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 11:46 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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 71/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AnnotationDbi 1.69.0 (landing page) Bioconductor Package Maintainer
| 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 AnnotationDbi package: - 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 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: AnnotationDbi |
Version: 1.69.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:AnnotationDbi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings AnnotationDbi_1.69.0.tar.gz |
StartedAt: 2024-12-24 03:40:38 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 03:48:59 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 500.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: AnnotationDbi.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:AnnotationDbi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings AnnotationDbi_1.69.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/AnnotationDbi.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 ‘AnnotationDbi/DESCRIPTION’ ... OK * this is package ‘AnnotationDbi’ version ‘1.69.0’ * 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 ... INFO 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 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 ... 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed AnnDbPkg-checker 52.568 0.962 60.925 * 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 ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/AnnotationDbi.Rcheck/00check.log’ for details.
AnnotationDbi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL AnnotationDbi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > require("AnnotationDbi") || stop("unable to load AnnotationDbi package") Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 object is masked from 'package:utils': findMatches 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 1:1 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: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 -- Tue Dec 24 03:48:54 2024 *********************************************** 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 252.023 38.860 292.126
AnnotationDbi.Rcheck/AnnotationDbi-Ex.timings
name | user | system | elapsed | |
AnnDbObj-class | 0.541 | 0.028 | 0.600 | |
AnnDbPkg-checker | 52.568 | 0.962 | 60.925 | |
AnnotationDb-class | 2.866 | 0.281 | 3.163 | |
Bimap-direction | 3.181 | 0.617 | 3.815 | |
Bimap-envirAPI | 0.312 | 0.064 | 0.377 | |
Bimap-keys | 0.860 | 0.008 | 0.869 | |
Bimap-toTable | 2.316 | 0.103 | 2.459 | |
Bimap | 1.638 | 0.349 | 1.990 | |
BimapFiltering | 0.142 | 0.004 | 0.146 | |
BimapFormatting | 0.329 | 0.020 | 0.349 | |
GOColsAndKeytypes | 0.191 | 0.000 | 0.191 | |
GOFrame | 1.144 | 0.268 | 1.437 | |
GOTerms-class | 0.000 | 0.000 | 0.001 | |
KEGGFrame | 0.069 | 0.034 | 0.662 | |
colsAndKeytypes | 0.200 | 0.024 | 0.231 | |
createSimpleBimap | 0.168 | 0.028 | 0.199 | |
inpIDMapper | 0 | 0 | 0 | |
makeGOGraph | 0.315 | 0.011 | 0.328 | |
make_eg_to_go_map | 0.178 | 0.013 | 0.190 | |
organismKEGGFrame | 0.135 | 0.015 | 2.054 | |
print.probetable | 0.482 | 0.140 | 0.627 | |
toSQLStringSet | 0.000 | 0.000 | 0.001 | |
unlist2 | 0.245 | 0.040 | 0.289 | |