Package: ViSEAGO

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ViSEAGO.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ViSEAGO_1.0.0.tar.gz

StartedAt: 2020-04-15 06:25:36 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:28:36 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 180.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ViSEAGO.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ViSEAGO.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ViSEAGO_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/ViSEAGO.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ViSEAGO/DESCRIPTION’ ... OK
* this is package ‘ViSEAGO’ version ‘1.0.0’
* 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 ‘ViSEAGO’ can be installed ... OK
* checking installed package size ... OK
* 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 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.
* 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 : <anonymous>: warning in getBM(attributes =
  c("ensembl_gene_id", "external_gene_name"), value = TRUE, mart =
  myspecies): partial argument match of 'value' to 'values'
MDSplot,ANY: no visible binding for global variable ‘text’
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 : <anonymous> : esummary : <anonymous>: no
  visible binding for global variable ‘start’
merge_enrich_terms,list : <anonymous> : esummary : <anonymous>: no
  visible binding for global variable ‘end’
Undefined global functions or variables:
  IC N end start text
Consider adding
  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 ... WARNING
Undocumented S4 methods:
  generic 'merge_enrich_terms' and siglist 'list'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
Ensembl2GO 1.071   0.23   8.574
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/ViSEAGO.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ViSEAGO
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ViSEAGO’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ViSEAGO)

name	user	system	elapsed
Bioconductor2GO	0.056	0.007	0.065
Custom2GO	0.811	0.014	0.335
Ensembl2GO	1.071	0.230	8.574
EntrezGene2GO	0.000	0.001	0.000
EntrezGene_orthologs	0	0	0
GOclusters_heatmap-methods	0.087	0.006	0.093
GOcount-methods	0.359	0.113	0.478
GOterms_heatmap-methods	0.074	0.006	0.080
MDSplot-methods	0.085	0.005	0.091
Uniprot2GO	0.005	0.003	1.489
Upset-methods	0.766	0.013	0.797
annotate-methods	0.000	0.000	0.002
available_organisms-methods	0.100	0.018	0.125
build_GO_SS-methods	0.090	0.006	0.173
clusters_cor-methods	0.069	0.006	0.075
compare_clusters-methods	0.069	0.005	0.075
compute_SS_distances-methods	0.079	0.004	0.084
create_topGOdata-methods	0.015	0.002	0.017
merge_enrich_terms-methods	0.026	0.004	0.030
overLapper	0	0	0
pkgdiagram	0.193	0.102	0.300
show_heatmap-methods	0.080	0.005	0.086
show_table-methods	0.339	0.039	0.403
taxonomy	1.748	0.015	0.291