Alexey Sergushichev
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/phantasus |
| Branch: RELEASE_3_10 |
| Last Commit: 80c7b42 |
| Last Changed Date: 2019-10-29 13:11:02 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:30:07 -0400 (Wed, 15 Apr 2020).
| Package 1253/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| phantasus 1.6.0 Alexey Sergushichev
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: phantasus |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:phantasus.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings phantasus_1.6.0.tar.gz |
| StartedAt: 2020-04-15 05:28:22 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:35:14 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 412.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: phantasus.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:phantasus.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings phantasus_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/phantasus.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.6.0'
* 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 27.5Mb
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 ... 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
loadSession: no visible binding for global variable 'es'
Undefined global functions or variables:
es
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'write.gct':
'...'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 or elapsed time > 5s
user system elapsed
getGSE 7.37 0.87 9.09
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getGSE 9.54 0.5 10.91
* 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: 1 WARNING, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/phantasus.Rcheck/00check.log'
for details.
phantasus.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/phantasus_1.6.0.tar.gz && rm -rf phantasus.buildbin-libdir && mkdir phantasus.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=phantasus.buildbin-libdir phantasus_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL phantasus_1.6.0.zip && rm phantasus_1.6.0.tar.gz phantasus_1.6.0.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 9775k 100 9775k 0 0 40.3M 0 --:--:-- --:--:-- --:--:-- 40.9M
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
checkGPLs html
collapseDataset html
convertByAnnotationDB html
createES html
es 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
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_1.6.0.zip
* DONE (phantasus)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'phantasus' successfully unpacked and MD5 sums checked
|
phantasus.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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-3.10-bioc/R/library/opencpu/config/defaults.conf
Loading config from C:\Users\biocbuild\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://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://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://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'
== testthat results ===========================================================
[ OK: 94 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 0 ]
>
> proc.time()
user system elapsed
85.50 6.03 106.21
|
phantasus.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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-3.10-bioc/R/library/opencpu/config/defaults.conf
Loading config from C:\Users\biocbuild\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://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://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://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'
== testthat results ===========================================================
[ OK: 94 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 0 ]
>
> proc.time()
user system elapsed
82.00 5.45 101.90
|
|
phantasus.Rcheck/examples_i386/phantasus-Ex.timings
|
phantasus.Rcheck/examples_x64/phantasus-Ex.timings
|