Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1535/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
phantasus 1.26.0 (landing page) Alexey Sergushichev
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the phantasus package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/phantasus.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: phantasus |
Version: 1.26.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:phantasus.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings phantasus_1.26.0.tar.gz |
StartedAt: 2024-12-20 07:34:42 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 07:46:08 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 685.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: phantasus.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:phantasus.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings phantasus_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/phantasus.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘phantasus/DESCRIPTION’ ... OK * this is package ‘phantasus’ version ‘1.26.0’ * 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 ... NOTE Found the following hidden files and directories: .env These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘phantasus’ can be installed ... OK * checking installed package size ... NOTE installed size is 29.0Mb sub-directories of 1Mb or more: testdata 5.0Mb www 23.5Mb * checking package 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 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 dependencies in R code ... NOTE Namespace in Imports field not imported from: 'rhdf5client' All declared Imports should be used. Unexported objects imported by ':::' calls: 'GEOquery:::.parseGPLTxt' 'GEOquery:::getDirListing' 'opencpu:::rookhandler' 'opencpu:::tmp_root' 'opencpu:::win_or_mac' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE filterPhenoAnnotations : parsePData: no visible binding for global variable 'value' generatePreloadedSession: no visible binding for global variable 'es' generatePreloadedSession: no visible binding for global variable 'heatmapJson' getCountsMetaPart: no visible binding for global variable 'file_name' getDesignMatrix: no visible binding for global variable 'id' getFileIndexDF: no visible global function definition for '.' getFileIndexDF: no visible binding for global variable 'Name' getFileIndexDF: no visible binding for global variable 'Last modified' getFileIndexDF: no visible binding for global variable 'Size' limmaAnalysisSimpleImpl: no visible binding for global variable 'ComparisonTarget' limmaAnalysisSimpleImpl: no visible binding for global variable 'ComparisonReference' loadCounts: no visible global function definition for '.' loadCounts: no visible binding for global variable 'directory' loadCounts: no visible binding for global variable 'DT_counts_meta' loadCounts: no visible binding for global variable 'accession' loadCounts: no visible binding for global variable 'collection_type' loadCounts: no visible binding for global variable 'file_name' loadSession: no visible binding for global variable 'es' servePhantasus: no visible global function definition for 'menu' servePhantasus: no visible global function definition for 'install.packages' setupPhantasus: no visible global function definition for 'menu' setupPhantasus: no visible global function definition for 'install.packages' validateCountsCollection: no visible binding for global variable 'file_name' Undefined global functions or variables: . ComparisonReference ComparisonTarget DT_counts_meta Last modified Name Size accession collection_type directory es file_name heatmapJson id install.packages menu value Consider adding importFrom("utils", "install.packages", "menu") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: convertByAnnotationDB.Rd:35-39: Dropping empty section \examples * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/phantasus.Rcheck/00check.log’ for details.
phantasus.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL phantasus ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘phantasus’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (phantasus)
phantasus.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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(testthat) > library(phantasus) Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) Loading config from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/opencpu/config/defaults.conf Loading config from /Users/biocbuild/Library/Preferences/org.R-project.R/R/opencpu/user.conf > > test_check("phantasus") trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53986/matrix/GSE53986_series_matrix.txt.gz' Content type 'application/x-gzip' length 2848655 bytes (2.7 MB) ================================================== downloaded 2.7 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL1nnn/GPL1261/annot/GPL1261.annot.gz' Content type 'application/x-gzip' length 8389179 bytes (8.0 MB) ================================================== downloaded 8.0 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107746/matrix/GSE107746_series_matrix.txt.gz' Content type 'application/x-gzip' length 7196 bytes ================================================== downloaded 7196 bytes trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL20795&form=text&view=data' downloaded 48 bytes trying URL 'https://alserglab.wustl.edu/files/phantasus/geo/series/GSE27nnn/GSE27112/matrix/GSE27112_series_matrix.txt.gz' trying URL 'https://alserglab.wustl.edu/files/phantasus/geo/series/GSE27nnn/GSE27112/matrix/GSE27112-GPL6103_series_matrix.txt.gz' Content type 'application/x-gzip' length 596707 bytes (582 KB) ================================================== downloaded 582 KB trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL6103&form=text&view=data' downloaded 3.4 MB trying URL 'https://alserglab.wustl.edu/files/phantasus/geo/series/GSE27nnn/GSE27112/matrix/GSE27112-GPL6885_series_matrix.txt.gz' Content type 'application/x-gzip' length 1273889 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL6885&form=text&view=data' downloaded 3.2 MB trying URL 'https://alserglab.wustl.edu/files/phantasus/geo/series/GSE14nnn/GSE14308/matrix/GSE14308_series_matrix.txt.gz' Content type 'application/x-gzip' length 1807552 bytes (1.7 MB) ================================================== downloaded 1.7 MB trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL1261&form=text&view=data' downloaded 9.5 MB trying URL 'https://alserglab.wustl.edu/files/phantasus/geo/datasets/GDS4nnn/GDS4885/soft/GDS4885.soft.gz' Content type 'application/x-gzip' length 1250109 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE14nnn/GSE14308/matrix/GSE14308_series_matrix.txt.gz' Content type 'application/x-gzip' length 1807570 bytes (1.7 MB) ================================================== downloaded 1.7 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS4nnn/GDS4885/soft/GDS4885.soft.gz' Content type 'application/x-gzip' length 1250109 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27112/matrix/GSE27112-GPL6103_series_matrix.txt.gz' Content type 'application/x-gzip' length 596708 bytes (582 KB) ================================================== downloaded 582 KB trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL6nnn/GPL6103/annot/GPL6103.annot.gz' Content type 'application/x-gzip' length 4652589 bytes (4.4 MB) ================================================== downloaded 4.4 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27112/matrix/GSE27112-GPL6885_series_matrix.txt.gz' Content type 'application/x-gzip' length 1273890 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL6nnn/GPL6885/annot/GPL6885.annot.gz' Content type 'application/x-gzip' length 4938348 bytes (4.7 MB) ================================================== downloaded 4.7 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27112/matrix/GSE27112_series_matrix.txt.gz' trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99709/matrix/GSE99709_series_matrix.txt.gz' Content type 'application/x-gzip' length 3386 bytes ================================================== downloaded 3386 bytes trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL17021&form=text&view=data' downloaded 48 bytes trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL17021&form=text&view=data' downloaded 48 bytes trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120978/matrix/GSE120978_series_matrix.txt.gz' Content type 'application/x-gzip' length 4192282 bytes (4.0 MB) ================================================== downloaded 4.0 MB trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL16985&form=text&view=data' downloaded 6.3 MB [ FAIL 0 | WARN 0 | SKIP 0 | PASS 111 ] > > proc.time() user system elapsed 154.608 21.361 226.037
phantasus.Rcheck/phantasus-Ex.timings
name | user | system | elapsed | |
adjustDataset | 0.001 | 0.000 | 0.001 | |
annotationDBMeta | 0.000 | 0.000 | 0.001 | |
calcPCA | 0.000 | 0.001 | 0.001 | |
checkGPLsFallback | 0.000 | 0.000 | 0.001 | |
collapseDataset | 0 | 0 | 0 | |
createES | 0.001 | 0.001 | 0.001 | |
es | 0.000 | 0.001 | 0.001 | |
generatePreloadedSession | 0.000 | 0.001 | 0.001 | |
getCountsMetaPart | 0.000 | 0.001 | 0.000 | |
getES | 0.000 | 0.001 | 0.001 | |
getGDS | 0.000 | 0.001 | 0.000 | |
getGSE | 0 | 0 | 0 | |
limmaAnalysis | 0.000 | 0.000 | 0.001 | |
loadGEO | 0.000 | 0.000 | 0.001 | |
performKmeans | 0 | 0 | 0 | |
queryAnnotationDBMeta | 0 | 0 | 0 | |
reparseCachedESs | 0.001 | 0.001 | 0.002 | |
reproduceInR | 0.001 | 0.001 | 0.001 | |
servePhantasus | 0.000 | 0.001 | 0.001 | |