Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-04 11:47 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 2049/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sparrow 1.14.0 (landing page) Steve Lianoglou
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the sparrow package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sparrow.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: sparrow |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sparrow.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sparrow_1.14.0.tar.gz |
StartedAt: 2025-08-02 11:38:31 -0400 (Sat, 02 Aug 2025) |
EndedAt: 2025-08-02 11:48:31 -0400 (Sat, 02 Aug 2025) |
EllapsedTime: 600.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sparrow.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sparrow.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sparrow_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/sparrow.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sparrow/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sparrow’ version ‘1.14.0’ * 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 ‘sparrow’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 whether startup messages can be suppressed ... 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 ... NOTE .map_ids_orthogene: no visible binding for global variable ‘gspecies’ .map_ids_orthogene: no visible binding for global variable ‘species’ .map_ids_orthogene: no visible binding for global variable ‘input_ensg’ .map_ids_orthogene: no visible binding for global variable ‘ortholog_ensg’ .map_ids_orthogene: no visible binding for global variable ‘ortholog_gene’ .map_ids_orthogene: no visible binding for global variable ‘symbol’ .map_ids_orthogene: no visible binding for global variable ‘input_id’ .map_ids_orthogene: no visible global function definition for ‘starts_with’ .map_ids_orthogene: no visible global function definition for ‘last_col’ .map_ids_orthogene: no visible binding for global variable ‘rm_na’ geneSetsStats: no visible binding for global variable ‘direction’ getMSigGeneSetDb: no visible binding for global variable ‘ncbi_gene’ getMSigGeneSetDb: no visible binding for global variable ‘db_species’ getMSigGeneSetDb: no visible binding for global variable ‘msigdb_collection’ getMSigGeneSetDb: no visible binding for global variable ‘gene_symbol’ getMSigGeneSetDb: no visible binding for global variable ‘gs_collection_name’ getMSigGeneSetDb: no visible binding for global variable ‘gs_url’ convertIdentifiers,GeneSetDb: no visible binding for global variable ‘.convert_ids_with_babelgene’ convertIdentifiers,GeneSetDb: no visible global function definition for ‘.map_ids_babelgene’ Undefined global functions or variables: .convert_ids_with_babelgene .map_ids_babelgene db_species direction gene_symbol gs_collection_name gs_url gspecies input_ensg input_id last_col msigdb_collection ncbi_gene ortholog_ensg ortholog_gene rm_na species starts_with symbol * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Non-topic package-anchored link(s) in Rd file 'GeneSetDb-class.Rd': ‘[GSEABase:GeneIdentifierType-constructors]{GSEABase::EntrezIdentifier()}’ Non-topic package-anchored link(s) in Rd file 'calculateIndividualLogFC.Rd': ‘[limma:ebayes]{limma::eBayes()}’ Non-topic package-anchored link(s) in Rd file 'collectionMetadata.Rd': ‘[GSEABase:GeneIdentifierType-constructors]{GSEABase::EntrezIdentifier()}’ Non-topic package-anchored link(s) in Rd file 'seas.Rd': ‘[limma:toptable]{limma::topTable()}’ ‘[limma:dupcor]{limma::duplicateCorrelation()}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: seas.Rd: BiocParallel Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed goseq 9.911 0.489 10.221 geneSetsStats 7.674 0.140 5.785 seas 7.250 0.431 7.200 scoreSingleSamples 6.146 0.307 6.443 annotateGeneSetMembership 5.788 0.133 4.918 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/sparrow.Rcheck/00check.log’ for details.
sparrow.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sparrow ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘sparrow’ ... ** this is package ‘sparrow’ version ‘1.14.0’ ** using staged installation ** R ** 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 (sparrow)
sparrow.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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("sparrow") > library("testthat") > library("data.table") > library("dplyr") Attaching package: 'dplyr' The following objects are masked from 'package:data.table': between, first, last The following object is masked from 'package:testthat': matches The following object is masked from 'package:sparrow': combine The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union > > test_check("sparrow") Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not [ FAIL 0 | WARN 0 | SKIP 6 | PASS 1491 ] ══ Skipped tests (6) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-MultiGSEAResult.R:3:1' • {misgdbdf} is not installed (5): 'test-get-msigdb.R:6:3', 'test-get-msigdb.R:14:3', 'test-get-msigdb.R:27:3', 'test-get-msigdb.R:65:3', 'test-get-msigdb.R:99:3' [ FAIL 0 | WARN 0 | SKIP 6 | PASS 1491 ] > > ## Remove temporary files that were generated > test.dir <- system.file('tests', package = "sparrow") > pdfs <- dir(test.dir, "\\.pdf$", full.names=TRUE) > if (length(pdfs)) { + unlink(pdfs) + } > > > proc.time() user system elapsed 324.842 15.676 306.111
sparrow.Rcheck/sparrow-Ex.timings
name | user | system | elapsed | |
GeneSetDb-class | 0.829 | 0.017 | 0.847 | |
SparrowResult-utilities | 4.745 | 0.223 | 4.390 | |
addGeneSetMetadata | 0.108 | 0.003 | 0.092 | |
annotateGeneSetMembership | 5.788 | 0.133 | 4.918 | |
calculateIndividualLogFC | 1.496 | 0.048 | 1.631 | |
collectionMetadata | 0.076 | 0.005 | 0.088 | |
combine-GeneSetDb-GeneSetDb-method | 0.140 | 0.011 | 0.154 | |
combine-SparrowResult-SparrowResult-method | 0.165 | 0.006 | 0.179 | |
conform | 1.240 | 0.033 | 1.272 | |
conversion | 0.718 | 0.036 | 0.694 | |
convertIdentifiers | 0.251 | 0.010 | 0.237 | |
corplot | 0.092 | 0.005 | 0.099 | |
eigenWeightedMean | 4.270 | 0.123 | 4.387 | |
examples | 0.337 | 0.070 | 0.407 | |
failWith | 0.000 | 0.000 | 0.001 | |
featureIdMap | 0.467 | 0.017 | 0.458 | |
featureIds | 0.477 | 0.022 | 0.481 | |
geneSet | 0.107 | 0.006 | 0.099 | |
geneSetCollectionURLfunction | 0.085 | 0.008 | 0.084 | |
geneSetSummaryByGenes | 3.222 | 0.120 | 2.941 | |
geneSets | 0.120 | 0.004 | 0.096 | |
geneSetsStats | 7.674 | 0.140 | 5.785 | |
getKeggCollection | 0.000 | 0.001 | 0.000 | |
getMSigCollection | 0 | 0 | 0 | |
getPantherCollection | 0 | 0 | 0 | |
getReactomeCollection | 0.000 | 0.001 | 0.000 | |
goseq | 9.911 | 0.489 | 10.221 | |
gsdScore | 0.981 | 0.046 | 1.000 | |
gskey | 0.003 | 0.001 | 0.005 | |
hasGeneSet | 0.116 | 0.004 | 0.094 | |
hasGeneSetCollection | 0.115 | 0.005 | 0.099 | |
incidenceMatrix | 1.128 | 0.062 | 1.167 | |
iplot | 2.582 | 0.103 | 2.686 | |
is.active | 0.392 | 0.046 | 0.416 | |
logFC | 4.702 | 0.129 | 3.776 | |
mgheatmap | 0 | 0 | 0 | |
mgheatmap2 | 0.000 | 0.001 | 0.000 | |
msg | 0.001 | 0.000 | 0.001 | |
ora | 0.308 | 0.017 | 0.326 | |
p.matrix | 0.122 | 0.002 | 0.125 | |
randomGeneSetDb | 0.087 | 0.008 | 0.096 | |
renameCollections | 0.091 | 0.002 | 0.082 | |
renameRows | 0.473 | 0.024 | 0.497 | |
results | 0.139 | 0.006 | 0.149 | |
scale_rows | 0.004 | 0.000 | 0.004 | |
scoreSingleSamples | 6.146 | 0.307 | 6.443 | |
seas | 7.250 | 0.431 | 7.200 | |
sparrow_methods | 0.003 | 0.001 | 0.004 | |
species_info | 0.005 | 0.003 | 0.009 | |
subset.GeneSetDb | 0.123 | 0.005 | 0.102 | |
subsetByFeatures | 0.181 | 0.006 | 0.140 | |
validateInputs | 0.154 | 0.012 | 0.153 | |
volcanoPlot | 2.280 | 0.082 | 2.373 | |
volcanoStatsTable | 0.094 | 0.002 | 0.098 | |
zScore | 0.851 | 0.039 | 0.847 | |