GeneAnswers 2.13.0
Lei Huang and Gang Feng
| Snapshot Date: 2015-10-21 20:20:05 -0400 (Wed, 21 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneAnswers | | Last Changed Rev: 109592 / Revision: 109826 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | 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 GeneAnswers_2.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/GeneAnswers.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.13.0’
* 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 ... [7s/8s] 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-3.3-bioc/meat/GeneAnswers.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 35.4Mb
sub-directories of 1Mb or more:
External 32.4Mb
data 1.0Mb
doc 1.6Mb
* 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’ ‘MASS’ ‘RColorBrewer’ ‘XML’ ‘igraph’
Please remove these calls from your code.
'library' or 'require' calls in package code:
‘GO.db’ ‘KEGG.db’ ‘biomaRt’ ‘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’
Undefined global functions or variables:
count.mappedkeys getLDS reactomePATHNAME2ID toTable useMart
* 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 ... [330s/364s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
geneAnswersReadable 40.895 1.843 43.538
GeneAnswers-class 22.469 1.246 23.776
buildNet 21.657 1.257 22.957
getMultiLayerGraphIDs 20.140 0.875 21.028
geneAnswersBuilder 19.989 0.990 21.009
getConnectedGraph 20.216 0.666 20.889
GeneAnswers-package 19.701 1.072 20.785
geneAnswersHomoMapping 19.502 0.625 20.133
geneAnswersConceptNet 19.385 0.662 20.059
geneAnswersChartPlots 19.158 0.875 20.051
geneAnswersConceptRelation 19.358 0.659 20.022
geneAnswersConcepts 19.250 0.627 19.884
geneAnswersHeatmap 18.732 0.571 19.310
geneAnswersSort 18.252 0.580 18.096
getGOList 9.895 1.085 44.041
* 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-3.3-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)