| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-07 11:33 -0400 (Thu, 07 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4879 |
| 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 2191/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TaxSEA 1.5.0 (landing page) Feargal Ryan
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| See other builds for TaxSEA in R Universe. | ||||||||||||||
|
To the developers/maintainers of the TaxSEA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TaxSEA.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. |
| Package: TaxSEA |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:TaxSEA.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings TaxSEA_1.5.0.tar.gz |
| StartedAt: 2026-05-07 05:12:42 -0400 (Thu, 07 May 2026) |
| EndedAt: 2026-05-07 05:18:28 -0400 (Thu, 07 May 2026) |
| EllapsedTime: 346.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: TaxSEA.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:TaxSEA.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings TaxSEA_1.5.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/TaxSEA.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-07 09:12:42 UTC
* checking for file ‘TaxSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TaxSEA’ version ‘1.5.0’
* package encoding: UTF-8
* 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 ‘TaxSEA’ 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 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 ... 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 ... WARNING
'::' or ':::' import not declared from: ‘methods’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get_ncbi_taxon_ids : get_ncbi_taxon_id: no visible global function
definition for ‘URLencode’
get_ncbi_taxon_ids: no visible global function definition for ‘data’
get_ncbi_taxon_ids: no visible binding for global variable ‘NCBI_ids’
get_taxon_sets: no visible global function definition for ‘data’
get_taxon_sets: no visible binding for global variable ‘TaxSEA_db’
get_taxon_sets: no visible binding for global variable ‘NCBI_ids’
ss_prepare: no visible binding for global variable ‘TaxSEA_db’
taxon_rank_sets: no visible global function definition for ‘is’
taxsea_KS : <anonymous>: no visible global function definition for
‘median’
taxsea_prepare: no visible binding for global variable ‘TaxSEA_db’
Undefined global functions or variables:
NCBI_ids TaxSEA_db URLencode data is median
Consider adding
importFrom("methods", "is")
importFrom("stats", "median")
importFrom("utils", "URLencode", "data")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
NCBI_ids.rda 136Kb 42Kb xz
TaxSEA_db.rda 48Kb 35Kb bzip2
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘TaxSEA-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TaxSEA
> ### Title: TaxSEA: Taxon Set Enrichment Analysis
> ### Aliases: TaxSEA
>
> ### ** Examples
>
> data("TaxSEA_test_data")
> res <- TaxSEA(taxon_ranks = TaxSEA_test_data)
Using cached version from 2026-04-26 20:35:38
Warning in ks.test.default(taxon_set_ranks, taxon_ranks) :
p-value will be approximate in the presence of ties
Warning in ks.test.default(taxon_set_ranks, taxon_ranks) :
p-value will be approximate in the presence of ties
Warning in ks.test.default(taxon_set_ranks, taxon_ranks) :
p-value will be approximate in the presence of ties
Warning in ks.test.default(taxon_set_ranks, taxon_ranks) :
p-value will be approximate in the presence of ties
Warning in ks.test.default(taxon_set_ranks, taxon_ranks) :
p-value will be approximate in the presence of ties
Warning in ks.test.default(taxon_set_ranks, taxon_ranks) :
p-value will be approximate in the presence of ties
Warning in ks.test.default(taxon_set_ranks, taxon_ranks) :
p-value will be approximate in the presence of ties
Warning in ks.test.default(taxon_set_ranks, taxon_ranks) :
p-value will be approximate in the presence of ties
Warning in ks.test.default(taxon_set_ranks, taxon_ranks) :
p-value will be approximate in the presence of ties
Warning in ks.test.default(taxon_set_ranks, taxon_ranks) :
p-value will be approximate in the presence of ties
Warning in ks.test.default(taxon_set_ranks, taxon_ranks) :
p-value will be approximate in the presence of ties
Warning in ks.test.default(taxon_set_ranks, taxon_ranks) :
p-value will be approximate in the presence of ties
Warning in ks.test.default(taxon_set_ranks, taxon_ranks) :
p-value will be approximate in the presence of ties
Warning in ks.test.default(taxon_set_ranks, taxon_ranks) :
p-value will be approximate in the presence of ties
> head(res$All_databases)
taxonSetName
1 GMRepoV2_Decreased_in_Liver_Cirrhosis
2 bsdb_bsdb:39237540/12/2_Aging:All-cohorts-(Increased-age-group)_vs_All-cohorts-(Decreased-age-group)_DOWN
3 bsdb_bsdb:39237540/13/2_Aging:All-cohorts-(Increased-age-group)_vs_All-cohorts-(Decreased-age-group)_DOWN
4 bsdb_bsdb:39237540/15/2_Aging:All-cohorts-(Increased-age-group)_vs_All-Cohorts-(Decreasing-age-group)_DOWN
5 bsdb_bsdb:39237540/4/2_Aging:All-Cohorts-(Increased-age-group)_vs_All-Cohorts-(Decreased-age-group)_DOWN
6 mBodyMap_Oral
median_rank_of_set_members PValue Test_statistic FDR
1 -3.6435 2.441190e-06 0.4555410 0.0007974835
2 -3.7530 6.403851e-06 0.5809088 0.0007974835
3 -3.7530 6.403851e-06 0.5809088 0.0007974835
4 -3.7530 6.403851e-06 0.5809088 0.0007974835
5 -3.8240 7.742558e-06 0.5426313 0.0007974835
6 1.7750 1.196178e-05 0.7080745 0.0010267198
TaxonSet
1 Faecalibacterium_prausnitzii, Bacteroides_uniformis, Roseburia_hominis, Alistipes_putredinis, Bacteroides_dorei, Eubacterium_rectale, Dorea_longicatena, Blautia_obeum, Eubacterium_eligens, Bacteroides_faecis, Dorea_formicigenerans, Roseburia_inulinivorans, Parasutterella_excrementihominis, Bacteroides_xylanisolvens, Collinsella_aerofaciens, Bacteroides_massiliensis, Odoribacter_splanchnicus, Eubacterium_hallii, Bilophila_wadsworthia, Eubacterium_ramulus, Eubacterium_ventriosum, Coprococcus_catus, Alistipes_shahii, Roseburia_intestinalis, Eubacterium_siraeum, Intestinibacter_bartlettii, Ruminococcus_bromii, Bifidobacterium_adolescentis, Coprococcus_comes, Bacteroides_cellulosilyticus, Ruminococcus_callidus, Coprococcus_eutactus, Ruminococcus_lactaris, Bacteroides_finegoldii, Barnesiella_intestinihominis, Alistipes_indistinctus, Alistipes_onderdonkii, Bacteroides_intestinalis
2 Faecalibacterium_prausnitzii, Roseburia_hominis, Eubacterium_rectale, Dorea_longicatena, Blautia_obeum, Eubacterium_eligens, Dorea_formicigenerans, Roseburia_inulinivorans, Parasutterella_excrementihominis, Eubacterium_hallii, Eubacterium_ventriosum, Coprococcus_catus, Roseburia_intestinalis, Bifidobacterium_pseudocatenulatum, Ruminococcus_bromii, Coprococcus_comes, Ruminococcus_torques, Ruminococcus_callidus, Ruminococcus_lactaris
3 Faecalibacterium_prausnitzii, Roseburia_hominis, Eubacterium_rectale, Dorea_longicatena, Blautia_obeum, Eubacterium_eligens, Dorea_formicigenerans, Roseburia_inulinivorans, Parasutterella_excrementihominis, Eubacterium_hallii, Eubacterium_ventriosum, Coprococcus_catus, Roseburia_intestinalis, Bifidobacterium_pseudocatenulatum, Ruminococcus_bromii, Coprococcus_comes, Ruminococcus_torques, Ruminococcus_callidus, Ruminococcus_lactaris
4 Faecalibacterium_prausnitzii, Roseburia_hominis, Eubacterium_rectale, Dorea_longicatena, Blautia_obeum, Eubacterium_eligens, Dorea_formicigenerans, Roseburia_inulinivorans, Parasutterella_excrementihominis, Eubacterium_hallii, Eubacterium_ventriosum, Coprococcus_catus, Roseburia_intestinalis, Bifidobacterium_pseudocatenulatum, Ruminococcus_bromii, Coprococcus_comes, Ruminococcus_torques, Ruminococcus_callidus, Ruminococcus_lactaris
5 Faecalibacterium_prausnitzii, Roseburia_hominis, Eubacterium_rectale, Ruminococcus_gnavus, Dorea_longicatena, Blautia_obeum, Eubacterium_eligens, Dorea_formicigenerans, Roseburia_inulinivorans, Parasutterella_excrementihominis, Collinsella_aerofaciens, Eubacterium_hallii, Eubacterium_ventriosum, Coprococcus_catus, Roseburia_intestinalis, Bifidobacterium_pseudocatenulatum, Ruminococcus_bromii, Bifidobacterium_adolescentis, Coprococcus_comes, Ruminococcus_torques, Ruminococcus_callidus, Ruminococcus_lactaris
6 Streptococcus_salivarius, Haemophilus_parainfluenzae, Streptococcus_parasanguinis, Actinomyces_oris, Veillonella_parvula, Veillonella_dispar, Streptococcus_mitis, Streptococcus_sanguinis, Rothia_mucilaginosa, Actinomyces_sp_HPA0247, Actinomyces_sp_ICM47
>
> # ORA example (toy): treat taxa with positive values as "hits"
> hits <- names(TaxSEA_test_data)
> res_ora <- TaxSEA(input_taxa = hits, mode = "ora")
Error while performing HEAD request.
Proceeding without cache information.
Error: download failed; see warnings()
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
‘/home/biocbuild/bbs-3.24-bioc/meat/TaxSEA.Rcheck/00check.log’
for details.
TaxSEA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL TaxSEA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’ * installing *source* package ‘TaxSEA’ ... ** this is package ‘TaxSEA’ version ‘1.5.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (TaxSEA)
TaxSEA.Rcheck/tests/testthat.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(TaxSEA)
> test_check("TaxSEA")
Error while performing HEAD request.
Proceeding without cache information.
Error while performing HEAD request.
Proceeding without cache information.
Using cached version from 2026-04-26 20:35:38
Detected SummarizedExperiment input. Extracting taxonomy from rowData().
Using mia::taxonomyRanks() to identify rank columns: Kingdom, Phylum, Class, Order, Family, Genus, Species
Detected SummarizedExperiment input. Extracting taxonomy from rowData().
Using mia::taxonomyRanks() to identify rank columns: Phylum, Genus, Species
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 53 ]
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 53 ]
>
> proc.time()
user system elapsed
16.263 0.938 122.822
TaxSEA.Rcheck/TaxSEA-Ex.timings
| name | user | system | elapsed | |
| NCBI_ids | 0.027 | 0.005 | 0.032 | |