Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-11-29 11:07:04 -0500 (Tue, 29 Nov 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4503
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4277
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4309
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 1919/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sparrow 1.4.0  (landing page)
Steve Lianoglou
Snapshot Date: 2022-11-28 14:00:06 -0500 (Mon, 28 Nov 2022)
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: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings sparrow_1.4.0.tar.gz
StartedAt: 2022-11-28 23:50:41 -0500 (Mon, 28 Nov 2022)
EndedAt: 2022-11-29 00:03:10 -0500 (Tue, 29 Nov 2022)
EllapsedTime: 748.6 seconds
RetCode: 0
Status:   OK  
CheckDir: sparrow.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings sparrow_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/sparrow.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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         8.196  0.216   7.510
geneSetsStats 6.113  0.080   4.530
seas          5.531  0.108   4.709
* 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-3.16-bioc/meat/sparrow.Rcheck/00check.log’
for details.



Installation output

sparrow.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL sparrow
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-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 4.2.2 (2022-10-31) -- "Innocent and Trusting"
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

[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 
386.030  34.574 332.767 

Example timings

sparrow.Rcheck/sparrow-Ex.timings

nameusersystemelapsed
GeneSetDb-class0.1240.0000.097
SparrowResult-utilities4.5390.1163.809
addGeneSetMetadata0.8390.0320.837
annotateGeneSetMembership4.5790.1043.800
calculateIndividualLogFC2.5460.1442.690
collectionMetadata0.1050.0000.077
combine-GeneSetDb-GeneSetDb-method0.1360.0000.087
combine-SparrowResult-SparrowResult-method0.1310.0120.136
conform0.4250.0080.409
conversion0.7190.0200.616
convertIdentifiers0.3010.0000.201
corplot0.0990.0000.100
eigenWeightedMean1.8250.0201.795
examples0.2900.0320.321
failWith0.0010.0000.001
featureIdMap1.1710.0721.218
featureIds0.4300.0000.394
geneSet0.1190.0000.087
geneSetCollectionURLfunction0.0760.0000.052
geneSetSummaryByGenes4.0920.1313.230
geneSets0.0810.0000.052
geneSetsStats6.1130.0804.530
getKeggCollection000
getMSigCollection000
getPantherCollection000
getReactomeCollection000
goseq8.1960.2167.510
gsdScore0.9240.0160.891
gskey0.0020.0000.003
hasGeneSet0.0770.0000.053
hasGeneSetCollection0.0720.0000.052
incidenceMatrix1.0830.0161.073
iplot2.1580.0842.196
is.active0.3270.0200.322
logFC3.8750.0973.087
mgheatmap0.0040.0000.000
mgheatmap2000
msg000
ora0.2390.0070.234
p.matrix0.0820.0000.082
randomGeneSetDb0.0730.0080.076
renameCollections0.1170.0000.075
renameRows0.4240.0080.429
results0.0910.0000.091
scale_rows0.0040.0000.004
scoreSingleSamples4.7040.2284.820
seas5.5310.1084.709
sparrow_methods0.0000.0030.003
species_info0.0050.0010.006
subset.GeneSetDb0.0850.0000.060
subsetByFeatures0.1140.0000.070
validateInputs0.1360.0000.106
volcanoPlot1.7940.0681.863
volcanoStatsTable0.0670.0000.068
zScore0.9250.0150.890