FGNet 3.4.0
Sara Aibar
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/FGNet | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | | |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings FGNet_3.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/FGNet.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FGNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FGNet’ version ‘3.4.0’
* 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 ‘FGNet’ can be installed ... [2s/2s] OK
* checking installed package size ... NOTE
installed size is 7.7Mb
sub-directories of 1Mb or more:
doc 7.2Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
FGNet_GUI: no visible global function definition for ‘gtkWindowNew’
FGNet_GUI: no visible global function definition for ‘gtkStatusbar’
FGNet_GUI: no visible global function definition for ‘gtkNotebookNew’
FGNet_GUI: no visible global function definition for
‘gtkNotebookInsertPage’
FGNet_GUI: no visible global function definition for ‘gtkLabelNew’
FGNet_GUI: no visible global function definition for ‘gtkVBoxNew’
FGNet_GUI: no visible global function definition for ‘gSignalConnect’
SOAPQuery: no visible global function definition for
‘basicTextGatherer’
SOAPQuery: no visible global function definition for ‘curlPerform’
SOAPQuery: no visible global function definition for ‘parseHTTPHeader’
actDeactGenes: no visible global function definition for
‘gtkWidgetSetSensitive’
buildGeneSets: no visible global function definition for ‘columns’
buildGeneSets: no visible global function definition for ‘keys’
buildGeneSets: no visible global function definition for ‘select’
buildGeneSets: no visible binding for global variable ‘GO.db’
buildGeneSets: no visible binding for global variable ‘KEGGPATHID2NAME’
buildGeneSets: no visible binding for global variable
‘reactomePATHID2EXTID’
buildGeneSets: no visible binding for global variable
‘reactomeEXTID2PATHID’
buildGeneSets: no visible binding for global variable
‘reactomePATHID2NAME’
fea_david: no visible binding for global variable ‘DAVIDWebService’
fea_david: no visible global function definition for ‘addList’
fea_david : <anonymous>: no visible global function definition for
‘getIdTypes’
fea_david: no visible global function definition for
‘setAnnotationCategories’
fea_david : <anonymous>: no visible global function definition for
‘getAllAnnotationCategoryNames’
fea_david: no visible global function definition for
‘getClusterReportFile’
fea_david: no visible global function definition for ‘getCurlHandle’
fea_david: no visible global function definition for ‘postForm’
fea_gage: no visible global function definition for ‘exprs’
fea_gage: no visible global function definition for ‘gage’
fea_gage: no visible global function definition for ‘esset.grp’
fea_gtLinker_getResults: no visible global function definition for
‘url.exists’
fea_topGO: no visible global function definition for ‘groupGOTerms’
fea_topGO: no visible binding for global variable ‘GOFisherTest’
fea_topGO: no visible binding for global variable ‘annFUN.gene2GO’
fea_topGO: no visible global function definition for ‘getSigGroups’
fea_topGO: no visible global function definition for ‘GenTable’
fea_topGO : <anonymous>: no visible global function definition for
‘genesInTerm’
fea_topGO : <anonymous>: no visible global function definition for
‘sigGenes’
fillCombosColumns : <anonymous>: no visible global function definition
for ‘gtkComboBoxAppendText’
formatResultsFile: no visible binding for global variable ‘rawResults’
format_david: no visible global function definition for ‘getURL’
generateNetwork: no visible global function definition for
‘gtkDialogNewWithButtons’
generateNetwork: no visible binding for global variable
‘GtkResponseType’
generateNetwork: no visible global function definition for ‘gtkLabel’
generateReport: no visible global function definition for
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generateReport: no visible binding for global variable
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generateReport: no visible global function definition for ‘gtkLabel’
goTreeLinks: no visible binding for global variable ‘GOBPPARENTS’
goTreeLinks: no visible binding for global variable ‘GOMFPARENTS’
goTreeLinks: no visible binding for global variable ‘GOCCPARENTS’
loadEset: no visible global function definition for ‘gtkCheckButton’
loadFileDialog: no visible global function definition for
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loadFileDialog: no visible binding for global variable
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loadFileDialog: no visible global function definition for
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loadFileDialog: no visible global function definition for
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loadFileDialog: no visible global function definition for
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loadInstPkg: no visible global function definition for
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loadInstPkg: no visible binding for global variable ‘GtkResponseType’
loadInstPkg: no visible global function definition for ‘gtkLabel’
loadInstPkg: no visible global function definition for ‘biocLite’
plotGoAncestors: no visible binding for global variable ‘GOBPPARENTS’
plotGoAncestors: no visible binding for global variable ‘GOMFPARENTS’
plotGoAncestors: no visible binding for global variable ‘GOCCPARENTS’
plotGoAncestors : <anonymous>: no visible binding for global variable
‘GOTERM’
plotKegg: no visible global function definition for ‘columns’
plotKegg: no visible global function definition for ‘keys’
plotKegg: no visible global function definition for ‘select’
plotKegg: no visible binding for global variable ‘KEGGPATHID2NAME’
plotKegg: no visible global function definition for ‘download_KEGGfile’
plotKegg: no visible global function definition for ‘parse_XMLfile’
plotKegg: no visible global function definition for ‘plot_profile’
processExpressionField: no visible global function definition for
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processExpressionField: no visible global function definition for
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processExpressionField: no visible global function definition for
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processExpressionField: no visible global function definition for
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processFile: no visible binding for '<<-' assignment to ‘rawResults’
processFile: no visible binding for global variable ‘rawResults’
processFile: no visible global function definition for
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processGenesField: no visible global function definition for
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processGenesField: no visible global function definition for
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processGenesField: no visible global function definition for
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processGenesField: no visible global function definition for
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readFEAresults: no visible global function definition for
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readFEAresults: no visible global function definition for
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readFEAresults: no visible global function definition for
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readFEAresults: no visible global function definition for
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readFEAresults: no visible global function definition for ‘gtkLabel’
refList: no visible global function definition for ‘columns’
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selectAPI: no visible global function definition for
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selectAPI: no visible global function definition for
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selectAPI: no visible global function definition for ‘gtkCheckButton’
selectNetworkTool: no visible global function definition for
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selectNetworkType: no visible global function definition for
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selectWs: no visible global function definition for
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selectWs_fillFields: no visible binding for global variable
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selectWs_fillFields: no visible global function definition for
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selectWs_fillFields: no visible global function definition for
‘getAllAnnotationCategoryNames’
selectWs_fillFields: no visible global function definition for
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selectWs_fillFields: no visible global function definition for
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selectWs_fillFields: no visible global function definition for
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selectWs_fillFields: no visible global function definition for
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selectWs_fillFields: no visible binding for global variable
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selectWs_fillFields: no visible global function definition for
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submitQuery: no visible global function definition for
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submitQuery: no visible global function definition for
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submitQuery: no visible binding for global variable ‘GtkResponseType’
submitQuery: no visible global function definition for ‘gtkLabel’
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submitQuery: no visible global function definition for ‘readList’
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submitQuery: no visible global function definition for
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submitQuery: no visible global function definition for
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tabDavid_fill: no visible global function definition for ‘gtkVBox’
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tabDavid_fill: no visible global function definition for ‘gtkHBox’
tabDavid_fill: no visible global function definition for
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tabDavid_fill: no visible global function definition for
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tabDavid_fill: no visible binding for global variable ‘GtkShadowType’
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tabDavid_fill: no visible global function definition for
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tabFEA_fill: no visible binding for global variable ‘GtkShadowType’
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tabFEA_fill: no visible global function definition for
‘pangoFontDescriptionFromString’
tabFEA_fill: no visible global function definition for
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tabFEA_fill: no visible global function definition for ‘gtkButton’
tabFEA_fill: no visible global function definition for ‘gSignalConnect’
tabFEA_fill: no visible global function definition for ‘gtkViewportNew’
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tabFEA_fill: no visible binding for '<<-' assignment to ‘rawResults’
tabFEA_fill: no visible global function definition for
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tabFEA_fill: no visible global function definition for ‘gtkLabelNew’
tabGTL_fill: no visible global function definition for ‘gtkVBox’
tabGTL_fill: no visible global function definition for
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tabGTL_fill: no visible global function definition for
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tabGTL_fill: no visible global function definition for
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tabGTL_fill: no visible binding for global variable ‘GtkShadowType’
tabGTL_fill: no visible global function definition for ‘gtkVBoxNew’
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tabGage_fill: no visible binding for global variable ‘GtkShadowType’
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tabGage_fill: no visible global function definition for
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tabGage_fill: no visible global function definition for
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tabHelp_fill: no visible global function definition for ‘gtkHBox’
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tabHelp_fill: no visible global function definition for ‘gtkFrame’
tabHelp_fill: no visible global function definition for
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tabHelp_fill: no visible binding for global variable ‘GtkShadowType’
tabHelp_fill: no visible global function definition for ‘gtkEntryNew’
tabNetwork_common_fill: no visible global function definition for
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tabNetwork_common_fill: no visible global function definition for
‘gtkTable’
tabNetwork_common_fill: no visible global function definition for
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tabNetwork_common_fill: no visible global function definition for
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tabNetwork_common_fill: no visible binding for global variable
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tabNetwork_common_fill: no visible global function definition for
‘gtkScrolledWindow’
tabNetwork_common_fill: no visible global function definition for
‘gtkTextViewNewWithBuffer’
tabNetwork_common_fill: no visible global function definition for
‘pangoFontDescriptionFromString’
tabNetwork_common_fill: no visible global function definition for
‘gtkTextBufferNew’
tabNetwork_common_fill: no visible global function definition for
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tabNetwork_common_fill: no visible global function definition for
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tabNetwork_common_fill: no visible global function definition for
‘gtkComboBoxNewText’
tabNetwork_common_fill: no visible global function definition for
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tabNetwork_common_fill: no visible global function definition for
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tabNetwork_common_fill: no visible global function definition for
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tabNetwork_common_fill: no visible global function definition for
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tabNetwork_common_fill: no visible global function definition for
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tabNetwork_common_fill: no visible global function definition for
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tabNetwork_common_fill: no visible global function definition for
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tabNetwork_common_fill: no visible global function definition for
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tabNetwork_common_fill: no visible global function definition for
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tabNetwork_fill: no visible global function definition for
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tabNetwork_fill: no visible global function definition for
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tabNetwork_fill: no visible global function definition for
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tabNetwork_fill: no visible global function definition for
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tabOther_fill: no visible global function definition for ‘gtkVBox’
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tabOther_fill: no visible global function definition for ‘gtkExpander’
tabOther_fill: no visible global function definition for ‘gtkHBox’
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tabOther_fill: no visible global function definition for
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tabOther_fill: no visible global function definition for
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tabOther_fill: no visible global function definition for ‘gtkFrame’
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tabOther_fill: no visible binding for global variable ‘GtkShadowType’
tabOther_fill: no visible global function definition for ‘gtkEntryNew’
tabOther_fill: no visible global function definition for ‘gtkButton’
tabOther_fill: no visible global function definition for
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tabOther_fill: no visible global function definition for
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tabTopGo_fill: no visible global function definition for ‘gtkVBoxNew’
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tabTopGo_fill: no visible global function definition for ‘gtkEntryNew’
tabTopGo_fill: no visible global function definition for
‘gtkLinkButtonNewWithLabel’
viewFile: no visible binding for global variable ‘rawResults’
* 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 ... ERROR
Running examples in ‘FGNet-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotKegg
> ### Title: Plot KEGG pathway
> ### Aliases: plotKegg
>
> ### ** Examples
>
>
> ###################################
> # Gene info
> genesYeast <- c("ADA2", "APC1", "APC11", "APC2", "APC4", "APC5", "APC9", "CDC16",
+ "CDC23", "CDC26", "CDC27", "CFT1", "CFT2", "DCP1", "DOC1", "FIP1",
+ "GCN5", "GLC7", "HFI1", "KEM1", "LSM1", "LSM2", "LSM3", "LSM4",
+ "LSM5", "LSM6", "LSM7", "LSM8", "MPE1", "NGG1", "PAP1", "PAT1",
+ "PFS2", "PTA1", "PTI1", "REF2", "RNA14", "RPN1", "RPN10", "RPN11",
+ "RPN13", "RPN2", "RPN3", "RPN5", "RPN6", "RPN8", "RPT1", "RPT3",
+ "RPT6", "SGF11", "SGF29", "SGF73", "SPT20", "SPT3", "SPT7", "SPT8",
+ "TRA1", "YSH1", "YTH1")
>
> # Gene expression (1=UP, -1=DW)
> genesYeastExpr <- setNames(c(rep(1,29), rep(-1,30)), genesYeast)
>
>
> ###################################
> # Plot pathway
>
> # Specific pathway
> plotKegg("sce04111", genesYeastExpr, geneIDtype="GENENAME")
Loading required package: DBI
KEGG.db contains mappings based on older data because the original
resource was removed from the the public domain before the most
recent update was produced. This package should now be considered
deprecated and future versions of Bioconductor may not have it
available. Users who want more current data are encouraged to look
at the KEGGREST or reactome.db packages
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
'select()' returned 1:1 mapping between keys and columns
[1] "Downloading files: 1/1"
trying URL 'http://www.genome.jp/kegg-bin/download?entry=sce04111&format=kgml'
Content type 'text/xml' length unknown
.......... .......... .......... .......... ..........
....
downloaded 54 KB
trying URL 'http://www.genome.jp/kegg/pathway/sce/sce04111.png'
Content type 'image/png' length 43060 bytes (42 KB)
==================================================
downloaded 42 KB
trying URL 'http://www.genome.jp/kegg/pathway/map/map04111.png'
Content type 'image/png' length 40513 bytes (39 KB)
==================================================
downloaded 39 KB
AttValue: " or ' expected
attributes construct error
Couldn't find end of Start Tag subtype line 1108
Premature end of data in tag relation line 1107
Premature end of data in tag pathway line 4
Error: 1: AttValue: " or ' expected
2: attributes construct error
3: Couldn't find end of Start Tag subtype line 1108
4: Premature end of data in tag relation line 1107
5: Premature end of data in tag pathway line 4
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [2s/11s]
[2s/12s] 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: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/FGNet.Rcheck/00check.log’
for details.