GeneAnswers 2.12.0
Lei Huang and Gang Feng
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/GeneAnswers | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GeneAnswers_2.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GeneAnswers.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneAnswers/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneAnswers’ version ‘2.12.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘igraph’ ‘RCurl’ ‘annotate’ ‘Biobase’ ‘XML’ ‘RSQLite’ ‘MASS’
‘Heatplus’ ‘RColorBrewer’
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 ‘GeneAnswers’ can be installed ... [13s/13s] WARNING
Found the following significant warnings:
Warning: replacing previous import by ‘igraph::decompose’ when loading ‘GeneAnswers’
Warning: replacing previous import by ‘igraph::spectrum’ when loading ‘GeneAnswers’
See ‘/Users/biocbuild/bbs-3.2-bioc/meat/GeneAnswers.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 35.4Mb
sub-directories of 1Mb or more:
data 1.0Mb
doc 1.6Mb
External 32.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘annotate’
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:
‘Biobase’ ‘Heatplus’ ‘igraph’ ‘MASS’ ‘RColorBrewer’ ‘XML’
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘biomaRt’ ‘GO.db’ ‘KEGG.db’ ‘reactome.db’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘GeneAnswers/R/zzz.R’:
.onLoad calls:
require(Biobase)
Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.
getHomoGeneIDs: no visible global function definition for ‘useMart’
getHomoGeneIDs: no visible global function definition for ‘getLDS’
getTotalGeneNumber: no visible global function definition for
‘count.mappedkeys’
getTotalGeneNumber: no visible global function definition for ‘toTable’
getTotalGeneNumber: no visible binding for global variable
‘reactomePATHNAME2ID’
* 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 ... [522s/548s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
geneAnswersReadable 71.689 4.043 75.736
GeneAnswers-class 34.349 2.520 36.992
buildNet 30.582 2.096 32.681
getConnectedGraph 31.447 1.168 32.617
GeneAnswers-package 30.406 2.156 32.568
geneAnswersBuilder 30.206 1.950 32.162
getMultiLayerGraphIDs 30.628 1.523 32.154
geneAnswersSort 30.851 1.160 32.011
geneAnswersHeatmap 30.197 1.155 31.353
geneAnswersHomoMapping 30.134 1.207 31.342
geneAnswersConceptNet 29.619 1.154 30.775
geneAnswersConceptRelation 29.274 1.334 30.609
geneAnswersChartPlots 28.858 1.506 30.366
geneAnswersConcepts 29.048 1.133 30.184
getGOList 15.995 1.688 43.366
* 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: 1 WARNING, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/GeneAnswers.Rcheck/00check.log’
for details.
* installing *source* package ‘GeneAnswers’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘igraph::decompose’ when loading ‘GeneAnswers’
Warning: replacing previous import by ‘igraph::spectrum’ when loading ‘GeneAnswers’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘igraph::decompose’ when loading ‘GeneAnswers’
Warning: replacing previous import by ‘igraph::spectrum’ when loading ‘GeneAnswers’
* DONE (GeneAnswers)