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This page was generated on 2024-05-08 11:41:25 -0400 (Wed, 08 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4707
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4484
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4514
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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 2024/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sparrow 1.10.1  (landing page)
Steve Lianoglou
Snapshot Date: 2024-05-07 14:00:20 -0400 (Tue, 07 May 2024)
git_url: https://git.bioconductor.org/packages/sparrow
git_branch: RELEASE_3_19
git_last_commit: d592783
git_last_commit_date: 2024-05-06 17:21:11 -0400 (Mon, 06 May 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  YES
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for sparrow on kunpeng2


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: 1.10.1
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings sparrow_1.10.1.tar.gz
StartedAt: 2024-05-08 12:08:20 -0000 (Wed, 08 May 2024)
EndedAt: 2024-05-08 12:20:42 -0000 (Wed, 08 May 2024)
EllapsedTime: 742.2 seconds
RetCode: 0
Status:   OK  
CheckDir: sparrow.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings sparrow_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/sparrow.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sparrow/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sparrow’ version ‘1.10.1’
* 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                     9.979  0.235   9.940
seas                      7.189  0.076   6.988
scoreSingleSamples        6.869  0.048   6.903
SparrowResult-utilities   5.739  0.172   5.623
geneSetsStats             5.847  0.053   5.351
annotateGeneSetMembership 5.678  0.136   5.556
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/sparrow.Rcheck/00check.log’
for details.


Installation output

sparrow.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL sparrow
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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.

> 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

Estimating GSVA scores for 76 gene sets.
Estimating ECDFs with Gaussian kernels

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Estimating PLAGE scores for 76 gene sets.

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Estimating ssGSEA scores for 76 gene sets.
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."

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[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1477 ]

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

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1477 ]
> 
> ## 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 
439.523  15.451 431.074 

Example timings

sparrow.Rcheck/sparrow-Ex.timings

nameusersystemelapsed
GeneSetDb-class0.2460.0080.255
SparrowResult-utilities5.7390.1725.623
addGeneSetMetadata0.0930.0000.084
annotateGeneSetMembership5.6780.1365.556
calculateIndividualLogFC2.4170.0162.438
collectionMetadata0.1040.0000.095
combine-GeneSetDb-GeneSetDb-method0.1280.0080.118
combine-SparrowResult-SparrowResult-method0.1260.0080.136
conform0.5800.0160.588
conversion0.8490.0040.818
convertIdentifiers0.2510.0040.220
corplot0.1070.0040.112
eigenWeightedMean4.2090.1154.316
examples0.4370.0160.453
failWith000
featureIdMap0.5830.0080.582
featureIds0.6310.0120.629
geneSet0.1070.0000.098
geneSetCollectionURLfunction0.0730.0040.068
geneSetSummaryByGenes4.4630.0954.231
geneSets0.1060.0040.100
geneSetsStats5.8470.0535.351
getKeggCollection000
getMSigCollection000
getPantherCollection0.0010.0000.000
getReactomeCollection000
goseq9.9790.2359.940
gsdScore1.3210.0281.336
gskey0.0030.0000.003
hasGeneSet0.0840.0000.075
hasGeneSetCollection0.0820.0000.073
incidenceMatrix1.5590.0081.560
iplot2.6600.0642.717
is.active0.3940.0520.438
logFC4.3260.0304.075
mgheatmap000
mgheatmap2000
msg0.0000.0010.001
ora0.2650.0120.277
p.matrix0.1020.0000.102
randomGeneSetDb0.1060.0000.106
renameCollections0.1390.0040.130
renameRows0.5170.0120.530
results0.1390.0040.144
scale_rows0.0050.0000.005
scoreSingleSamples6.8690.0486.903
seas7.1890.0766.988
sparrow_methods0.0040.0000.003
species_info0.0070.0000.007
subset.GeneSetDb0.0930.0000.082
subsetByFeatures0.1190.0000.102
validateInputs0.2160.0040.210
volcanoPlot2.4570.0352.499
volcanoStatsTable0.0760.0010.077
zScore1.2360.0041.226