| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-06 11:45 -0400 (Sat, 06 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4643 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3833 |
| 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 1971/2243 | 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 | |||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | NA | OK | ERROR | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: sparrow |
| Version: 1.11.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --no-vignettes --timings sparrow_1.11.0.tar.gz |
| StartedAt: 2024-07-06 08:39:49 -0000 (Sat, 06 Jul 2024) |
| EndedAt: 2024-07-06 08:52:40 -0000 (Sat, 06 Jul 2024) |
| EllapsedTime: 770.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: sparrow.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --no-vignettes --timings sparrow_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/sparrow.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
R 1.0Mb
doc 1.8Mb
extdata 2.1Mb
* 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
goseq 10.462 0.167 10.383
seas 6.860 0.128 6.782
scoreSingleSamples 6.712 0.203 6.909
SparrowResult-utilities 5.597 0.191 5.531
annotateGeneSetMembership 5.629 0.137 5.515
geneSetsStats 5.603 0.056 5.183
* 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 1496 ]
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, 4 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/sparrow.Rcheck/00check.log’
for details.
sparrow.Rcheck/00install.out
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 3 | WARN 0 | SKIP 1 | PASS 1496 ]
══ 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 1496 ]
Error: Test failures
Execution halted
sparrow.Rcheck/sparrow-Ex.timings
| name | user | system | elapsed | |
| GeneSetDb-class | 0.255 | 0.004 | 0.259 | |
| SparrowResult-utilities | 5.597 | 0.191 | 5.531 | |
| addGeneSetMetadata | 0.089 | 0.000 | 0.080 | |
| annotateGeneSetMembership | 5.629 | 0.137 | 5.515 | |
| calculateIndividualLogFC | 2.391 | 0.028 | 2.424 | |
| collectionMetadata | 0.106 | 0.000 | 0.096 | |
| combine-GeneSetDb-GeneSetDb-method | 0.125 | 0.004 | 0.111 | |
| combine-SparrowResult-SparrowResult-method | 0.131 | 0.000 | 0.131 | |
| conform | 0.594 | 0.008 | 0.594 | |
| conversion | 0.842 | 0.028 | 0.839 | |
| convertIdentifiers | 0.238 | 0.004 | 0.214 | |
| corplot | 0.112 | 0.000 | 0.112 | |
| eigenWeightedMean | 4.188 | 0.088 | 4.271 | |
| examples | 0.426 | 0.024 | 0.450 | |
| failWith | 0 | 0 | 0 | |
| featureIdMap | 0.576 | 0.008 | 0.576 | |
| featureIds | 0.618 | 0.008 | 0.612 | |
| geneSet | 0.111 | 0.000 | 0.102 | |
| geneSetCollectionURLfunction | 0.079 | 0.000 | 0.071 | |
| geneSetSummaryByGenes | 4.509 | 0.075 | 4.283 | |
| geneSets | 0.107 | 0.000 | 0.098 | |
| geneSetsStats | 5.603 | 0.056 | 5.183 | |
| getKeggCollection | 0 | 0 | 0 | |
| getMSigCollection | 0.001 | 0.000 | 0.001 | |
| getPantherCollection | 0 | 0 | 0 | |
| getReactomeCollection | 0.001 | 0.000 | 0.000 | |
| goseq | 10.462 | 0.167 | 10.383 | |
| gsdScore | 1.294 | 0.024 | 1.306 | |
| gskey | 0.003 | 0.000 | 0.003 | |
| hasGeneSet | 0.079 | 0.000 | 0.071 | |
| hasGeneSetCollection | 0.075 | 0.004 | 0.070 | |
| incidenceMatrix | 1.478 | 0.004 | 1.477 | |
| iplot | 2.595 | 0.060 | 2.648 | |
| is.active | 0.434 | 0.040 | 0.466 | |
| logFC | 4.011 | 0.087 | 3.849 | |
| mgheatmap | 0 | 0 | 0 | |
| mgheatmap2 | 0 | 0 | 0 | |
| msg | 0.001 | 0.000 | 0.001 | |
| ora | 0.247 | 0.028 | 0.275 | |
| p.matrix | 0.089 | 0.008 | 0.097 | |
| randomGeneSetDb | 0.104 | 0.000 | 0.104 | |
| renameCollections | 0.098 | 0.005 | 0.093 | |
| renameRows | 0.522 | 0.016 | 0.539 | |
| results | 0.116 | 0.000 | 0.116 | |
| scale_rows | 0.004 | 0.000 | 0.004 | |
| scoreSingleSamples | 6.712 | 0.203 | 6.909 | |
| seas | 6.860 | 0.128 | 6.782 | |
| sparrow_methods | 0.000 | 0.003 | 0.004 | |
| species_info | 0.006 | 0.000 | 0.006 | |
| subset.GeneSetDb | 0.087 | 0.000 | 0.079 | |
| subsetByFeatures | 0.106 | 0.000 | 0.094 | |
| validateInputs | 0.229 | 0.003 | 0.226 | |
| volcanoPlot | 2.365 | 0.032 | 2.402 | |
| volcanoStatsTable | 0.073 | 0.000 | 0.073 | |
| zScore | 1.173 | 0.004 | 1.166 | |