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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 2009/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sparrow 1.12.0  (landing page)
Steve Lianoglou
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/sparrow
git_branch: RELEASE_3_20
git_last_commit: df6e04d
git_last_commit_date: 2024-10-29 11:04:59 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 1.12.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings sparrow_1.12.0.tar.gz
StartedAt: 2024-12-20 05:40:05 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 05:50:56 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 650.6 seconds
RetCode: 0
Status:   OK  
CheckDir: sparrow.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings sparrow_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/sparrow.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘sparrow/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sparrow’ version ‘1.12.0’
* 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
geneSetsStats: no visible binding for global variable ‘direction’
Undefined global functions or variables:
  direction
* checking Rd files ... OK
* 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 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         7.443  0.165   6.720
seas          6.518  0.096   5.713
geneSetsStats 5.572  0.046   3.947
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/sparrow.Rcheck/00check.log’
for details.


Installation output

sparrow.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL sparrow
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘sparrow’ ...
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 1 | PASS 1501 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-MultiGSEAResult.R:3:1'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1501 ]
> 
> ## 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 
306.104  13.552 274.520 

Example timings

sparrow.Rcheck/sparrow-Ex.timings

nameusersystemelapsed
GeneSetDb-class0.0800.0010.065
SparrowResult-utilities3.9980.0523.192
addGeneSetMetadata0.0800.0000.056
annotateGeneSetMembership4.4280.0563.627
calculateIndividualLogFC1.4080.0081.416
collectionMetadata0.0840.0000.060
combine-GeneSetDb-GeneSetDb-method0.1320.0000.083
combine-SparrowResult-SparrowResult-method0.1410.0010.139
conform0.3990.0010.376
conversion0.6380.0030.533
convertIdentifiers0.2510.0010.155
corplot0.0830.0000.083
eigenWeightedMean2.9300.0042.881
examples0.2690.0170.287
failWith0.0000.0000.001
featureIdMap0.3900.0020.366
featureIds0.5330.0150.506
geneSet0.1020.0000.068
geneSetCollectionURLfunction0.0730.0000.049
geneSetSummaryByGenes4.2750.0183.303
geneSets0.0740.0010.048
geneSetsStats5.5720.0463.947
getKeggCollection000
getMSigCollection0.0010.0000.000
getPantherCollection000
getReactomeCollection000
goseq7.4430.1656.720
gsdScore0.8320.0000.784
gskey0.0020.0000.003
hasGeneSet0.0720.0010.049
hasGeneSetCollection0.0710.0000.046
incidenceMatrix0.9290.0010.903
iplot1.0560.0231.032
is.active0.3160.0210.301
logFC3.3190.0652.526
mgheatmap000
mgheatmap2000
msg0.0000.0000.001
ora0.2490.0010.245
p.matrix0.0820.0010.083
randomGeneSetDb0.1430.0030.140
renameCollections0.1010.0000.066
renameRows0.3310.0070.334
results0.0920.0000.094
scale_rows0.0030.0000.003
scoreSingleSamples3.8220.0283.745
seas6.5180.0965.713
sparrow_methods0.0030.0000.003
species_info0.0050.0000.005
subset.GeneSetDb0.0840.0000.056
subsetByFeatures0.1170.0000.067
validateInputs0.1320.0060.112
volcanoPlot1.6100.0251.635
volcanoStatsTable0.0590.0010.060
zScore0.7260.0450.721