Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-27 11:36:18 -0400 (Wed, 27 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4667 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4403 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4426 |
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 2001/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sparrow 1.8.0 (landing page) Steve Lianoglou
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.8.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings sparrow_1.8.0.tar.gz |
StartedAt: 2024-03-26 02:42:44 -0400 (Tue, 26 Mar 2024) |
EndedAt: 2024-03-26 02:54:14 -0400 (Tue, 26 Mar 2024) |
EllapsedTime: 690.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sparrow.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:sparrow.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings sparrow_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/sparrow.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 ‘1.8.0’ * 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 ... 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 loading without being on the library search path ... OK * checking 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 ... 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 goseq 8.168 0.222 7.491 seas 5.186 0.104 4.367 geneSetsStats 5.129 0.026 3.455 SparrowResult-utilities 4.897 0.140 4.151 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘sparrow.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/sparrow.Rcheck/00check.log’ for details.
sparrow.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL sparrow ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-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
R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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 [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..." [1] "Calculating ranks..." [1] "Calculating absolute values from ranks..." [1] "Normalizing..." [ FAIL 0 | WARN 11 | SKIP 1 | PASS 1523 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-MultiGSEAResult.R:3:1' [ FAIL 0 | WARN 11 | SKIP 1 | PASS 1523 ] > > ## Remove temporary files that were generated > test.dir <- system.file('tests', package = "sparrow") > pdfs <- dir(test.dir, "\\.pdf$", full.names=TRUE) > if (length(pdfs)) { + unlink(pdfs) + } > > > proc.time() user system elapsed 326.624 14.522 294.402
sparrow.Rcheck/sparrow-Ex.timings
name | user | system | elapsed | |
GeneSetDb-class | 0.092 | 0.000 | 0.076 | |
SparrowResult-utilities | 4.897 | 0.140 | 4.151 | |
addGeneSetMetadata | 0.083 | 0.000 | 0.059 | |
annotateGeneSetMembership | 4.452 | 0.118 | 3.696 | |
calculateIndividualLogFC | 1.977 | 0.213 | 2.191 | |
collectionMetadata | 0.088 | 0.004 | 0.067 | |
combine-GeneSetDb-GeneSetDb-method | 0.133 | 0.000 | 0.085 | |
combine-SparrowResult-SparrowResult-method | 0.092 | 0.028 | 0.116 | |
conform | 0.409 | 0.016 | 0.401 | |
conversion | 0.680 | 0.000 | 0.561 | |
convertIdentifiers | 0.254 | 0.000 | 0.157 | |
corplot | 0.092 | 0.000 | 0.093 | |
eigenWeightedMean | 2.461 | 0.035 | 2.447 | |
examples | 0.284 | 0.008 | 0.292 | |
failWith | 0.000 | 0.000 | 0.001 | |
featureIdMap | 0.424 | 0.000 | 0.398 | |
featureIds | 0.441 | 0.000 | 0.402 | |
geneSet | 0.107 | 0.000 | 0.073 | |
geneSetCollectionURLfunction | 0.098 | 0.000 | 0.069 | |
geneSetSummaryByGenes | 4.733 | 0.127 | 3.837 | |
geneSets | 0.087 | 0.000 | 0.055 | |
geneSetsStats | 5.129 | 0.026 | 3.455 | |
getKeggCollection | 0 | 0 | 0 | |
getMSigCollection | 0 | 0 | 0 | |
getPantherCollection | 0 | 0 | 0 | |
getReactomeCollection | 0 | 0 | 0 | |
goseq | 8.168 | 0.222 | 7.491 | |
gsdScore | 0.900 | 0.004 | 0.854 | |
gskey | 0.003 | 0.000 | 0.003 | |
hasGeneSet | 0.078 | 0.000 | 0.053 | |
hasGeneSetCollection | 0.076 | 0.000 | 0.052 | |
incidenceMatrix | 1.051 | 0.000 | 1.024 | |
iplot | 1.104 | 0.051 | 1.095 | |
is.active | 0.350 | 0.024 | 0.351 | |
logFC | 3.534 | 0.047 | 2.710 | |
mgheatmap | 0 | 0 | 0 | |
mgheatmap2 | 0 | 0 | 0 | |
msg | 0.002 | 0.001 | 0.000 | |
ora | 0.248 | 0.000 | 0.243 | |
p.matrix | 0.081 | 0.000 | 0.080 | |
randomGeneSetDb | 1.126 | 0.055 | 1.176 | |
renameCollections | 0.102 | 0.000 | 0.069 | |
renameRows | 0.343 | 0.004 | 0.343 | |
results | 0.085 | 0.004 | 0.090 | |
scale_rows | 0.003 | 0.000 | 0.004 | |
scoreSingleSamples | 4.470 | 0.112 | 4.484 | |
seas | 5.186 | 0.104 | 4.367 | |
sparrow_methods | 0.003 | 0.000 | 0.003 | |
species_info | 0.003 | 0.002 | 0.006 | |
subset.GeneSetDb | 0.114 | 0.014 | 0.095 | |
subsetByFeatures | 0.113 | 0.000 | 0.070 | |
validateInputs | 0.172 | 0.000 | 0.143 | |
volcanoPlot | 1.793 | 0.028 | 1.821 | |
volcanoStatsTable | 0.060 | 0.000 | 0.059 | |
zScore | 0.761 | 0.000 | 0.710 | |