Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 2235/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ViSEAGO 1.21.0 (landing page) Aurelien Brionne
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the ViSEAGO package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: ViSEAGO |
Version: 1.21.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ViSEAGO.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ViSEAGO_1.21.0.tar.gz |
StartedAt: 2024-12-24 12:31:23 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 12:36:20 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 297.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ViSEAGO.Rcheck |
Warnings: 9 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:ViSEAGO.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ViSEAGO_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ViSEAGO.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ViSEAGO/DESCRIPTION’ ... OK * this is package ‘ViSEAGO’ version ‘1.21.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 23 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 Warning: replacing previous import ‘data.table::set’ by ‘dendextend::set’ when loading ‘ViSEAGO’ Warning: replacing previous import ‘dendextend::cutree’ by ‘stats::cutree’ when loading ‘ViSEAGO’ Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘ViSEAGO’ See ‘/home/biocbuild/bbs-3.21-bioc/meat/ViSEAGO.Rcheck/00install.out’ for details. * checking installed package size ... INFO installed size is 12.4Mb sub-directories of 1Mb or more: extdata 10.6Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: GPL-3 bioconductor.org Standardizable: FALSE * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... WARNING Warning: program compiled against libxml 212 using older 211 '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 ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 GOterms_heatmap,GO_SS: no visible binding for global variable ‘GO.ID’ MDSplot,ANY: no visible binding for global variable ‘GO.cluster’ 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 ‘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 : <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’ Undefined global functions or variables: . ENTREZID ES EVIDENCE GO.ID GO.cluster IC Id N NES ONTOLOGY Significant_genes genes_frequency leadingEdge log2err nMoreExtreme padj pathway pval size * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: overLapper.Rd: upset Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... WARNING Warning: program compiled against libxml 212 using older 211 * 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 516Kb xz * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 9 WARNINGs, 5 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/ViSEAGO.Rcheck/00check.log’ for details.
ViSEAGO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ViSEAGO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘ViSEAGO’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 Warning: replacing previous import ‘data.table::set’ by ‘dendextend::set’ when loading ‘ViSEAGO’ Warning: replacing previous import ‘dendextend::cutree’ by ‘stats::cutree’ when loading ‘ViSEAGO’ Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘ViSEAGO’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 Warning: replacing previous import ‘data.table::set’ by ‘dendextend::set’ when loading ‘ViSEAGO’ Warning: replacing previous import ‘dendextend::cutree’ by ‘stats::cutree’ when loading ‘ViSEAGO’ Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘ViSEAGO’ ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 Warning: replacing previous import ‘data.table::set’ by ‘dendextend::set’ when loading ‘ViSEAGO’ Warning: replacing previous import ‘dendextend::cutree’ by ‘stats::cutree’ when loading ‘ViSEAGO’ Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘ViSEAGO’ ** testing if installed package keeps a record of temporary installation path * DONE (ViSEAGO)
ViSEAGO.Rcheck/ViSEAGO-Ex.timings
name | user | system | elapsed | |
Bioconductor2GO | 0.036 | 0.009 | 0.087 | |
Custom2GO | 0 | 0 | 0 | |
Ensembl2GO | 0 | 0 | 0 | |
EntrezGene2GO | 0.001 | 0.000 | 0.000 | |
EntrezGene_orthologs | 0 | 0 | 0 | |
GOclusters_heatmap-methods | 0.041 | 0.000 | 0.041 | |
GOcount-methods | 0.269 | 0.023 | 0.296 | |
GOterms_heatmap-methods | 0.034 | 0.000 | 0.035 | |
MDSplot-methods | 0.034 | 0.000 | 0.034 | |
Uniprot2GO | 0 | 0 | 0 | |
Upset-methods | 2.490 | 0.080 | 3.208 | |
annotate-methods | 0 | 0 | 0 | |
available_organisms-methods | 0.119 | 0.012 | 0.168 | |
build_GO_SS-methods | 0.035 | 0.000 | 0.035 | |
clusters_cor-methods | 0.036 | 0.000 | 0.036 | |
compare_clusters-methods | 0.035 | 0.000 | 0.035 | |
compute_SS_distances-methods | 0.036 | 0.000 | 0.035 | |
create_topGOdata-methods | 0.016 | 0.001 | 0.040 | |
merge_enrich_terms-methods | 0.096 | 0.022 | 0.350 | |
overLapper | 0 | 0 | 0 | |
pkgdiagram | 0.115 | 0.033 | 0.306 | |
runfgsea-methods | 0.025 | 0.000 | 0.040 | |
show_heatmap-methods | 0.037 | 0.000 | 0.069 | |
show_table-methods | 0.241 | 0.009 | 0.414 | |
taxonomy | 0.047 | 0.004 | 1.868 | |