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This page was generated on 2024-03-28 11:36:52 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 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 1530/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phantasus 1.23.4  (landing page)
Alexey Sergushichev
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/phantasus
git_branch: devel
git_last_commit: 261f353
git_last_commit_date: 2024-03-06 16:29:21 -0400 (Wed, 06 Mar 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    TIMEOUT  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for phantasus on nebbiolo1


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.

raw results


Summary

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: 2024-03-28 01:22:42 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 02:02:42 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 2400.1 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: phantasus.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### 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’

Installation output

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)

Tests output

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


Example timings

phantasus.Rcheck/phantasus-Ex.timings

nameusersystemelapsed
adjustDataset000
annotationDBMeta000
calcPCA000
checkGPLsFallback000
collapseDataset000
createES000
es000
generatePreloadedSession0.0000.0000.001
getCountsMetaPart0.0010.0000.000
getES000
getGDS000
getGSE000
limmaAnalysis000
loadGEO000
performKmeans000
queryAnnotationDBMeta0.0000.0000.001
read.gct0.0680.0080.076
reparseCachedESs000
reproduceInR000
servePhantasus0.0000.0000.001
write.gct0.0450.0200.065