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CHECK report for phantasus on tokay1

This page was generated on 2021-05-06 12:32:44 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the phantasus package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1334/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phantasus 1.10.0  (landing page)
Alexey Sergushichev
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/phantasus
Branch: RELEASE_3_12
Last Commit: efcdf05
Last Changed Date: 2020-10-27 11:33:27 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: phantasus
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:phantasus.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings phantasus_1.10.0.tar.gz
StartedAt: 2021-05-06 05:30:12 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:38:33 -0400 (Thu, 06 May 2021)
EllapsedTime: 501.1 seconds
RetCode: 0
Status:   OK   
CheckDir: phantasus.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:phantasus.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings phantasus_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/phantasus.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.10.0'
* 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 ... OK
* checking for portable file names ... 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   4.2Mb
    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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
getGSE 10.19   1.12   12.55
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
getGSE 8.31   0.48    10.3
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/phantasus.Rcheck/00check.log'
for details.

Installation output

phantasus.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/phantasus_1.10.0.tar.gz && rm -rf phantasus.buildbin-libdir && mkdir phantasus.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=phantasus.buildbin-libdir phantasus_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL phantasus_1.10.0.zip && rm phantasus_1.10.0.tar.gz phantasus_1.10.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 10.3M  100 10.3M    0     0  21.5M      0 --:--:-- --:--:-- --:--:-- 21.6M

install for i386

* 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  
    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

install for x64

* installing *source* package 'phantasus' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'phantasus' as phantasus_1.10.0.zip
* DONE (phantasus)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'phantasus' successfully unpacked and MD5 sums checked

Tests output

phantasus.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 C:/Users/biocbuild/bbs-3.12-bioc/R/library/opencpu/config/defaults.conf
Loading config from C:\Users\BIOCBU~1\AppData\Local/opencpu/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'
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 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'
 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'
 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=quick'
Content type 'geo/text' length unknown
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downloaded 7.1 MB

[ FAIL 0 | WARN 19 | SKIP 0 | PASS 95 ]
> 
> proc.time()
   user  system elapsed 
 106.87   10.45  143.18

phantasus.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 C:/Users/biocbuild/bbs-3.12-bioc/R/library/opencpu/config/defaults.conf
Loading config from C:\Users\BIOCBU~1\AppData\Local/opencpu/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'
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 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'
 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'
 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=quick'
Content type 'geo/text' length unknown
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downloaded 7.1 MB

[ FAIL 0 | WARN 19 | SKIP 0 | PASS 95 ]
> 
> proc.time()
   user  system elapsed 
  98.98    5.85  121.18

Example timings

phantasus.Rcheck/examples_i386/phantasus-Ex.timings

nameusersystemelapsed
adjustDataset000
annotationDBMeta000
calcPCA000
checkGPLsFallback000
collapseDataset000
createES000
es000
generatePreloadedSession1.520.063.22
getES2.210.162.87
getGDS1.020.061.08
getGSE10.19 1.1212.55
limmaAnalysis000
loadGEO000
performKmeans000
queryAnnotationDBMeta000
read.gct0.050.000.05
reparseCachedESs1.690.071.75
reproduceInR000
servePhantasus000
write.gct0.040.000.05

phantasus.Rcheck/examples_x64/phantasus-Ex.timings

nameusersystemelapsed
adjustDataset000
annotationDBMeta000
calcPCA000
checkGPLsFallback000
collapseDataset000
createES000
es000
generatePreloadedSession1.090.032.91
getES1.050.101.54
getGDS0.580.060.64
getGSE 8.31 0.4810.30
limmaAnalysis000
loadGEO000
performKmeans000
queryAnnotationDBMeta000
read.gct0.030.000.03
reparseCachedESs0.970.031.00
reproduceInR000
servePhantasus000
write.gct0.030.000.03