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This page was generated on 2025-09-20 12:07 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 2045/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sparrow 1.15.0  (landing page)
Steve Lianoglou
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 2025)
git_url: https://git.bioconductor.org/packages/sparrow
git_branch: devel
git_last_commit: fd4225d
git_last_commit_date: 2025-04-15 12:39:51 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for sparrow on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: sparrow
Version: 1.15.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sparrow_1.15.0.tar.gz
StartedAt: 2025-09-19 13:44:26 -0000 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 14:00:38 -0000 (Fri, 19 Sep 2025)
EllapsedTime: 972.2 seconds
RetCode: 0
Status:   OK  
CheckDir: sparrow.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sparrow_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/sparrow.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 ‘sparrow/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sparrow’ version ‘1.15.0’
* 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 loading without being on the library search path ... 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
scoreSingleSamples        13.152  0.141  15.861
goseq                      9.698  0.244  15.042
seas                       7.009  0.156  11.752
eigenWeightedMean          6.435  0.146   8.280
geneSetsStats              5.833  0.159   9.136
SparrowResult-utilities    5.117  0.137   6.834
annotateGeneSetMembership  4.964  0.175   6.202
geneSetSummaryByGenes      4.333  0.121   7.364
logFC                      3.915  0.100   5.721
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/sparrow.Rcheck/00check.log’
for details.


Installation output

sparrow.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL sparrow
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘sparrow’ ...
** this is package ‘sparrow’ version ‘1.15.0’
** 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)

Tests output

sparrow.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 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.

> 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 1479 ]

══ 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 1479 ]
> 
> ## 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 
338.379   8.407 476.716 

Example timings

sparrow.Rcheck/sparrow-Ex.timings

nameusersystemelapsed
GeneSetDb-class0.0950.0040.178
SparrowResult-utilities5.1170.1376.834
addGeneSetMetadata0.0880.0000.088
annotateGeneSetMembership4.9640.1756.202
calculateIndividualLogFC2.3590.0443.223
collectionMetadata0.0900.0000.155
combine-GeneSetDb-GeneSetDb-method0.1240.0040.128
combine-SparrowResult-SparrowResult-method0.1290.0040.208
conform0.5290.0160.547
conversion0.7900.0161.135
convertIdentifiers0.2740.0040.311
corplot0.1060.0040.111
eigenWeightedMean6.4350.1468.280
examples0.3620.0190.766
failWith0.0010.0000.006
featureIdMap0.5460.0131.111
featureIds0.5870.0000.643
geneSet0.1150.0000.116
geneSetCollectionURLfunction0.1020.0000.102
geneSetSummaryByGenes4.3330.1217.364
geneSets0.0840.0000.084
geneSetsStats5.8330.1599.136
getKeggCollection000
getMSigCollection0.0010.0000.000
getPantherCollection000
getReactomeCollection0.0010.0000.000
goseq 9.698 0.24415.042
gsdScore1.3580.0132.729
gskey0.0030.0000.007
hasGeneSet0.0860.0000.167
hasGeneSetCollection0.0820.0010.082
incidenceMatrix2.4360.0712.725
iplot2.2480.0922.447
is.active0.4240.0160.477
logFC3.9150.1005.721
mgheatmap000
mgheatmap2000
msg000
ora0.3210.0040.327
p.matrix0.1010.0000.100
randomGeneSetDb0.1980.0040.202
renameCollections0.1070.0000.108
renameRows0.4450.0000.535
results0.1220.0030.127
scale_rows0.0050.0000.005
scoreSingleSamples13.152 0.14115.861
seas 7.009 0.15611.752
sparrow_methods0.0040.0000.004
species_info0.0070.0000.012
subset.GeneSetDb0.0940.0040.099
subsetByFeatures0.1260.0000.126
validateInputs0.2010.0070.209
volcanoPlot3.1200.0284.227
volcanoStatsTable0.0760.0000.075
zScore1.1010.0411.412