Alexey Sergushichev
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/phantasus |
| git_branch: master |
| git_last_commit: 373c171 |
| git_last_commit_date: 2022-02-15 07:10:33 -0400 (Tue, 15 Feb 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:17 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 phantasus package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1411/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| phantasus 1.15.4 (landing page) Alexey Sergushichev
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: phantasus |
| Version: 1.15.4 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:phantasus.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings phantasus_1.15.4.tar.gz |
| StartedAt: 2022-03-17 19:51:23 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:57:33 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 370.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: phantasus.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:phantasus.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings phantasus_1.15.4.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/phantasus.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'phantasus/DESCRIPTION' ... OK
* this is package 'phantasus' version '1.15.4'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'phantasus' can be installed ... OK
* checking installed package size ... NOTE
installed size is 28.9Mb
sub-directories of 1Mb or more:
testdata 5.0Mb
www 23.4Mb
* 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 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 ... NOTE
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
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'
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'
safeDownload: no visible binding for global variable 'tempDestFile'
validateCountsCollection: no visible binding for global variable
'file_name'
Undefined global functions or variables:
. DT_counts_meta accession collection_type directory es file_name
heatmapJson tempDestFile
* checking Rd files ... NOTE
prepare_Rd: convertByAnnotationDB.Rd:36-41: 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getGSE 3.78 1.44 14.62
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
`expected`: TRUE
-- Failure (testcounts.R:115:5): updateCountsMeta create good meta files for archs4 --
file.exists(arch_meta_file) is not TRUE
`actual`: FALSE
`expected`: TRUE
-- Error (testcounts.R:116:5): updateCountsMeta create good meta files for archs4 --
Error in `fread(arch_meta_file)`: File 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpcbMivb/test_counts/counts/archs4/meta.txt' does not exist or is non-readable. getwd()=='D:/biocbuild/bbs-3.15-bioc/meat/phantasus.Rcheck/tests/testthat'
Backtrace:
x
1. \-data.table::fread(arch_meta_file) at testcounts.R:116:4
[ FAIL 4 | WARN 9 | SKIP 0 | PASS 110 ]
Error: Test failures
Execution halted
* 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 ERROR, 4 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/phantasus.Rcheck/00check.log'
for details.
phantasus.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL phantasus
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/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
converting help for package 'phantasus'
finding HTML links ... done
adjustDataset html
annotationDBMeta html
calcPCA html
calculatedAnnotation html
checkGPLsFallback html
colMeansByGroups html
collapseDataset html
convertByAnnotationDB html
createES html
es html
fgseaExample html
generatePreloadedSession html
getArchs4Files html
getES html
getGDS html
getGSE html
gseaPlot html
limmaAnalysis html
loadCounts html
loadFromARCHS4 html
loadGEO html
loadPreloaded html
performKmeans html
queryAnnotationDBMeta html
read.gct html
reparseCachedESs html
reproduceInR html
servePhantasus html
shinyGAMAnalysis html
subsetES html
write.gct html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'MIGSA' is missing or broken
done
phantasus.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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(testthat)
> library(phantasus)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading config from D:/biocbuild/bbs-3.15-bioc/R/library/opencpu/config/defaults.conf
Loading config from C:\Users\biocbuild\AppData\Roaming/R/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'
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'
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 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 length 596707 bytes (582 KB)
==================================================
downloaded 582 KB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL6nnn/GPL6103/annot/GPL6103.annot.gz'
length 4652589 bytes (4.4 MB)
==================================================
downloaded 4.4 MB
trying URL 'https://genome.ifmo.ru/files/software/phantasus/geo/series/GSE27nnn/GSE27112/matrix/GSE27112-GPL6885_series_matrix.txt.gz'
length 1273889 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL6nnn/GPL6885/annot/GPL6885.annot.gz'
length 4938348 bytes (4.7 MB)
==================================================
downloaded 4.7 MB
trying URL 'https://genome.ifmo.ru/files/software/phantasus/geo/series/GSE14nnn/GSE14308/matrix/GSE14308_series_matrix.txt.gz'
length 1807552 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
trying URL 'https://genome.ifmo.ru/files/software/phantasus/geo/datasets/GDS4nnn/GDS4885/soft/GDS4885.soft.gz'
length 1250109 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27112/matrix/GSE27112_series_matrix.txt.gz'
trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL17021&form=text&view=data'
downloaded 48 bytes
[ FAIL 4 | WARN 9 | SKIP 0 | PASS 110 ]
== Failed tests ================================================================
-- Failure (testcounts.R:88:5): loadCounts returns result ----------------------
nrow(ess[[1]]) is not strictly more than 0. Difference: 0
-- Failure (testcounts.R:113:5): updateCountsMeta create good meta files for archs4 --
file.exists(meta_file) is not TRUE
`actual`: FALSE
`expected`: TRUE
-- Failure (testcounts.R:115:5): updateCountsMeta create good meta files for archs4 --
file.exists(arch_meta_file) is not TRUE
`actual`: FALSE
`expected`: TRUE
-- Error (testcounts.R:116:5): updateCountsMeta create good meta files for archs4 --
Error in `fread(arch_meta_file)`: File 'D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpcbMivb/test_counts/counts/archs4/meta.txt' does not exist or is non-readable. getwd()=='D:/biocbuild/bbs-3.15-bioc/meat/phantasus.Rcheck/tests/testthat'
Backtrace:
x
1. \-data.table::fread(arch_meta_file) at testcounts.R:116:4
[ FAIL 4 | WARN 9 | SKIP 0 | PASS 110 ]
Error: Test failures
Execution halted
phantasus.Rcheck/phantasus-Ex.timings
| name | user | system | elapsed | |
| adjustDataset | 0 | 0 | 0 | |
| annotationDBMeta | 0 | 0 | 0 | |
| calcPCA | 0 | 0 | 0 | |
| checkGPLsFallback | 0 | 0 | 0 | |
| collapseDataset | 0 | 0 | 0 | |
| createES | 0 | 0 | 0 | |
| es | 0 | 0 | 0 | |
| generatePreloadedSession | 0 | 0 | 0 | |
| getES | 0.98 | 0.35 | 3.50 | |
| getGDS | 0.29 | 0.31 | 1.33 | |
| getGSE | 3.78 | 1.44 | 14.62 | |
| limmaAnalysis | 0 | 0 | 0 | |
| loadGEO | 0 | 0 | 0 | |
| performKmeans | 0 | 0 | 0 | |
| queryAnnotationDBMeta | 0 | 0 | 0 | |
| read.gct | 0.01 | 0.00 | 0.02 | |
| reparseCachedESs | 0.50 | 0.32 | 1.77 | |
| reproduceInR | 0 | 0 | 0 | |
| servePhantasus | 0 | 0 | 0 | |
| write.gct | 0.02 | 0.00 | 0.01 | |