Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-02-03 11:07:08 -0500 (Fri, 03 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4511
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4289
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4318
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

CHECK results for sparrow on lconway


To the developers/maintainers of the sparrow package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1919/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sparrow 1.4.0  (landing page)
Steve Lianoglou
Snapshot Date: 2023-02-02 14:00:04 -0500 (Thu, 02 Feb 2023)
git_url: https://git.bioconductor.org/packages/sparrow
git_branch: RELEASE_3_16
git_last_commit: 71b4d4c
git_last_commit_date: 2022-11-01 11:25:47 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: sparrow
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sparrow.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sparrow_1.4.0.tar.gz
StartedAt: 2023-02-02 23:07:33 -0500 (Thu, 02 Feb 2023)
EndedAt: 2023-02-02 23:16:36 -0500 (Thu, 02 Feb 2023)
EllapsedTime: 543.0 seconds
RetCode: 0
Status:   OK  
CheckDir: sparrow.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sparrow.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sparrow_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/sparrow.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sparrow/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sparrow’ version ‘1.4.0’
* 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 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 6.589  0.302   7.037
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/sparrow.Rcheck/00check.log’
for details.



Installation output

sparrow.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sparrow
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 1503 ]

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

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1503 ]
> 
> ## 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 
288.040  29.994 308.033 

Example timings

sparrow.Rcheck/sparrow-Ex.timings

nameusersystemelapsed
GeneSetDb-class0.0870.0120.107
SparrowResult-utilities3.2330.0993.373
addGeneSetMetadata0.6240.0080.633
annotateGeneSetMembership3.0650.1663.266
calculateIndividualLogFC1.6890.0661.770
collectionMetadata0.0530.0010.054
combine-GeneSetDb-GeneSetDb-method0.0620.0010.064
combine-SparrowResult-SparrowResult-method0.1400.0080.151
conform0.8560.0270.890
conversion0.4660.0250.494
convertIdentifiers0.1290.0050.134
corplot0.0690.0040.073
eigenWeightedMean1.5200.0661.594
examples0.2490.0680.321
failWith0.0010.0000.001
featureIdMap0.4110.0270.441
featureIds0.3420.0160.358
geneSet0.0730.0020.076
geneSetCollectionURLfunction0.0710.0070.079
geneSetSummaryByGenes3.4130.0973.530
geneSets0.0490.0020.051
geneSetsStats3.6970.1243.835
getKeggCollection000
getMSigCollection0.0010.0000.000
getPantherCollection000
getReactomeCollection000
goseq6.5890.3027.037
gsdScore0.8200.0430.868
gskey0.0020.0010.004
hasGeneSet0.0450.0010.045
hasGeneSetCollection0.0770.0050.082
incidenceMatrix0.9860.0451.042
iplot1.9580.1852.224
is.active0.2970.0510.351
logFC2.7560.1132.890
mgheatmap000
mgheatmap2000
msg0.0010.0010.001
ora1.1390.0311.174
p.matrix0.0740.0020.076
randomGeneSetDb0.0600.0060.067
renameCollections0.0580.0070.065
renameRows0.2920.0120.304
results0.0840.0040.088
scale_rows0.0050.0010.005
scoreSingleSamples3.0190.4173.488
seas4.1470.1434.315
sparrow_methods0.0030.0020.004
species_info0.0040.0020.010
subset.GeneSetDb0.1010.0180.121
subsetByFeatures0.0530.0010.054
validateInputs0.1120.0200.133
volcanoPlot1.6540.1421.843
volcanoStatsTable0.0580.0020.061
zScore0.7090.0370.750