Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2022-04-13 12:05:59 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 nebbiolo2


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 1839/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sparrow 1.0.3  (landing page)
Steve Lianoglou
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/sparrow
git_branch: RELEASE_3_14
git_last_commit: 7cde579
git_last_commit_date: 2022-03-23 14:09:29 -0400 (Wed, 23 Mar 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: sparrow
Version: 1.0.3
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings sparrow_1.0.3.tar.gz
StartedAt: 2022-04-12 09:28:23 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 09:37:22 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 539.6 seconds
RetCode: 0
Status:   OK  
CheckDir: sparrow.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings sparrow_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/sparrow.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.0.3’
* 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                     7.567  0.228   6.885
seas                      5.493  0.144   4.718
geneSetsStats             5.512  0.108   3.916
SparrowResult-utilities   5.313  0.180   4.596
annotateGeneSetMembership 5.073  0.152   4.370
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/sparrow.Rcheck/00check.log’
for details.



Installation output

sparrow.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL sparrow
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1479 ]

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

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 1479 ]
> 
> ## 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 
354.692  20.233 319.319 

Example timings

sparrow.Rcheck/sparrow-Ex.timings

nameusersystemelapsed
GeneSetDb-class0.0920.0040.070
SparrowResult-utilities5.3130.1804.596
addGeneSetMetadata0.0840.0000.060
annotateGeneSetMembership5.0730.1524.370
calculateIndividualLogFC1.7210.0601.781
collectionMetadata0.0960.0040.073
combine-GeneSetDb-GeneSetDb-method0.1740.0000.125
combine-SparrowResult-SparrowResult-method0.1200.0080.124
conform0.4350.0200.428
conversion0.6640.0040.554
convertIdentifiers0.2420.0000.147
corplot0.0870.0000.087
eigenWeightedMean1.7440.0601.754
examples0.2720.0120.284
failWith000
featureIdMap0.3980.0040.376
featureIds0.4380.0000.400
geneSet0.1050.0000.071
geneSetCollectionURLfunction0.0760.0000.052
geneSetSummaryByGenes4.7640.1463.939
geneSets0.0740.0000.048
geneSetsStats5.5120.1083.916
getKeggCollection000
getMSigCollection000
getPantherCollection000
getReactomeCollection000
goseq7.5670.2286.885
gsdScore0.8830.0040.839
gskey0.0020.0000.002
hasGeneSet0.0740.0000.051
hasGeneSetCollection0.0680.0000.048
incidenceMatrix1.9830.0361.995
iplot0.9490.0320.928
is.active0.3460.0080.330
logFC3.7870.0522.962
mgheatmap000
mgheatmap2000
msg0.0010.0000.000
ora0.2540.0080.252
p.matrix0.0780.0040.082
randomGeneSetDb0.1580.0040.159
renameCollections0.1070.0000.069
renameRows0.3270.0120.333
results0.1010.0000.101
scale_rows0.0030.0000.003
scoreSingleSamples4.7510.1084.756
seas5.4930.1444.718
sparrow_methods0.0030.0000.002
species_info0.0040.0000.005
subset.GeneSetDb0.0870.0040.064
subsetByFeatures0.1240.0040.078
validateInputs0.1620.0120.147
volcanoPlot1.6860.0401.725
volcanoStatsTable0.0590.0040.063
zScore0.8870.0320.868