Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:08:39 -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 machv2


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: /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_1.0.2.tar.gz
StartedAt: 2022-01-13 18:22:40 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 18:39:12 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 991.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: sparrow.Rcheck
Warnings: NA

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


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/sparrow.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.0.2’
* 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                      14.111  4.166  12.049
goseq                     12.235  0.269  12.517
SparrowResult-utilities    7.688  0.219   7.915
scoreSingleSamples         6.926  0.430   7.361
geneSetsStats              6.777  0.047   6.828
annotateGeneSetMembership  6.561  0.112   6.676
geneSetSummaryByGenes      6.241  0.109   6.355
logFC                      5.967  0.106   6.078
* 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:
  71/76 mismatches (average diff: 0.0282)
  [1] 0.0996 - 0.1036 == -0.00398
  [2] 0.0717 - 0.0398 ==  0.03187
  [3] 0.1833 - 0.1673 ==  0.01594
  [4] 0.8446 - 0.8008 ==  0.04382
  [5] 0.8725 - 0.8486 ==  0.02390
  [6] 0.3267 - 0.3028 ==  0.02390
  [7] 0.7371 - 0.7092 ==  0.02789
  [8] 0.1673 - 0.1793 == -0.01195
  [9] 0.3546 - 0.3307 ==  0.02390
  ...
  
  [ FAIL 10 | WARN 0 | SKIP 1 | PASS 1473 ]
  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
  ‘/Users/biocbuild/bbs-3.14-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/4.1/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.fail


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

══ 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: 0.0141)
[1] -1.56 - -1.584 ==  0.02463
[2] -2.09 - -2.107 ==  0.01950
[3] -1.77 - -1.797 ==  0.02338
[4] -1.01 - -1.023 ==  0.01029
[5]  1.52 -  1.536 == -0.01823
[6] -1.86 - -1.880 ==  0.02241
[7]  0.64 -  0.658 == -0.01779
[8] -1.58 - -1.592 ==  0.01462
[9] -1.22 - -1.221 == -0.00286
...
── Failure (test-fgsea.R:64:3): seas calculate t and preranked t match fgsea results ──
mgres$pval not equal to rest$pval.
70/76 mismatches (average diff: 0.00978)
[1] 0.028626 - 0.030758 == -2.13e-03
[2] 0.000013 - 0.000017 == -3.96e-06
[3] 0.002125 - 0.001563 ==  5.62e-04
[4] 0.457746 - 0.446337 ==  1.14e-02
[5] 0.030975 - 0.034707 == -3.73e-03
[6] 0.000654 - 0.000284 ==  3.69e-04
[7] 0.910486 - 0.905612 ==  4.87e-03
[8] 0.025518 - 0.031313 == -5.80e-03
[9] 0.026289 - 0.030488 == -4.20e-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: 0.07198068
── 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: 0.07007989
── Failure (test-romer.R:44:3): romer runs equivalently from do.romer vs direct call ──
res$pval.up not equal to expected[, "Up"].
72/76 mismatches (average diff: 0.0237)
[2]  0.972 - 0.960 ==  0.01195
[3]  0.849 - 0.888 == -0.03984
[4]  0.801 - 0.825 == -0.02390
[5]  0.279 - 0.259 ==  0.01992
[6]  0.873 - 0.892 == -0.01992
[7]  0.390 - 0.490 == -0.09960
[8]  0.960 - 0.964 == -0.00398
[9]  0.566 - 0.562 ==  0.00398
[10] 0.996 - 0.980 ==  0.01594
...
── Failure (test-romer.R:45:3): romer runs equivalently from do.romer vs direct call ──
res$pval.down not equal to expected[, "Down"].
72/76 mismatches (average diff: 0.0238)
[2]  0.03187 - 0.0438 == -0.01195
[3]  0.15538 - 0.1155 ==  0.03984
[4]  0.20319 - 0.1793 ==  0.02390
[5]  0.72510 - 0.7450 == -0.01992
[6]  0.13147 - 0.1116 ==  0.01992
[7]  0.61355 - 0.5139 ==  0.09960
[8]  0.04382 - 0.0398 ==  0.00398
[9]  0.43825 - 0.4422 == -0.00398
[10] 0.00797 - 0.0239 == -0.01594
...
── Failure (test-romer.R:46:3): romer runs equivalently from do.romer vs direct call ──
res$pval not equal to expected[, "Mixed"].
71/76 mismatches (average diff: 0.0282)
[1] 0.0996 - 0.1036 == -0.00398
[2] 0.0717 - 0.0398 ==  0.03187
[3] 0.1833 - 0.1673 ==  0.01594
[4] 0.8446 - 0.8008 ==  0.04382
[5] 0.8725 - 0.8486 ==  0.02390
[6] 0.3267 - 0.3028 ==  0.02390
[7] 0.7371 - 0.7092 ==  0.02789
[8] 0.1673 - 0.1793 == -0.01195
[9] 0.3546 - 0.3307 ==  0.02390
...

[ FAIL 10 | WARN 0 | SKIP 1 | PASS 1473 ]
Error: Test failures
Execution halted

Example timings

sparrow.Rcheck/sparrow-Ex.timings

nameusersystemelapsed
GeneSetDb-class0.1150.0070.123
SparrowResult-utilities7.6880.2197.915
addGeneSetMetadata0.1350.0030.138
annotateGeneSetMembership6.5610.1126.676
calculateIndividualLogFC4.7690.0524.825
collectionMetadata0.1160.0010.117
combine-GeneSetDb-GeneSetDb-method0.1340.0030.137
combine-SparrowResult-SparrowResult-method0.2120.0060.219
conform0.7010.0200.721
conversion1.4620.0291.492
convertIdentifiers0.2640.0030.268
corplot0.1230.0040.127
eigenWeightedMean2.9970.0633.062
examples0.4890.1040.593
failWith0.0000.0000.001
featureIdMap0.6470.0250.672
featureIds0.6830.0250.709
geneSet0.1080.0050.112
geneSetCollectionURLfunction0.0960.0020.098
geneSetSummaryByGenes6.2410.1096.355
geneSets0.0910.0020.092
geneSetsStats6.7770.0476.828
getKeggCollection000
getMSigCollection0.0000.0010.000
getPantherCollection000
getReactomeCollection0.0000.0000.001
goseq12.235 0.26912.517
gsdScore1.5080.0351.543
gskey0.0040.0010.005
hasGeneSet0.0950.0020.098
hasGeneSetCollection0.0830.0010.083
incidenceMatrix2.7030.0472.754
iplot1.4340.1461.588
is.active0.5600.0350.597
logFC5.9670.1066.078
mgheatmap000
mgheatmap2000
msg0.0000.0000.001
ora0.3620.0130.376
p.matrix0.1490.0010.151
randomGeneSetDb0.1570.0080.166
renameCollections0.1150.0010.115
renameRows0.5730.0160.588
results0.1870.0070.194
scale_rows0.0060.0010.007
scoreSingleSamples6.9260.4307.361
seas14.111 4.16612.049
sparrow_methods0.0040.0020.007
species_info0.0060.0020.009
subset.GeneSetDb0.0680.0040.072
subsetByFeatures1.3040.2551.560
validateInputs0.1830.0090.193
volcanoPlot3.0460.2083.257
volcanoStatsTable0.1110.0030.115
zScore1.4830.0711.555