Back to Multiple platform build/check report for BioC 3.9
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

CHECK report for phantasus on malbec2

This page was generated on 2019-04-09 11:50:16 -0400 (Tue, 09 Apr 2019).

Package 1177/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phantasus 1.3.4
Alexey Sergushichev
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/phantasus
Branch: master
Last Commit: d5d3a2a
Last Changed Date: 2019-02-02 08:32:57 -0400 (Sat, 02 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: phantasus
Version: 1.3.4
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:phantasus.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings phantasus_1.3.4.tar.gz
StartedAt: 2019-04-09 02:39:56 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:43:49 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 233.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: phantasus.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:phantasus.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings phantasus_1.3.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/phantasus.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.3.4’
* 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:
  .dockerignore
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 27.4Mb
  sub-directories of 1Mb or more:
    testdata   4.1Mb
    www       23.0Mb
* 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 ... WARNING
Found the following file with non-ASCII characters:
  gseaPlot.R
Portable packages must use only ASCII characters in their R code,
except perhaps in comments.
Use \uxxxx escapes for other characters.
* 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 ... NOTE
prepare_Rd: convertByAnnotationDB.Rd:24-29: 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 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 7.581   0.22   8.759
* 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: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/phantasus.Rcheck/00check.log’
for details.



Installation output

phantasus.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL phantasus
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-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
Loading config from /home/biocbuild/bbs-3.9-bioc/R/library/opencpu/config/defaults.conf
Loading config from /home/biocbuild/.local/share/opencpu/user.conf
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'phantasus'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Loading config from /home/biocbuild/bbs-3.9-bioc/R/library/opencpu/config/defaults.conf
Loading config from /home/biocbuild/.local/share/opencpu/user.conf
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'phantasus'
** testing if installed package can be loaded from final location
Loading config from /home/biocbuild/bbs-3.9-bioc/R/library/opencpu/config/defaults.conf
Loading config from /home/biocbuild/.local/share/opencpu/user.conf
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'phantasus'
** testing if installed package keeps a record of temporary installation path
* DONE (phantasus)

Tests output

phantasus.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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-3.9-bioc/R/library/opencpu/config/defaults.conf
Loading config from /home/biocbuild/.local/share/opencpu/user.conf
Warning message:
replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'phantasus' 
> 
> 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'
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 98 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 76.094   1.528  92.397 

Example timings

phantasus.Rcheck/phantasus-Ex.timings

nameusersystemelapsed
adjustDataset000
annotationDBMeta000
calcPCA000
checkGPLs000
collapseDataset0.0000.0000.001
createES0.0000.0000.001
es000
getES1.4810.0282.011
getGDS0.6410.0000.641
getGSE7.5810.2208.759
limmaAnalysis0.0000.0000.001
loadGEO000
performKmeans0.0000.0000.001
queryAnnotationDBMeta000
read.gct0.0260.0030.038
reparseCachedESs1.2950.0231.318
servePhantasus000
write.gct0.0290.0000.030