| Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:45 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 2024/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| sparrow 1.10.1 (landing page) Steve Lianoglou
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
|
To the developers/maintainers of the sparrow package: - 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: 1.10.1 |
| 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_1.10.1.tar.gz |
| StartedAt: 2024-05-07 01:07:28 -0400 (Tue, 07 May 2024) |
| EndedAt: 2024-05-07 01:10:44 -0400 (Tue, 07 May 2024) |
| EllapsedTime: 196.1 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_1.10.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/sparrow.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sparrow/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sparrow’ version ‘1.10.1’
* 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 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
* 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 1476 ]
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-3.19-bioc-mac-arm64/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-arm64/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 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 1476 ]
══ 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 1476 ]
Error: Test failures
Execution halted
sparrow.Rcheck/sparrow-Ex.timings
| name | user | system | elapsed | |
| GeneSetDb-class | 0.024 | 0.001 | 0.027 | |
| SparrowResult-utilities | 1.054 | 0.034 | 1.089 | |
| addGeneSetMetadata | 0.027 | 0.002 | 0.029 | |
| annotateGeneSetMembership | 1.199 | 0.046 | 1.250 | |
| calculateIndividualLogFC | 0.468 | 0.020 | 0.488 | |
| collectionMetadata | 0.022 | 0.001 | 0.023 | |
| combine-GeneSetDb-GeneSetDb-method | 0.287 | 0.006 | 0.292 | |
| combine-SparrowResult-SparrowResult-method | 0.048 | 0.002 | 0.052 | |
| conform | 0.134 | 0.007 | 0.143 | |
| conversion | 0.181 | 0.008 | 0.189 | |
| convertIdentifiers | 0.054 | 0.005 | 0.059 | |
| corplot | 0.025 | 0.001 | 0.026 | |
| eigenWeightedMean | 0.937 | 0.025 | 0.965 | |
| examples | 0.111 | 0.024 | 0.134 | |
| failWith | 0.000 | 0.000 | 0.001 | |
| featureIdMap | 0.150 | 0.006 | 0.156 | |
| featureIds | 0.147 | 0.005 | 0.152 | |
| geneSet | 0.031 | 0.002 | 0.033 | |
| geneSetCollectionURLfunction | 0.019 | 0.000 | 0.020 | |
| geneSetSummaryByGenes | 1.192 | 0.024 | 1.220 | |
| geneSets | 0.018 | 0.001 | 0.019 | |
| geneSetsStats | 1.361 | 0.036 | 1.399 | |
| getKeggCollection | 0 | 0 | 0 | |
| getMSigCollection | 0 | 0 | 0 | |
| getPantherCollection | 0 | 0 | 0 | |
| getReactomeCollection | 0 | 0 | 0 | |
| goseq | 1.871 | 0.107 | 1.983 | |
| gsdScore | 0.351 | 0.009 | 0.360 | |
| gskey | 0.001 | 0.001 | 0.001 | |
| hasGeneSet | 0.017 | 0.000 | 0.017 | |
| hasGeneSetCollection | 0.031 | 0.003 | 0.034 | |
| incidenceMatrix | 0.285 | 0.012 | 0.297 | |
| iplot | 0.361 | 0.026 | 0.389 | |
| is.active | 0.105 | 0.012 | 0.117 | |
| logFC | 0.778 | 0.022 | 0.800 | |
| mgheatmap | 0 | 0 | 0 | |
| mgheatmap2 | 0 | 0 | 0 | |
| msg | 0 | 0 | 0 | |
| ora | 0.491 | 0.006 | 0.497 | |
| p.matrix | 0.030 | 0.001 | 0.031 | |
| randomGeneSetDb | 0.022 | 0.002 | 0.024 | |
| renameCollections | 0.022 | 0.001 | 0.023 | |
| renameRows | 0.126 | 0.005 | 0.131 | |
| results | 0.035 | 0.002 | 0.038 | |
| scale_rows | 0.001 | 0.001 | 0.002 | |
| scoreSingleSamples | 1.217 | 0.106 | 1.323 | |
| seas | 1.423 | 0.069 | 1.491 | |
| sparrow_methods | 0.001 | 0.000 | 0.001 | |
| species_info | 0.002 | 0.001 | 0.002 | |
| subset.GeneSetDb | 0.019 | 0.001 | 0.020 | |
| subsetByFeatures | 0.022 | 0.001 | 0.022 | |
| validateInputs | 0.038 | 0.003 | 0.040 | |
| volcanoPlot | 1.217 | 0.046 | 1.262 | |
| volcanoStatsTable | 0.029 | 0.001 | 0.030 | |
| zScore | 0.247 | 0.010 | 0.257 | |