Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:52 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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 |
To the developers/maintainers of the sparrow package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1899/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
sparrow 1.5.0 (landing page) Steve Lianoglou
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
Package: sparrow |
Version: 1.5.0 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sparrow.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings sparrow_1.5.0.tar.gz |
StartedAt: 2022-12-29 03:44:59 -0500 (Thu, 29 Dec 2022) |
EndedAt: 2022-12-29 03:55:54 -0500 (Thu, 29 Dec 2022) |
EllapsedTime: 655.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: sparrow.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sparrow.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings sparrow_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/sparrow.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'sparrow/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'sparrow' version '1.5.0' * 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 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 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 6.44 0.53 6.75 seas 5.27 0.47 5.59 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/sparrow.Rcheck/00check.log' for details.
sparrow.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL sparrow ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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 0 | SKIP 1 | PASS 1479 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • empty test (1) [ FAIL 0 | WARN 0 | SKIP 1 | PASS 1479 ] > > ## 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 282.29 17.51 448.95
sparrow.Rcheck/sparrow-Ex.timings
name | user | system | elapsed | |
GeneSetDb-class | 0.06 | 0.00 | 0.06 | |
SparrowResult-utilities | 3.74 | 0.31 | 3.89 | |
addGeneSetMetadata | 0.03 | 0.02 | 0.04 | |
annotateGeneSetMembership | 3.60 | 0.36 | 3.80 | |
calculateIndividualLogFC | 1.68 | 0.14 | 1.82 | |
collectionMetadata | 0.05 | 0.04 | 0.07 | |
combine-GeneSetDb-GeneSetDb-method | 0.09 | 0.00 | 0.09 | |
combine-SparrowResult-SparrowResult-method | 0.08 | 0.00 | 0.09 | |
conform | 0.41 | 0.01 | 0.43 | |
conversion | 0.51 | 0.05 | 0.56 | |
convertIdentifiers | 0.13 | 0.03 | 0.15 | |
corplot | 0.06 | 0.00 | 0.07 | |
eigenWeightedMean | 1.56 | 0.03 | 1.59 | |
examples | 0.38 | 0.03 | 0.41 | |
failWith | 0 | 0 | 0 | |
featureIdMap | 0.44 | 0.03 | 0.47 | |
featureIds | 0.50 | 0.07 | 0.54 | |
geneSet | 0.06 | 0.00 | 0.06 | |
geneSetCollectionURLfunction | 0.05 | 0.00 | 0.05 | |
geneSetSummaryByGenes | 3.59 | 0.18 | 3.67 | |
geneSets | 0.06 | 0.00 | 0.07 | |
geneSetsStats | 3.80 | 0.63 | 3.90 | |
getKeggCollection | 0 | 0 | 0 | |
getMSigCollection | 0 | 0 | 0 | |
getPantherCollection | 0 | 0 | 0 | |
getReactomeCollection | 0 | 0 | 0 | |
goseq | 6.44 | 0.53 | 6.75 | |
gsdScore | 0.73 | 0.04 | 0.76 | |
gskey | 0 | 0 | 0 | |
hasGeneSet | 0.05 | 0.02 | 0.05 | |
hasGeneSetCollection | 0.05 | 0.00 | 0.03 | |
incidenceMatrix | 0.95 | 0.03 | 1.00 | |
iplot | 1.00 | 0.17 | 1.41 | |
is.active | 0.32 | 0.03 | 0.73 | |
logFC | 3.47 | 0.13 | 3.57 | |
mgheatmap | 0 | 0 | 0 | |
mgheatmap2 | 0 | 0 | 0 | |
msg | 0 | 0 | 0 | |
ora | 0.20 | 0.03 | 0.29 | |
p.matrix | 0.08 | 0.00 | 0.08 | |
randomGeneSetDb | 0.06 | 0.01 | 0.17 | |
renameCollections | 0.06 | 0.00 | 0.07 | |
renameRows | 0.35 | 0.03 | 0.37 | |
results | 0.07 | 0.00 | 0.08 | |
scale_rows | 0 | 0 | 0 | |
scoreSingleSamples | 2.94 | 0.24 | 3.17 | |
seas | 5.27 | 0.47 | 5.59 | |
sparrow_methods | 0 | 0 | 0 | |
species_info | 0 | 0 | 0 | |
subset.GeneSetDb | 0.04 | 0.01 | 0.07 | |
subsetByFeatures | 0.08 | 0.00 | 0.06 | |
validateInputs | 0.11 | 0.00 | 0.19 | |
volcanoPlot | 1.69 | 0.08 | 1.76 | |
volcanoStatsTable | 0.05 | 0.00 | 0.05 | |
zScore | 0.82 | 0.00 | 0.83 | |