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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ViSEAGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ViSEAGO_1.4.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ViSEAGO.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ViSEAGO/DESCRIPTION' ... OK
* this is package 'ViSEAGO' version '1.4.0'
* 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 whether package 'ViSEAGO' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'data.table::set' by 'dendextend::set' when loading 'ViSEAGO'
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ViSEAGO.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 12.5Mb
sub-directories of 1Mb or more:
extdata 10.6Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... WARNING
'library' or 'require' call not declared from: 'topGO'
'library' or 'require' call to 'topGO' 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: 'processx'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotate,character-genomic_ressource: warning in getBM(attributes =
c("ensembl_gene_id", "go_id", "go_linkage_type", "namespace_1003"),
filters = unlist(go_filter[grep("with GO ID", ignore.case = TRUE,
go_filter$description), "name", with = FALSE]), value = TRUE, mart =
myspecies): partial argument match of 'value' to 'values'
compute_SS_distances,ANY-character: warning in select(GO.db, keys =
onto$values, column = "TERM"): partial argument match of 'column' to
'columns'
merge_enrich_terms,list : genes_symbols_add: warning in
getBM(attributes = c("ensembl_gene_id", "external_gene_name"), value
= TRUE, mart = myspecies): partial argument match of 'value' to
'values'
GOcount,ANY: no visible global function definition for 'orca'
GOterms_heatmap,GO_SS: no visible binding for global variable 'GO.ID'
MDSplot,ANY: no visible binding for global variable 'text'
MDSplot,ANY: no visible binding for global variable 'GO.cluster'
MDSplot,ANY: no visible global function definition for 'orca'
Upset,ANY: no visible global function definition for 'png'
Upset,ANY: no visible global function definition for 'dev.off'
annotate,character-genomic_ressource: no visible global function
definition for '.'
annotate,character-genomic_ressource: no visible binding for global
variable 'ENTREZID'
annotate,character-genomic_ressource: no visible binding for global
variable 'GO'
annotate,character-genomic_ressource: no visible binding for global
variable 'EVIDENCE'
annotate,character-genomic_ressource: no visible binding for global
variable 'ONTOLOGY'
compute_SS_distances,ANY-character: no visible binding for global
variable 'N'
compute_SS_distances,ANY-character: no visible binding for global
variable 'IC'
merge_enrich_terms,list : genes_symbols_add : esummary : <anonymous>:
no visible binding for global variable 'start'
merge_enrich_terms,list : genes_symbols_add : esummary : <anonymous>:
no visible binding for global variable 'end'
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable 'pval'
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable 'pathway'
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable 'Id'
merge_enrich_terms,list : <anonymous>: no visible global function
definition for '.'
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable 'padj'
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable 'nMoreExtreme'
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable 'ES'
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable 'NES'
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable 'size'
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable 'genes_frequency'
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable 'log2err'
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable 'leadingEdge'
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable 'Significant_genes'
merge_enrich_terms,list : <anonymous>: no visible binding for global
variable 'GO.ID'
runfgsea,ANY-gene2GO-character: no visible binding for global variable
'genes_frequency'
runfgsea,ANY-gene2GO-character: no visible binding for global variable
'leadingEdge'
runfgsea,ANY-gene2GO-character: no visible binding for global variable
'size'
runfgsea,ANY-gene2GO-character: no visible binding for global variable
'pathway'
show_heatmap,GO_clusters-character: no visible global function
definition for 'orca'
Undefined global functions or variables:
. ENTREZID ES EVIDENCE GO GO.ID GO.cluster IC Id N NES ONTOLOGY
Significant_genes dev.off end genes_frequency leadingEdge log2err
nMoreExtreme orca padj pathway png pval size start text
Consider adding
importFrom("grDevices", "dev.off", "png")
importFrom("graphics", "text")
importFrom("stats", "end", "start")
to your NAMESPACE file.
* 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 ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
myGOs.RData 876Kb 517Kb xz
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/ViSEAGO.Rcheck/00check.log'
for details.
