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This page was generated on 2023-05-31 05:44:44 -0000 (Wed, 31 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4219
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CHECK results for sparrow on kunpeng1


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1934/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sparrow 1.7.0  (landing page)
Steve Lianoglou
Snapshot Date: 2023-05-29 10:19:22 -0000 (Mon, 29 May 2023)
git_url: https://git.bioconductor.org/packages/sparrow
git_branch: devel
git_last_commit: 56993db
git_last_commit_date: 2023-04-25 15:33:16 -0000 (Tue, 25 Apr 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

Package: sparrow
Version: 1.7.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings sparrow_1.7.0.tar.gz
StartedAt: 2023-05-30 19:44:40 -0000 (Tue, 30 May 2023)
EndedAt: 2023-05-30 20:01:13 -0000 (Tue, 30 May 2023)
EllapsedTime: 992.2 seconds
RetCode: 0
Status:   OK  
CheckDir: sparrow.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings sparrow_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/sparrow.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘sparrow/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sparrow’ version ‘1.7.0’
* 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 ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 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                     10.127  0.236  10.115
seas                       7.614  0.072   7.461
scoreSingleSamples         6.691  0.176   6.842
SparrowResult-utilities    6.028  0.141   5.939
geneSetsStats              6.052  0.102   5.704
annotateGeneSetMembership  5.908  0.156   5.821
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘sparrow.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/sparrow.Rcheck/00check.log’
for details.



Installation output

sparrow.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL sparrow
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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

[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..."
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1471 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1471 ]
> 
> ## 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 
451.325  16.698 444.008 

Example timings

sparrow.Rcheck/sparrow-Ex.timings

nameusersystemelapsed
GeneSetDb-class0.0920.0000.092
SparrowResult-utilities6.0280.1415.939
addGeneSetMetadata0.0740.0120.078
annotateGeneSetMembership5.9080.1565.821
calculateIndividualLogFC3.4590.0793.539
collectionMetadata0.0990.0010.089
combine-GeneSetDb-GeneSetDb-method0.1130.0110.107
combine-SparrowResult-SparrowResult-method0.1430.0120.159
conform0.6190.0320.641
conversion0.8310.0130.810
convertIdentifiers0.2570.0080.234
corplot0.1020.0080.110
eigenWeightedMean3.4610.0673.514
examples0.4330.0400.473
failWith0.0010.0000.001
featureIdMap0.6370.0080.636
featureIds1.6280.0521.665
geneSet0.1070.0000.098
geneSetCollectionURLfunction0.0780.0000.069
geneSetSummaryByGenes4.7200.0844.530
geneSets0.0680.0150.075
geneSetsStats6.0520.1025.704
getKeggCollection000
getMSigCollection000
getPantherCollection0.0000.0000.001
getReactomeCollection000
goseq10.127 0.23610.115
gsdScore1.3460.0241.356
gskey0.0030.0000.003
hasGeneSet0.0740.0000.067
hasGeneSetCollection0.0710.0040.067
incidenceMatrix1.4450.0201.458
iplot1.4760.0521.515
is.active0.4650.0200.478
logFC4.7510.0154.501
mgheatmap000
mgheatmap20.0000.0010.000
msg0.0000.0010.000
ora0.3310.0180.351
p.matrix0.1090.0000.109
randomGeneSetDb0.0970.0040.101
renameCollections1.3330.0481.370
renameRows0.5110.0040.515
results0.1150.0040.119
scale_rows0.0050.0000.005
scoreSingleSamples6.6910.1766.842
seas7.6140.0727.461
sparrow_methods0.0040.0000.003
species_info0.0070.0000.008
subset.GeneSetDb0.0860.0000.078
subsetByFeatures0.1060.0000.093
validateInputs0.2240.0040.219
volcanoPlot2.3750.0672.442
volcanoStatsTable0.0790.0000.078
zScore1.2590.0441.290