Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-31 19:29:28 -0400 (Fri, 31 May 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" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 1963/2233 | 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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings sparrow_1.11.0.tar.gz |
StartedAt: 2024-05-31 08:25:42 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 08:37:27 -0400 (Fri, 31 May 2024) |
EllapsedTime: 704.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: sparrow.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings sparrow_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/sparrow.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed goseq 7.820 0.172 7.072 scoreSingleSamples 5.679 0.172 5.744 seas 5.529 0.140 4.683 geneSetsStats 5.464 0.055 3.760 SparrowResult-utilities 4.866 0.196 4.142 annotateGeneSetMembership 4.872 0.135 4.110 * 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 1480 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/sparrow.Rcheck/00check.log’ for details.
sparrow.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL sparrow ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 RC (2024-04-16 r86468) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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 | | | 0% | |= | 1% | |== | 3% | |=== | 4% | |==== | 5% | |===== | 7% | |====== | 8% | |====== | 9% | |======= | 11% | |======== | 12% | |========= | 13% | |========== | 14% | |=========== | 16% | |============ | 17% | |============= | 18% | |============== | 20% | |=============== | 21% | |================ | 22% | |================= | 24% | |================== | 25% | |================== | 26% | |=================== | 28% | |==================== | 29% | |===================== | 30% | |====================== | 32% | |======================= | 33% | |======================== | 34% | |========================= | 36% | |========================== | 37% | |=========================== | 38% | |============================ | 39% | |============================= | 41% | |============================= | 42% | |============================== | 43% | |=============================== | 45% | |================================ | 46% | 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|===================================================================== | 99% | |======================================================================| 100% Estimating ssGSEA scores for 76 gene sets. [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." | | | 0% | |==== | 6% | |======== | 11% | |============ | 17% | |================ | 22% | |=================== | 28% | |======================= | 33% | |=========================== | 39% | |=============================== | 44% | |=================================== | 50% | |======================================= | 56% | |=========================================== | 61% | |=============================================== | 67% | |=================================================== | 72% | |====================================================== | 78% | |========================================================== | 83% | |============================================================== | 89% | |================================================================== | 94% | |======================================================================| 100% [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 1480 ] ══ 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 1480 ] Error: Test failures Execution halted
sparrow.Rcheck/sparrow-Ex.timings
name | user | system | elapsed | |
GeneSetDb-class | 0.227 | 0.004 | 0.215 | |
SparrowResult-utilities | 4.866 | 0.196 | 4.142 | |
addGeneSetMetadata | 0.090 | 0.004 | 0.067 | |
annotateGeneSetMembership | 4.872 | 0.135 | 4.110 | |
calculateIndividualLogFC | 1.431 | 0.032 | 1.463 | |
collectionMetadata | 0.100 | 0.000 | 0.072 | |
combine-GeneSetDb-GeneSetDb-method | 0.132 | 0.005 | 0.088 | |
combine-SparrowResult-SparrowResult-method | 0.116 | 0.003 | 0.118 | |
conform | 0.421 | 0.001 | 0.395 | |
conversion | 0.682 | 0.000 | 0.571 | |
convertIdentifiers | 0.273 | 0.000 | 0.172 | |
corplot | 0.098 | 0.000 | 0.098 | |
eigenWeightedMean | 3.534 | 0.104 | 3.585 | |
examples | 0.306 | 0.000 | 0.307 | |
failWith | 0.000 | 0.000 | 0.001 | |
featureIdMap | 0.423 | 0.012 | 0.407 | |
featureIds | 0.478 | 0.000 | 0.437 | |
geneSet | 0.113 | 0.000 | 0.079 | |
geneSetCollectionURLfunction | 0.084 | 0.000 | 0.057 | |
geneSetSummaryByGenes | 3.982 | 0.104 | 3.026 | |
geneSets | 0.082 | 0.004 | 0.055 | |
geneSetsStats | 5.464 | 0.055 | 3.760 | |
getKeggCollection | 0 | 0 | 0 | |
getMSigCollection | 0 | 0 | 0 | |
getPantherCollection | 0 | 0 | 0 | |
getReactomeCollection | 0 | 0 | 0 | |
goseq | 7.820 | 0.172 | 7.072 | |
gsdScore | 0.884 | 0.044 | 0.874 | |
gskey | 0.003 | 0.000 | 0.003 | |
hasGeneSet | 1.190 | 0.016 | 1.177 | |
hasGeneSetCollection | 0.079 | 0.000 | 0.053 | |
incidenceMatrix | 0.972 | 0.012 | 0.956 | |
iplot | 1.191 | 0.024 | 1.168 | |
is.active | 0.377 | 0.048 | 0.387 | |
logFC | 3.641 | 0.072 | 2.777 | |
mgheatmap | 0 | 0 | 0 | |
mgheatmap2 | 0 | 0 | 0 | |
msg | 0 | 0 | 0 | |
ora | 0.312 | 0.004 | 0.311 | |
p.matrix | 0.089 | 0.000 | 0.089 | |
randomGeneSetDb | 0.088 | 0.000 | 0.082 | |
renameCollections | 0.111 | 0.000 | 0.075 | |
renameRows | 0.376 | 0.012 | 0.383 | |
results | 0.100 | 0.004 | 0.104 | |
scale_rows | 0.004 | 0.000 | 0.005 | |
scoreSingleSamples | 5.679 | 0.172 | 5.744 | |
seas | 5.529 | 0.140 | 4.683 | |
sparrow_methods | 0.004 | 0.000 | 0.003 | |
species_info | 0.006 | 0.000 | 0.006 | |
subset.GeneSetDb | 0.093 | 0.004 | 0.071 | |
subsetByFeatures | 0.129 | 0.008 | 0.084 | |
validateInputs | 0.183 | 0.000 | 0.158 | |
volcanoPlot | 1.965 | 0.064 | 2.028 | |
volcanoStatsTable | 0.068 | 0.000 | 0.068 | |
zScore | 0.798 | 0.000 | 0.746 | |