Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:03:19 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 2239/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
UniProt.ws 2.44.0 (landing page) Marcel Ramos
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the UniProt.ws package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/UniProt.ws.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: UniProt.ws |
Version: 2.44.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:UniProt.ws.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings UniProt.ws_2.44.0.tar.gz |
StartedAt: 2024-05-31 09:16:58 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 09:19:50 -0400 (Fri, 31 May 2024) |
EllapsedTime: 171.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: UniProt.ws.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:UniProt.ws.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings UniProt.ws_2.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/UniProt.ws.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘UniProt.ws/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘UniProt.ws’ version ‘2.44.0’ * 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 ‘UniProt.ws’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) mapUniprot.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) mapUniprot.Rd:107-108: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) mapUniprot.Rd:109: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) mapUniprot.Rd:110-111: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) utilities.Rd:49-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) utilities.Rd:52-54: Lost braces in \itemize; meant \describe ? checkRd: (-1) utilities.Rd:55-62: Lost braces in \itemize; meant \describe ? checkRd: (-1) utilities.Rd:63-69: Lost braces in \itemize; meant \describe ? * 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘UniProt.ws-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: UniProt.ws-objects > ### Title: UniProt.ws objects and their related methods and functions > ### Aliases: UniProt.ws class:UniProt.ws UniProt.ws-class > ### show,UniProt.ws-method species species,UniProt.ws-method taxId > ### taxId,UniProt.ws-method taxId<- taxId<-,UniProt.ws-method columns > ### columns,UniProt.ws-method keytypes keytypes,UniProt.ws-method keys > ### keys,UniProt.ws-method select select,UniProt.ws-method > ### availableUniprotSpecies lookupUniprotSpeciesFromTaxId > ### Keywords: classes methods > > ### ** Examples > > ## Make a UniProt.ws object > up <- UniProt.ws(taxId=9606) > > ## look at the object > up UniProt.ws interface object: Taxonomy ID: 9606 Species name: Homo sapiens (Human) List species with 'availableUniprotSpecies()' > > ## get the current species > species(up) [1] "Homo sapiens (Human)" > > ## look up available species with their tax ids > availableUniprotSpecies("musculus") kingdom Taxon Node Official (scientific) name ANTMS E 520121 Anthocoris musculus ANTMU E 208057 Anthoscopus musculus APOMU E 238007 Apomys musculus BAIMU E 213557 Baiomys musculus BALMU E 9771 Balaenoptera musculus BLEMU E 197864 Blepharisma musculus MOUSE E 10090 Mus musculus MUSMB E 35531 Mus musculus bactrianus MUSMC E 10091 Mus musculus castaneus MUSMM E 57486 Mus musculus molossinus MUSMS E 186842 Mus musculus x Mus spretus MUSMX E 477816 Mus musculus musculus x Mus musculus castaneus POVM1 V 1891730 Mus musculus polyomavirus 1 > > ## get the current taxId > taxId(up) [1] 9606 > > ## look up the species that goes with a tax id > lookupUniprotSpeciesFromTaxId(9606) [1] "Homo sapiens" > > ## set the taxId to something else > taxId(up) <- 10090 > up UniProt.ws interface object: Taxonomy ID: 10090 Species name: Mus musculus (Mouse) List species with 'availableUniprotSpecies()' > > ## list the possible key types > head(keytypes(up)) [1] "Allergome" "ArachnoServer" "Araport" "BioCyc" [5] "BioGRID" "BioMuta" > > ## list of possible columns > head(columns(up)) [1] "absorption" "accession" [3] "annotation_score" "cc_activity_regulation" [5] "cc_allergen" "cc_alternative_products" > > ## list all possible keys of type entrez gene ID > egs <- keys(up, "GeneID") Error: 'idmapping_run' failed: Internal Server Error (HTTP 500). Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘UniProt.ws_unit_tests.R’ ERROR Running the tests in ‘tests/UniProt.ws_unit_tests.R’ failed. Last 13 lines of output: test_select_1 test_select_2 test_select_3 test_select_4 test_select_5 test_select_6 test_select_8 test_serviceAccessors.R test_mapUniProt Error in BiocGenerics:::testPackage("UniProt.ws") : unit tests failed for package UniProt.ws Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘UniProt.ws.Rmd’ using rmarkdown Quitting from lines 119-124 [select] (UniProt.ws.Rmd) Error: processing vignette 'UniProt.ws.Rmd' failed with diagnostics: 'idmapping_run' failed: Internal Server Error (HTTP 500). --- failed re-building ‘UniProt.ws.Rmd’ SUMMARY: processing the following file failed: ‘UniProt.ws.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 3 ERRORs, 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/UniProt.ws.Rcheck/00check.log’ for details.
UniProt.ws.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL UniProt.ws ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘UniProt.ws’ ... ** using staged installation ** R ** 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 (UniProt.ws)
UniProt.ws.Rcheck/tests/UniProt.ws_unit_tests.Rout.fail
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 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. > BiocGenerics:::testPackage("UniProt.ws") Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Timing stopped at: 0.078 0.008 5.389 Error : 'idmapping_run' failed: Internal Server Error (HTTP 500). Timing stopped at: 0.019 0 4.851 Error : 'idmapping_run' failed: Internal Server Error (HTTP 500). Timing stopped at: 0.032 0 4.885 Error : 'idmapping_run' failed: Internal Server Error (HTTP 500). Timing stopped at: 0.031 0 4.901 Error : 'idmapping_run' failed: Internal Server Error (HTTP 500). Timing stopped at: 0.034 0 4.905 Error : 'idmapping_run' failed: Internal Server Error (HTTP 500). Timing stopped at: 0.029 0 4.905 Error : 'idmapping_run' failed: Internal Server Error (HTTP 500). Timing stopped at: 0.383 0.14 5.399 Error : 'idmapping_run' failed: Internal Server Error (HTTP 500). Timing stopped at: 0.015 0.004 4.891 Error : 'idmapping_run' failed: Internal Server Error (HTTP 500). Timing stopped at: 0.005 0 4.871 Error : 'idmapping_run' failed: Internal Server Error (HTTP 500). RUNIT TEST PROTOCOL -- Fri May 31 09:19:30 2024 *********************************************** Number of test functions: 23 Number of errors: 9 Number of failures: 0 1 Test Suite : UniProt.ws RUnit Tests - 23 test functions, 9 errors, 0 failures ERROR in test_mapUniProt: Error : 'idmapping_run' failed: Internal Server Error (HTTP 500). ERROR in test_select_1: Error : 'idmapping_run' failed: Internal Server Error (HTTP 500). ERROR in test_select_2: Error : 'idmapping_run' failed: Internal Server Error (HTTP 500). ERROR in test_select_3: Error : 'idmapping_run' failed: Internal Server Error (HTTP 500). ERROR in test_select_4: Error : 'idmapping_run' failed: Internal Server Error (HTTP 500). ERROR in test_select_5: Error : 'idmapping_run' failed: Internal Server Error (HTTP 500). ERROR in test_select_6: Error : 'idmapping_run' failed: Internal Server Error (HTTP 500). ERROR in test_select_8: Error : 'idmapping_run' failed: Internal Server Error (HTTP 500). ERROR in test_mapUniProt: Error : 'idmapping_run' failed: Internal Server Error (HTTP 500). Test files with failing tests test_mapUniProt.R test_mapUniProt test_select.R test_select_1 test_select_2 test_select_3 test_select_4 test_select_5 test_select_6 test_select_8 test_serviceAccessors.R test_mapUniProt Error in BiocGenerics:::testPackage("UniProt.ws") : unit tests failed for package UniProt.ws Execution halted
UniProt.ws.Rcheck/UniProt.ws-Ex.timings
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