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CHECK results for phantasus on machv2

This page was generated on 2021-06-14 14:05:49 -0400 (Mon, 14 Jun 2021).

Package 1377/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phantasus 1.12.0  (landing page)
Alexey Sergushichev
Snapshot Date: 2021-06-13 06:50:09 -0400 (Sun, 13 Jun 2021)
URL: https://git.bioconductor.org/packages/phantasus
Branch: RELEASE_3_13
Last Commit: e2115e2
Last Changed Date: 2021-05-19 12:34:17 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
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.

Summary

Package: phantasus
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:phantasus.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings phantasus_1.12.0.tar.gz
StartedAt: 2021-06-13 21:54:31 -0400 (Sun, 13 Jun 2021)
EndedAt: 2021-06-13 22:00:41 -0400 (Sun, 13 Jun 2021)
EllapsedTime: 370.4 seconds
RetCode: 0
Status:   OK  
CheckDir: phantasus.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:phantasus.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings phantasus_1.12.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/phantasus.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phantasus/DESCRIPTION’ ... OK
* this is package ‘phantasus’ version ‘1.12.0’
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
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 28.0Mb
  sub-directories of 1Mb or more:
    testdata   4.3Mb
    www       23.3Mb
* 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:::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'
loadSession: no visible binding for global variable 'es'
reproduceInR: no visible global function definition for 'object.size'
safeDownload: no visible binding for global variable 'tempDestFile'
Undefined global functions or variables:
  es heatmapJson object.size tempDestFile
Consider adding
  importFrom("utils", "object.size")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: convertByAnnotationDB.Rd:27-32: 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 7.693  0.636  10.078
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/phantasus.Rcheck/00check.log’
for details.



Installation output

phantasus.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL phantasus
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)

Tests output

phantasus.Rcheck/tests/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 /Library/Frameworks/R.framework/Versions/4.1/Resources/library/opencpu/config/defaults.conf
Loading config from ~/Library/Application Support/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://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://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://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://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://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://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/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=quick'
downloaded 7.2 MB

[ FAIL 0 | WARN 17 | SKIP 0 | PASS 95 ]
> 
> proc.time()
   user  system elapsed 
100.199   6.543 146.915 

Example timings

phantasus.Rcheck/phantasus-Ex.timings

nameusersystemelapsed
adjustDataset000
annotationDBMeta0.0000.0000.001
calcPCA0.0000.0010.000
checkGPLsFallback000
collapseDataset0.0010.0000.000
createES000
es000
generatePreloadedSession1.4270.1553.563
getES1.8000.1252.330
getGDS0.8300.0610.891
getGSE 7.693 0.63610.078
limmaAnalysis000
loadGEO0.0000.0010.000
performKmeans0.0000.0000.001
queryAnnotationDBMeta000
read.gct0.0430.0010.044
reparseCachedESs1.7390.0901.835
reproduceInR000
servePhantasus000
write.gct0.0340.0010.035