Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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: 2024-06-12 14:00 -0400 (Wed, 12 Jun 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  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for sparrow on nebbiolo1

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.

raw results


Summary

Package: sparrow
Version: 1.10.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings sparrow_1.10.1.tar.gz
StartedAt: 2024-06-13 03:49:16 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 04:00:37 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 681.3 seconds
RetCode: 0
Status:   OK  
CheckDir: sparrow.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --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 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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              8.131  0.441   7.665
scoreSingleSamples 6.436  0.208   6.531
geneSetsStats      5.239  0.072   3.565
seas               5.101  0.115   4.273
* 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 re-building of vignette outputs ... OK
* 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/bbs-3.19-bioc/R/bin/R CMD INSTALL sparrow
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
319.607  14.415 287.596 

Example timings

sparrow.Rcheck/sparrow-Ex.timings

nameusersystemelapsed
GeneSetDb-class0.2150.0010.200
SparrowResult-utilities4.4750.2043.793
addGeneSetMetadata0.0820.0000.058
annotateGeneSetMembership4.3520.1633.635
calculateIndividualLogFC1.3150.0521.367
collectionMetadata0.0870.0040.066
combine-GeneSetDb-GeneSetDb-method0.1250.0000.079
combine-SparrowResult-SparrowResult-method0.1070.0050.110
conform0.4000.0270.402
conversion0.6600.0040.558
convertIdentifiers0.2520.0040.164
corplot0.0930.0000.093
eigenWeightedMean3.2190.1733.342
examples0.2940.0710.365
failWith0.0010.0000.000
featureIdMap0.3960.0120.384
featureIds0.4320.0320.424
geneSet0.1180.0000.081
geneSetCollectionURLfunction0.0790.0000.055
geneSetSummaryByGenes3.7770.1072.838
geneSets0.0890.0000.057
geneSetsStats5.2390.0723.565
getKeggCollection0.0040.0000.000
getMSigCollection000
getPantherCollection000
getReactomeCollection000
goseq8.1310.4417.665
gsdScore2.0090.0482.002
gskey0.0020.0010.002
hasGeneSet0.0770.0030.054
hasGeneSetCollection0.0730.0000.049
incidenceMatrix0.9640.0000.938
iplot1.1310.0441.120
is.active0.3540.0280.357
logFC3.4540.1092.672
mgheatmap0.0000.0000.001
mgheatmap2000
msg000
ora0.2450.0080.248
p.matrix0.0790.0000.079
randomGeneSetDb0.0780.0000.073
renameCollections0.1060.0000.071
renameRows0.3820.0080.384
results0.0940.0040.098
scale_rows0.0040.0000.004
scoreSingleSamples6.4360.2086.531
seas5.1010.1154.273
sparrow_methods0.0000.0030.004
species_info0.0000.0070.007
subset.GeneSetDb0.0850.0010.060
subsetByFeatures0.1210.0040.072
validateInputs0.1830.0000.159
volcanoPlot1.7130.0201.734
volcanoStatsTable0.0620.0000.063
zScore0.8050.0080.765