Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:35 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the AnnotationDbi package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AnnotationDbi.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 55/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AnnotationDbi 1.61.0 (landing page) Bioconductor Package Maintainer
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: AnnotationDbi |
Version: 1.61.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:AnnotationDbi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings AnnotationDbi_1.61.0.tar.gz |
StartedAt: 2023-02-27 20:19:01 -0000 (Mon, 27 Feb 2023) |
EndedAt: 2023-02-27 20:24:02 -0000 (Mon, 27 Feb 2023) |
EllapsedTime: 301.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: AnnotationDbi.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:AnnotationDbi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings AnnotationDbi_1.61.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/AnnotationDbi.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘AnnotationDbi/DESCRIPTION’ ... OK * this is package ‘AnnotationDbi’ version ‘1.61.0’ * 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 ‘AnnotationDbi’ can be installed ... OK * checking installed package size ... NOTE installed size is 8.3Mb sub-directories of 1Mb or more: R 1.1Mb extdata 6.0Mb * 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 ... NOTE Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE createORGANISMSeeds: no visible global function definition for ‘makeAnnDbMapSeeds’ Undefined global functions or variables: makeAnnDbMapSeeds * checking Rd files ... WARNING checkRd: (5) AnnDbObj-class.Rd:58-61: \item in \describe must have non-empty label checkRd: (5) AnnDbObj-class.Rd:64-68: \item in \describe must have non-empty label checkRd: (5) AnnDbObj-class.Rd:71-75: \item in \describe must have non-empty label checkRd: (5) AnnDbObj-class.Rd:78-89: \item in \describe must have non-empty label checkRd: (5) AnnDbObj-class.Rd:92-96: \item in \describe must have non-empty label checkRd: (5) Bimap.Rd:79-82: \item in \describe must have non-empty label checkRd: (5) Bimap.Rd:84-87: \item in \describe must have non-empty label checkRd: (-1) inpIDMapper.Rd:91: Escaped LaTeX specials: \# checkRd: (-1) inpIDMapper.Rd:95: Escaped LaTeX specials: \# checkRd: (-1) inpIDMapper.Rd:99: Escaped LaTeX specials: \# * 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 ‘AnnotationDbi-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: KEGGFrame > ### Title: KEGGFrame objects > ### Aliases: KEGGFrame class:KEGGFrame KEGGFrame-class KEGGFrame > ### KEGGFrame,data.frame,character-method > ### KEGGFrame,data.frame,missing-method getKEGGFrameData > ### getKEGGFrameData,KEGGFrame-method > ### getKEGGFrameData,KEGGAllFrame-method > ### Keywords: classes interface > > ### ** Examples > > ## Make up an example > genes = c(2,9,9,10) > KEGGIds = c("04610","00232","00983","00232") > frameData = data.frame(cbind(KEGGIds,genes)) > > library(AnnotationDbi) > frame=KEGGFrame(frameData,organism="Homo sapiens") Error in KEGGFrame(frameData, organism = "Homo sapiens") : None of elements in the 1st column of your data.frame object are legitimate KEGG IDs. Calls: KEGGFrame -> KEGGFrame Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘AnnotationDbi_unit_tests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘AnnotationDbi.Rnw’ using ‘UTF-8’... OK ‘IntroToAnnotationPackages.Rnw’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/AnnotationDbi.Rcheck/00check.log’ for details.
AnnotationDbi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL AnnotationDbi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘AnnotationDbi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’ Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’ Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’ Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’ Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’ ** 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 (AnnotationDbi)
AnnotationDbi.Rcheck/tests/AnnotationDbi_unit_tests.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) 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. > require("AnnotationDbi") || stop("unable to load AnnotationDbi package") Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics 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, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname [1] TRUE > > AnnotationDbi:::.test() Loading required package: org.Hs.eg.db 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns Loading required package: RSQLite Loading required package: org.At.tair.db Loading required package: org.Sc.sgd.db Loading required package: GO.db Loading required package: hgu95av2.db 'select()' returned many:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned many:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned many:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned many:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns Warning: You have selected the following columns that can have a many to one relationship with the primary key: ACCNUM, ALIAS, ENSEMBL, ENSEMBLPROT, ENSEMBLTRANS, ENZYME, EVIDENCE, EVIDENCEALL, GO, GOALL, IPI, MAP, OMIM, ONTOLOGY, ONTOLOGYALL, PATH, PFAM, PMID, PROSITE, REFSEQ, UCSCKG, UNIPROT . Because you have selected more than a few such columns there is a risk that this selection may balloon up into a very large result as the number of rows returned multiplies accordingly. To experience smaller/more manageable results and faster retrieval times, you might want to consider selecting these columns separately. 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned many:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned many:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned many:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns Loading required package: reactome.db 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns RUNIT TEST PROTOCOL -- Mon Feb 27 20:23:07 2023 *********************************************** Number of test functions: 64 Number of errors: 0 Number of failures: 0 1 Test Suite : AnnotationDbi RUnit Tests - 64 test functions, 0 errors, 0 failures Number of test functions: 64 Number of errors: 0 Number of failures: 0 Warning messages: 1: In .local(x, ...) : returned vector has duplicated names 2: In .local(x, ...) : returned vector has duplicated names 3: call dbDisconnect() when finished working with a connection 4: In .deprecatedColsMessage() : Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is deprecated. Please use a range based accessor like genes(), or select() with columns values like TXCHROM and TXSTART on a TxDb or OrganismDb object instead. 5: In .deprecatedColsMessage() : Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is deprecated. Please use a range based accessor like genes(), or select() with columns values like TXCHROM and TXSTART on a TxDb or OrganismDb object instead. 6: In .deprecatedColsMessage() : Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is deprecated. Please use a range based accessor like genes(), or select() with columns values like TXCHROM and TXSTART on a TxDb or OrganismDb object instead. > > proc.time() user system elapsed 67.614 3.295 70.973
AnnotationDbi.Rcheck/AnnotationDbi-Ex.timings
name | user | system | elapsed | |
AnnDbObj-class | 0.460 | 0.045 | 0.505 | |
AnnDbPkg-checker | 49.836 | 1.011 | 51.313 | |
AnnotationDb-class | 2.223 | 0.196 | 2.422 | |
Bimap-direction | 3.213 | 0.556 | 3.795 | |
Bimap-envirAPI | 0.360 | 0.148 | 0.508 | |
Bimap-keys | 0.755 | 0.040 | 0.796 | |
Bimap-toTable | 2.343 | 0.100 | 2.456 | |
Bimap | 1.698 | 0.316 | 2.013 | |
BimapFiltering | 0.144 | 0.004 | 0.148 | |
BimapFormatting | 0.339 | 0.008 | 0.347 | |
GOColsAndKeytypes | 0.191 | 0.004 | 0.195 | |
GOFrame | 1.461 | 0.348 | 1.809 | |
GOTerms-class | 0.001 | 0.000 | 0.001 | |