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CHECK report for phantasus on malbec1

This page was generated on 2019-04-16 11:53:23 -0400 (Tue, 16 Apr 2019).

Package 1148/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phantasus 1.2.1
Alexey Sergushichev
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/phantasus
Branch: RELEASE_3_8
Last Commit: 05217c4
Last Changed Date: 2018-12-11 16:13:22 -0400 (Tue, 11 Dec 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: phantasus
Version: 1.2.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:phantasus.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings phantasus_1.2.1.tar.gz
StartedAt: 2019-04-16 02:03:42 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:06:44 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 182.4 seconds
RetCode: 0
Status:  OK 
CheckDir: phantasus.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:phantasus.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings phantasus_1.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/phantasus.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phantasus/DESCRIPTION’ ... OK
* this is package ‘phantasus’ version ‘1.2.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘phantasus’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 21.5Mb
  sub-directories of 1Mb or more:
    www  20.8Mb
* 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 ... OK
* checking Rd files ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
getGSE 8.744  0.272   10.14
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/phantasus.Rcheck/00check.log’
for details.



Installation output

phantasus.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL phantasus
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘phantasus’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Loading config from /home/biocbuild/bbs-3.8-bioc/R/library/opencpu/config/defaults.conf
Loading config from /home/biocbuild/.local/share/opencpu/user.conf
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Loading config from /home/biocbuild/bbs-3.8-bioc/R/library/opencpu/config/defaults.conf
Loading config from /home/biocbuild/.local/share/opencpu/user.conf
* DONE (phantasus)

Tests output

phantasus.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 /home/biocbuild/bbs-3.8-bioc/R/library/opencpu/config/defaults.conf
Loading config from /home/biocbuild/.local/share/opencpu/user.conf
> 
> test_check("phantasus")
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://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://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/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/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 3390 bytes
==================================================
downloaded 3390 bytes

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 97 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 68.872   1.424  89.844 

Example timings

phantasus.Rcheck/phantasus-Ex.timings

nameusersystemelapsed
adjustDataset000
calcPCA000
checkGPLs000
collapseDataset000
createES000
es000
getES1.1600.0482.687
getGDS0.5160.0120.532
getGSE 8.744 0.27210.140
limmaAnalysis000
loadGEO000
performKmeans000
read.gct0.0360.0000.047
reparseCachedESs0.8720.0280.902
servePhantasus000
write.gct0.0240.0080.032