Mulder2012 0.8.0
Xin Wang
| Snapshot Date: 2015-10-07 07:15:35 -0700 (Wed, 07 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_1/experiment/pkgs/Mulder2012 | | Last Changed Rev: 3279 / Revision: 3442 | | Last Changed Date: 2015-04-16 13:16:53 -0700 (Thu, 16 Apr 2015) |
| 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 | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings Mulder2012_0.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-data-experiment/meat/Mulder2012.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘0.8.0’
* 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 ... [14s/21s] 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 binding for global variable ‘bm_Arora2010’
Arora2010.fig: no visible binding for global variable ‘pan_Arora2010’
Arora2010.hypergeo : Arora2010.pathway: no visible binding for global
variable ‘KEGGPATHID2NAME’
Arora2010.pipeline: no visible binding for global variable ‘Arora2010’
Mulder2012.PPIPre: no visible binding for global variable
‘PINdbProteins’
Mulder2012.PPIPre : <anonymous>: no visible binding for global variable
‘PINdbProteins’
Mulder2012.fig: no visible binding for global variable ‘bm_Mulder2012’
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’
parPvclust4PAN: no visible global function definition for ‘parLapply’
* 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 ... [8s/14s] 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-3.1-data-experiment/meat/Mulder2012.Rcheck/00check.log’
for details.
* installing *source* package ‘Mulder2012’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Warning: replacing previous import by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
Note: the specification for class “numeric_Or_integer” in package ‘PANR’ seems equivalent to one from package ‘HTSanalyzeR’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Warning: replacing previous import by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
Note: the specification for class “numeric_Or_integer” in package ‘PANR’ seems equivalent to one from package ‘HTSanalyzeR’: not turning on duplicate class definitions for this class.
* DONE (Mulder2012)