BioC experimental data: CHECK report for Mulder2012 on linux2.bioconductor.org
This page was generated on 2015-10-24 19:25:31 -0400 (Sat, 24 Oct 2015).
Mulder2012 0.11.0 Xin Wang
Snapshot Date: 2015-10-24 10:15:05 -0400 (Sat, 24 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/Mulder2012 | Last Changed Rev: 3462 / Revision: 3473 | Last Changed Date: 2015-10-13 16:20:35 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
Package: Mulder2012 |
Version: 0.11.0 |
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Mulder2012_0.11.0.tar.gz |
StartedAt: 2015-10-24 12:30:50 -0400 (Sat, 24 Oct 2015) |
EndedAt: 2015-10-24 12:33:23 -0400 (Sat, 24 Oct 2015) |
EllapsedTime: 152.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Mulder2012.Rcheck |
Warnings: 0 |
Command output
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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_0.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-data-experiment/meat/Mulder2012.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘0.11.0’
* 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 ... [13s/13s] OK
* checking installed package size ... NOTE
installed size is 22.4Mb
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’
Undefined global functions or variables:
Arora2010 KEGGPATHID2NAME Mulder2012 PINdbProteins PPI bm_Arora2010
bm_Mulder2012 bm_ext_Mulder2012 pan_Arora2010 pan_ext_Mulder2012
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] 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.
Mulder2012.Rcheck/00install.out:
* installing *source* package ‘Mulder2012’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 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 by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
* DONE (Mulder2012)
Mulder2012.Rcheck/Mulder2012-Ex.timings:
name | user | system | elapsed
|
Arora2010.BMfitting | 0 | 0 | 0 |
|
Arora2010.InferPAN | 0 | 0 | 0 |
|
Arora2010.ModuleSearchByPvclust | 0 | 0 | 0 |
|
Arora2010.fig | 0 | 0 | 0 |
|
Arora2010.hypergeo | 0.001 | 0.000 | 0.001 |
|
Arora2010.module.visualize | 0.001 | 0.000 | 0.001 |
|
Arora2010.pipeline | 0 | 0 | 0 |
|
GSEARandomWalkFig | 0 | 0 | 0 |
|
Mulder2012.BMfitting | 0.001 | 0.000 | 0.001 |
|
Mulder2012.InferPAN | 0.001 | 0.000 | 0.001 |
|
Mulder2012.ModuleSearchByPvclust | 0 | 0 | 0 |
|
Mulder2012.PPIPre | 0 | 0 | 0 |
|
Mulder2012.PPIenrich | 0.000 | 0.000 | 0.001 |
|
Mulder2012.RNAiPre | 0.001 | 0.000 | 0.001 |
|
Mulder2012.fig | 0 | 0 | 0 |
|
Mulder2012.module.visualize | 0 | 0 | 0 |
|
Mulder2012.pipeline | 0 | 0 | 0 |
|
data-Arora2010 | 0.900 | 0.024 | 0.924 |
|
data-Mulder2012 | 0.922 | 0.007 | 0.932 |
|