapply pdf sd
Consider adding
importFrom("grDevices", "graphics.off", "pdf")
importFrom("graphics", "barplot", "par")
importFrom("stats", "as.dist", "cor", "dist", "hclust", "na.omit",
"p.adjust", "sd")
importFrom("utils", "data", "getFromNamespace")
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
‘/home/biocbuild/bbs-3.3-data-experiment/meat/Mulder2012.Rcheck/00check.log’
for details.
* installing *source* package ‘Mulder2012’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
* DONE (Mulder2012)