| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 1968/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sparrow 1.11.0 (landing page) Steve Lianoglou
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
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. |
| Package: sparrow |
| Version: 1.11.0 |
| 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_1.11.0.tar.gz |
| StartedAt: 2024-06-10 10:24:36 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 10:46:18 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 1302.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: sparrow.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sparrow.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sparrow/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sparrow’ version ‘1.11.0’
* 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 ... 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 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 ... NOTE
checkRd: (-1) convertIdentifiers.Rd:118: Lost braces; missing escapes or markup?
118 | rely on the {babelgene} package for the conversion, so you will have to
| ^
* 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 14.429 0.492 17.097
seas 12.791 0.539 14.821
scoreSingleSamples 10.271 0.391 11.851
annotateGeneSetMembership 8.317 0.140 9.516
SparrowResult-utilities 7.936 0.283 9.510
geneSetsStats 8.046 0.115 9.174
geneSetSummaryByGenes 6.984 0.278 8.262
logFC 6.729 0.192 8.055
eigenWeightedMean 6.434 0.119 7.355
volcanoPlot 5.297 0.227 6.079
calculateIndividualLogFC 4.590 0.069 5.259
* 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:
GSVA::plage
── Failure ('test-scoreSingleSamples.R:27:5'): do.scoreSingleSamples.gsva produces correct gsva,plage,ssGSEA scores ──
`res` not equal to `ex`.
Attributes: < Component "geneSets": Component "c2;;HUPER_BREAST_BASAL_VS_LUMINAL_UP": 33 string mismatches >
Attributes: < Component "geneSets": Component "c6;;CYCLIN_D1_UP.V1_DN": 108 string mismatches >
Attributes: < Component "geneSets": Component "c6;;KRAS.600.LUNG.BREAST_UP.V1_UP": 146 string mismatches >
Attributes: < Component "geneSets": Component "c6;;KRAS.BREAST_UP.V1_UP": 56 string mismatches >
Attributes: < Component "geneSets": Component "c6;;KRAS.LUNG.BREAST_UP.V1_UP": 73 string mismatches >
Attributes: < Component "geneSets": Component "c7;;GSE37416_CTRL_VS_0H_F_TULARENSIS_LVS_NEUTROPHIL_DN": 59 string mismatches >
Attributes: < Component "geneSets": Component "c7;;GSE3982_BCELL_VS_TH2_DN": 50 string mismatches >
GSVA::ssgsea
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 1504 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/sparrow.Rcheck/00check.log’
for details.
sparrow.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sparrow ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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)
sparrow.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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 3 | WARN 0 | SKIP 1 | PASS 1504 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-MultiGSEAResult.R:3:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-scoreSingleSamples.R:27:5'): do.scoreSingleSamples.gsva produces correct gsva,plage,ssGSEA scores ──
`res` not equal to `ex`.
Attributes: < Component "geneSets": Component "c2;;HUPER_BREAST_BASAL_VS_LUMINAL_UP": 33 string mismatches >
Attributes: < Component "geneSets": Component "c6;;CYCLIN_D1_UP.V1_DN": 108 string mismatches >
Attributes: < Component "geneSets": Component "c6;;KRAS.600.LUNG.BREAST_UP.V1_UP": 146 string mismatches >
Attributes: < Component "geneSets": Component "c6;;KRAS.BREAST_UP.V1_UP": 56 string mismatches >
Attributes: < Component "geneSets": Component "c6;;KRAS.LUNG.BREAST_UP.V1_UP": 73 string mismatches >
Attributes: < Component "geneSets": Component "c7;;GSE37416_CTRL_VS_0H_F_TULARENSIS_LVS_NEUTROPHIL_DN": 59 string mismatches >
Attributes: < Component "geneSets": Component "c7;;GSE3982_BCELL_VS_TH2_DN": 50 string mismatches >
GSVA::gsva
── Failure ('test-scoreSingleSamples.R:27:5'): do.scoreSingleSamples.gsva produces correct gsva,plage,ssGSEA scores ──
`res` not equal to `ex`.
Attributes: < Component "geneSets": Component "c2;;HUPER_BREAST_BASAL_VS_LUMINAL_UP": 33 string mismatches >
Attributes: < Component "geneSets": Component "c6;;CYCLIN_D1_UP.V1_DN": 108 string mismatches >
Attributes: < Component "geneSets": Component "c6;;KRAS.600.LUNG.BREAST_UP.V1_UP": 146 string mismatches >
Attributes: < Component "geneSets": Component "c6;;KRAS.BREAST_UP.V1_UP": 56 string mismatches >
Attributes: < Component "geneSets": Component "c6;;KRAS.LUNG.BREAST_UP.V1_UP": 73 string mismatches >
Attributes: < Component "geneSets": Component "c7;;GSE37416_CTRL_VS_0H_F_TULARENSIS_LVS_NEUTROPHIL_DN": 59 string mismatches >
Attributes: < Component "geneSets": Component "c7;;GSE3982_BCELL_VS_TH2_DN": 50 string mismatches >
GSVA::plage
── Failure ('test-scoreSingleSamples.R:27:5'): do.scoreSingleSamples.gsva produces correct gsva,plage,ssGSEA scores ──
`res` not equal to `ex`.
Attributes: < Component "geneSets": Component "c2;;HUPER_BREAST_BASAL_VS_LUMINAL_UP": 33 string mismatches >
Attributes: < Component "geneSets": Component "c6;;CYCLIN_D1_UP.V1_DN": 108 string mismatches >
Attributes: < Component "geneSets": Component "c6;;KRAS.600.LUNG.BREAST_UP.V1_UP": 146 string mismatches >
Attributes: < Component "geneSets": Component "c6;;KRAS.BREAST_UP.V1_UP": 56 string mismatches >
Attributes: < Component "geneSets": Component "c6;;KRAS.LUNG.BREAST_UP.V1_UP": 73 string mismatches >
Attributes: < Component "geneSets": Component "c7;;GSE37416_CTRL_VS_0H_F_TULARENSIS_LVS_NEUTROPHIL_DN": 59 string mismatches >
Attributes: < Component "geneSets": Component "c7;;GSE3982_BCELL_VS_TH2_DN": 50 string mismatches >
GSVA::ssgsea
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 1504 ]
Error: Test failures
Execution halted
sparrow.Rcheck/sparrow-Ex.timings
| name | user | system | elapsed | |
| GeneSetDb-class | 0.308 | 0.009 | 0.368 | |
| SparrowResult-utilities | 7.936 | 0.283 | 9.510 | |
| addGeneSetMetadata | 0.124 | 0.002 | 0.145 | |
| annotateGeneSetMembership | 8.317 | 0.140 | 9.516 | |
| calculateIndividualLogFC | 4.590 | 0.069 | 5.259 | |
| collectionMetadata | 0.145 | 0.006 | 0.167 | |
| combine-GeneSetDb-GeneSetDb-method | 0.161 | 0.003 | 0.190 | |
| combine-SparrowResult-SparrowResult-method | 0.208 | 0.007 | 0.244 | |
| conform | 0.835 | 0.022 | 0.962 | |
| conversion | 1.183 | 0.037 | 1.366 | |
| convertIdentifiers | 0.327 | 0.006 | 0.389 | |
| corplot | 0.168 | 0.008 | 0.194 | |
| eigenWeightedMean | 6.434 | 0.119 | 7.355 | |
| examples | 0.635 | 0.206 | 0.996 | |
| failWith | 0.001 | 0.001 | 0.001 | |
| featureIdMap | 0.802 | 0.014 | 0.871 | |
| featureIds | 0.872 | 0.035 | 1.019 | |
| geneSet | 0.167 | 0.006 | 0.198 | |
| geneSetCollectionURLfunction | 0.116 | 0.003 | 0.133 | |
| geneSetSummaryByGenes | 6.984 | 0.278 | 8.262 | |
| geneSets | 0.109 | 0.002 | 0.123 | |
| geneSetsStats | 8.046 | 0.115 | 9.174 | |
| getKeggCollection | 0 | 0 | 0 | |
| getMSigCollection | 0.000 | 0.000 | 0.001 | |
| getPantherCollection | 0 | 0 | 0 | |
| getReactomeCollection | 0 | 0 | 0 | |
| goseq | 14.429 | 0.492 | 17.097 | |
| gsdScore | 1.890 | 0.057 | 2.207 | |
| gskey | 0.005 | 0.001 | 0.006 | |
| hasGeneSet | 1.231 | 0.022 | 1.452 | |
| hasGeneSetCollection | 0.113 | 0.003 | 0.134 | |
| incidenceMatrix | 2.266 | 0.046 | 2.624 | |
| iplot | 2.428 | 0.239 | 3.031 | |
| is.active | 0.747 | 0.094 | 0.958 | |
| logFC | 6.729 | 0.192 | 8.055 | |
| mgheatmap | 0.001 | 0.001 | 0.001 | |
| mgheatmap2 | 0 | 0 | 0 | |
| msg | 0.000 | 0.001 | 0.002 | |
| ora | 0.520 | 0.025 | 0.595 | |
| p.matrix | 0.154 | 0.003 | 0.170 | |
| randomGeneSetDb | 0.153 | 0.012 | 0.181 | |
| renameCollections | 0.143 | 0.003 | 0.158 | |
| renameRows | 0.695 | 0.011 | 0.765 | |
| results | 0.202 | 0.011 | 0.230 | |
| scale_rows | 0.008 | 0.001 | 0.011 | |
| scoreSingleSamples | 10.271 | 0.391 | 11.851 | |
| seas | 12.791 | 0.539 | 14.821 | |
| sparrow_methods | 0.006 | 0.003 | 0.011 | |
| species_info | 0.012 | 0.005 | 0.024 | |
| subset.GeneSetDb | 0.129 | 0.005 | 0.145 | |
| subsetByFeatures | 0.149 | 0.006 | 0.166 | |
| validateInputs | 0.299 | 0.018 | 0.355 | |
| volcanoPlot | 5.297 | 0.227 | 6.079 | |
| volcanoStatsTable | 0.123 | 0.004 | 0.146 | |
| zScore | 1.754 | 0.037 | 1.958 | |