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This page was generated on 2025-09-30 12:04 -0400 (Tue, 30 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4843
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4575
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 2048/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sparrow 1.15.0  (landing page)
Steve Lianoglou
Snapshot Date: 2025-09-29 13:45 -0400 (Mon, 29 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 nebbiolo2

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.

raw results


Summary

Package: sparrow
Version: 1.15.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings sparrow_1.15.0.tar.gz
StartedAt: 2025-09-30 04:44:46 -0400 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 04:55:01 -0400 (Tue, 30 Sep 2025)
EllapsedTime: 615.5 seconds
RetCode: 0
Status:   OK  
CheckDir: sparrow.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings sparrow_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/sparrow.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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
geneSetsStats             40.589  0.083   5.073
goseq                     26.447  0.278   8.163
seas                      25.189  0.140   6.470
geneSetSummaryByGenes     23.101  0.129   3.320
logFC                     22.829  0.118   4.521
annotateGeneSetMembership 22.697  0.219   4.453
SparrowResult-utilities   22.720  0.136   4.423
scoreSingleSamples         5.878  0.037   4.988
* 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 re-building of vignette outputs ... OK
* 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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL sparrow
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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.

> 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 1487 ]

══ 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 1487 ]
> 
> ## 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 
896.681  10.541 258.863 

Example timings

sparrow.Rcheck/sparrow-Ex.timings

nameusersystemelapsed
GeneSetDb-class0.0870.0000.071
SparrowResult-utilities22.720 0.136 4.423
addGeneSetMetadata0.3320.0010.066
annotateGeneSetMembership22.697 0.219 4.453
calculateIndividualLogFC1.4320.0131.445
collectionMetadata0.3360.0000.069
combine-GeneSetDb-GeneSetDb-method0.5750.0020.102
combine-SparrowResult-SparrowResult-method0.1180.0010.117
conform0.6590.0020.388
conversion1.8070.0300.594
convertIdentifiers1.3130.0100.219
corplot0.0900.0030.094
eigenWeightedMean4.5300.0434.047
examples0.2700.0050.274
failWith0.0010.0000.001
featureIdMap0.6630.0000.392
featureIds0.7840.0030.439
geneSet0.3830.0020.086
geneSetCollectionURLfunction0.3610.0010.079
geneSetSummaryByGenes23.101 0.129 3.320
geneSets0.3400.0110.059
geneSetsStats40.589 0.083 5.073
getKeggCollection000
getMSigCollection000
getPantherCollection000
getReactomeCollection000
goseq26.447 0.278 8.163
gsdScore1.4530.0040.938
gskey0.0030.0000.003
hasGeneSet0.2950.0000.060
hasGeneSetCollection0.3270.0010.061
incidenceMatrix2.2170.0091.966
iplot2.6800.0761.790
is.active0.6230.0090.334
logFC22.829 0.118 4.521
mgheatmap0.0000.0000.001
mgheatmap2000
msg0.0010.0000.001
ora0.2060.0150.214
p.matrix0.0790.0010.079
randomGeneSetDb0.1040.0010.098
renameCollections0.4950.0010.082
renameRows0.3570.0060.350
results0.0990.0000.099
scale_rows0.0030.0000.004
scoreSingleSamples5.8780.0374.988
seas25.189 0.140 6.470
sparrow_methods0.0030.0000.002
species_info0.0050.0000.006
subset.GeneSetDb0.3160.0010.069
subsetByFeatures0.5970.0010.092
validateInputs0.4150.0090.134
volcanoPlot2.2430.0442.287
volcanoStatsTable0.0690.0000.069
zScore1.4650.0130.912