Aurelien Brionne
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/ViSEAGO |
| git_branch: RELEASE_3_13 |
| git_last_commit: 320ba38 |
| git_last_commit_date: 2021-05-19 12:44:50 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:27 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the ViSEAGO package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ViSEAGO.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2008/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ViSEAGO 1.6.0 (landing page) Aurelien Brionne
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: ViSEAGO |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ViSEAGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ViSEAGO_1.6.0.tar.gz |
| StartedAt: 2021-10-15 07:13:10 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 07:17:38 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 267.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ViSEAGO.Rcheck |
| Warnings: 3 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ViSEAGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ViSEAGO_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ViSEAGO.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.6.0'
* 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:
Note: possible error in 'listEnsembl(host = host, ': unused argument (host = host)
Warning: replacing previous import 'data.table::set' by 'dendextend::set' when loading 'ViSEAGO'
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ViSEAGO.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* checking installed package size ... NOTE
installed size is 12.6Mb
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'
Ensembl2GO: possible error in listEnsembl(host = host, version =
version): unused argument (host = host)
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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
merge_enrich_terms-methods 0.22 0.01 6.3
** 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-3.13-bioc/meat/ViSEAGO.Rcheck/00check.log'
for details.
ViSEAGO.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ViSEAGO_1.6.0.tar.gz && rm -rf ViSEAGO.buildbin-libdir && mkdir ViSEAGO.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ViSEAGO.buildbin-libdir ViSEAGO_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ViSEAGO_1.6.0.zip && rm ViSEAGO_1.6.0.tar.gz ViSEAGO_1.6.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
1 6604k 1 94287 0 0 456k 0 0:00:14 --:--:-- 0:00:14 455k
58 6604k 58 3840k 0 0 3177k 0 0:00:02 0:00:01 0:00:01 3178k
100 6604k 100 6604k 0 0 3698k 0 0:00:01 0:00:01 --:--:-- 3697k
install for i386
* installing *source* package 'ViSEAGO' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'data.table::set' by 'dendextend::set' when loading 'ViSEAGO'
Note: possible error in 'listEnsembl(host = host, ': unused argument (host = host)
** help
*** installing help indices
converting help for package 'ViSEAGO'
finding HTML links ... done
Bioconductor2GO html
Custom2GO html
Ensembl2GO html
EntrezGene2GO html
EntrezGene_orthologs html
GO_SS-class html
GO_clusters-class html
GOclusters_heatmap-methods html
GOcount-methods html
GOterms_heatmap-methods html
MDSplot-methods html
Uniprot2GO html
Upset-methods html
ViSEAGO html
annotate-methods html
available_organisms-methods html
build_GO_SS-methods html
clusters_cor-methods html
compare_clusters-methods html
compute_SS_distances-methods html
create_topGOdata-methods html
enrich_GO_terms-class html
fgsea-class html
gene2GO-class html
genomic_ressource-class html
merge_enrich_terms-methods html
myGOs html
overLapper html
finding level-2 HTML links ... done
pkgdiagram html
runfgsea-methods html
show_heatmap-methods html
show_table-methods html
taxonomy html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'data.table::set' by 'dendextend::set' when loading 'ViSEAGO'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'data.table::set' by 'dendextend::set' when loading 'ViSEAGO'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'ViSEAGO' ...
** testing if installed package can be loaded
Warning: replacing previous import 'data.table::set' by 'dendextend::set' when loading 'ViSEAGO'
* MD5 sums
packaged installation of 'ViSEAGO' as ViSEAGO_1.6.0.zip
* DONE (ViSEAGO)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ViSEAGO' successfully unpacked and MD5 sums checked
|
ViSEAGO.Rcheck/examples_i386/ViSEAGO-Ex.timings
|
ViSEAGO.Rcheck/examples_x64/ViSEAGO-Ex.timings
|