Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:05:48 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 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? here 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 1.0.2  (landing page)
Steve Lianoglou
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/sparrow
git_branch: RELEASE_3_14
git_last_commit: 3329966
git_last_commit_date: 2022-01-05 17:20:42 -0500 (Wed, 05 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: sparrow
Version: 1.0.2
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_1.0.2.tar.gz
StartedAt: 2022-01-13 09:43:18 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 09:52:35 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 556.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: sparrow.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### 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_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/sparrow.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.0.2’
* 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
seas                    7.135  1.417   6.101
goseq                   8.163  0.312   7.573
geneSetsStats           6.296  0.122   4.733
SparrowResult-utilities 5.728  0.210   5.115
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  73/76 mismatches (average diff: 0.0288)
  [1] 0.0996 - 0.1036 == -0.00398
  [2] 0.0637 - 0.0398 ==  0.02390
  [3] 0.2032 - 0.1673 ==  0.03586
  [4] 0.8446 - 0.8008 ==  0.04382
  [5] 0.8884 - 0.8486 ==  0.03984
  [6] 0.2749 - 0.3028 == -0.02789
  [7] 0.7052 - 0.7092 == -0.00398
  [8] 0.1952 - 0.1793 ==  0.01594
  [9] 0.3426 - 0.3307 ==  0.01195
  ...
  
  [ FAIL 10 | WARN 0 | SKIP 1 | PASS 1485 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 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.fail


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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

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

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-fgsea.R:16:3): seas calculate t and preranked t match fgsea results ──
`{ ... }` did not produce any warnings.
── Failure (test-fgsea.R:63:3): seas calculate t and preranked t match fgsea results ──
mgres$NES not equal to rest$NES.
76/76 mismatches (average diff: 0.02)
[1] -1.582 - -1.584 ==  0.002245
[2] -2.076 - -2.107 ==  0.030225
[3] -1.751 - -1.797 ==  0.046604
[4] -1.018 - -1.023 ==  0.005185
[5]  1.537 -  1.536 ==  0.000518
[6] -1.845 - -1.880 ==  0.034444
[7]  0.653 -  0.658 == -0.004513
[8] -1.570 - -1.592 ==  0.022086
[9] -1.222 - -1.221 == -0.001217
...
── Failure (test-fgsea.R:64:3): seas calculate t and preranked t match fgsea results ──
mgres$pval not equal to rest$pval.
71/76 mismatches (average diff: 0.0116)
[1] 4.26e-02 - 0.030758 ==  1.18e-02
[2] 1.07e-05 - 0.000017 == -6.27e-06
[3] 2.15e-03 - 0.001563 ==  5.82e-04
[4] 4.57e-01 - 0.446337 ==  1.07e-02
[5] 2.66e-02 - 0.034707 == -8.13e-03
[6] 4.84e-04 - 0.000284 ==  1.99e-04
[7] 9.13e-01 - 0.905612 ==  7.43e-03
[8] 2.99e-02 - 0.031313 == -1.38e-03
[9] 2.85e-02 - 0.030488 == -1.97e-03
...
── Failure (test-fgsea.R:67:3): seas calculate t and preranked t match fgsea results ──
`{ ... }` did not produce any warnings.
── Failure (test-fgsea.R:75:3): seas calculate t and preranked t match fgsea results ──
rpre[, comp.cols] not equal to mgres[, comp.cols].
Component "pval": Mean relative difference: 0.04540071
── Failure (test-fgsea.R:78:3): seas calculate t and preranked t match fgsea results ──
`{ ... }` did not produce any warnings.
── Failure (test-fgsea.R:85:3): seas calculate t and preranked t match fgsea results ──
res.df[, comp.cols] not equal to mgres[, comp.cols].
Component "pval": Mean relative difference: 0.06233509
── Failure (test-romer.R:44:3): romer runs equivalently from do.romer vs direct call ──
res$pval.up not equal to expected[, "Up"].
69/76 mismatches (average diff: 0.02)
[1]  0.988 - 0.996 == -0.00797
[2]  0.980 - 0.960 ==  0.01992
[3]  0.884 - 0.888 == -0.00398
[4]  0.837 - 0.825 ==  0.01195
[5]  0.267 - 0.259 ==  0.00797
[6]  0.932 - 0.892 ==  0.03984
[7]  0.482 - 0.490 == -0.00797
[9]  0.598 - 0.562 ==  0.03586
[10] 0.992 - 0.980 ==  0.01195
...
── Failure (test-romer.R:45:3): romer runs equivalently from do.romer vs direct call ──
res$pval.down not equal to expected[, "Down"].
69/76 mismatches (average diff: 0.02)
[1]  0.0159 - 0.00797 ==  0.00797
[2]  0.0239 - 0.04382 == -0.01992
[3]  0.1195 - 0.11554 ==  0.00398
[4]  0.1673 - 0.17928 == -0.01195
[5]  0.7371 - 0.74502 == -0.00797
[6]  0.0717 - 0.11155 == -0.03984
[7]  0.5219 - 0.51394 ==  0.00797
[9]  0.4064 - 0.44223 == -0.03586
[10] 0.0120 - 0.02390 == -0.01195
...
── Failure (test-romer.R:46:3): romer runs equivalently from do.romer vs direct call ──
res$pval not equal to expected[, "Mixed"].
73/76 mismatches (average diff: 0.0288)
[1] 0.0996 - 0.1036 == -0.00398
[2] 0.0637 - 0.0398 ==  0.02390
[3] 0.2032 - 0.1673 ==  0.03586
[4] 0.8446 - 0.8008 ==  0.04382
[5] 0.8884 - 0.8486 ==  0.03984
[6] 0.2749 - 0.3028 == -0.02789
[7] 0.7052 - 0.7092 == -0.00398
[8] 0.1952 - 0.1793 ==  0.01594
[9] 0.3426 - 0.3307 ==  0.01195
...

[ FAIL 10 | WARN 0 | SKIP 1 | PASS 1485 ]
Error: Test failures
Execution halted

Example timings

sparrow.Rcheck/sparrow-Ex.timings

nameusersystemelapsed
GeneSetDb-class0.1330.0000.104
SparrowResult-utilities5.7280.2105.115
addGeneSetMetadata0.1210.0040.098
annotateGeneSetMembership4.3650.0753.603
calculateIndividualLogFC2.5330.1602.693
collectionMetadata0.0930.0000.067
combine-GeneSetDb-GeneSetDb-method0.1260.0040.082
combine-SparrowResult-SparrowResult-method0.1170.0120.123
conform0.4210.0080.405
conversion0.6990.0000.591
convertIdentifiers0.2810.0080.191
corplot0.0890.0000.089
eigenWeightedMean2.4520.0602.460
examples0.2520.0200.272
failWith000
featureIdMap0.4060.0000.380
featureIds0.4290.0040.396
geneSet0.1040.0040.076
geneSetCollectionURLfunction0.0830.0000.057
geneSetSummaryByGenes4.1400.0993.250
geneSets0.0920.0000.060
geneSetsStats6.2960.1224.733
getKeggCollection000
getMSigCollection0.0010.0000.000
getPantherCollection000
getReactomeCollection000
goseq8.1630.3127.573
gsdScore1.9830.0441.972
gskey0.0030.0000.002
hasGeneSet0.0800.0000.054
hasGeneSetCollection0.0730.0040.053
incidenceMatrix1.0180.0040.997
iplot1.0040.0240.982
is.active0.3760.0040.354
logFC3.9260.0483.087
mgheatmap000
mgheatmap2000
msg0.0010.0000.001
ora0.3240.0000.319
p.matrix0.0920.0000.092
randomGeneSetDb0.0800.0000.075
renameCollections0.1130.0000.077
renameRows0.3380.0120.345
results0.1350.0040.138
scale_rows0.0060.0000.005
scoreSingleSamples3.6300.0763.603
seas7.1351.4176.101
sparrow_methods0.0000.0030.004
species_info0.0060.0000.006
subset.GeneSetDb0.0940.0040.073
subsetByFeatures0.1290.0080.084
validateInputs0.1860.0160.174
volcanoPlot1.7790.0721.851
volcanoStatsTable0.0640.0000.063
zScore2.3220.1642.434