Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-27 11:37:06 -0400 (Wed, 27 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4698 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4436 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4461 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4376 |
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 1524/2264 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
phantasus 1.23.4 (landing page) Alexey Sergushichev
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 1.23.4 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:phantasus.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings phantasus_1.23.4.tar.gz |
StartedAt: 2024-03-27 01:21:15 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 01:31:03 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 588.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: phantasus.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:phantasus.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings phantasus_1.23.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/phantasus.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * 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 ‘phantasus/DESCRIPTION’ ... OK * this is package ‘phantasus’ version ‘1.23.4’ * 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 15.7Mb sub-directories of 1Mb or more: testdata 1.6Mb www 13.6Mb * 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 loading without being on the library search path ... OK * checking dependencies in R code ... WARNING '::' or ':::' imports not declared from: 'XML' 'fs' 'yaml' 'library' or 'require' calls not declared from: 'org.Hs.eg.db' 'org.Mm.eg.db' 'library' or 'require' calls in package code: 'org.Hs.eg.db' 'org.Mm.eg.db' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. 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 configureAnnotDB : <anonymous>: no visible global function definition for 'org.Mm.eg_dbfile' configureAnnotDB : <anonymous>: no visible global function definition for 'org.Hs.eg_dbfile' 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' 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 org.Hs.eg_dbfile org.Mm.eg_dbfile * checking Rd files ... NOTE prepare_Rd: convertByAnnotationDB.Rd:35-40: 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 ... WARNING Undocumented arguments in Rd file 'isHSDS.Rd' ‘url’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 4 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/phantasus.Rcheck/00check.log’ for details.
phantasus.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL phantasus ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 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(testthat) > library(phantasus) Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) Loading config from /home/biocbuild/bbs-3.19-bioc/R/site-library/opencpu/config/defaults.conf Loading config from /home/biocbuild/.config/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://genome.ifmo.ru/files/software/phantasus/geo/series/GSE27nnn/GSE27112/matrix/GSE27112_series_matrix.txt.gz' trying URL 'https://genome.ifmo.ru/files/software/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://genome.ifmo.ru/files/software/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://genome.ifmo.ru/files/software/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://genome.ifmo.ru/files/software/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' 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 [ FAIL 0 | WARN 11 | SKIP 0 | PASS 115 ] [ FAIL 0 | WARN 11 | SKIP 0 | PASS 115 ] > > proc.time() user system elapsed 81.320 6.382 434.832
phantasus.Rcheck/phantasus-Ex.timings
name | user | system | elapsed | |
adjustDataset | 0 | 0 | 0 | |
annotationDBMeta | 0 | 0 | 0 | |
calcPCA | 0.001 | 0.000 | 0.000 | |
checkGPLsFallback | 0 | 0 | 0 | |
collapseDataset | 0 | 0 | 0 | |
createES | 0.000 | 0.000 | 0.001 | |
es | 0 | 0 | 0 | |
generatePreloadedSession | 0 | 0 | 0 | |
getCountsMetaPart | 0.000 | 0.000 | 0.001 | |
getES | 0 | 0 | 0 | |
getGDS | 0.001 | 0.000 | 0.000 | |
getGSE | 0.000 | 0.000 | 0.001 | |
limmaAnalysis | 0 | 0 | 0 | |
loadGEO | 0 | 0 | 0 | |
performKmeans | 0 | 0 | 0 | |
queryAnnotationDBMeta | 0.001 | 0.000 | 0.000 | |
read.gct | 0.054 | 0.012 | 0.066 | |
reparseCachedESs | 0 | 0 | 0 | |
reproduceInR | 0 | 0 | 0 | |
servePhantasus | 0 | 0 | 0 | |
write.gct | 0.057 | 0.000 | 0.057 | |