Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2021-11-30 13:54:44 -0500 (Tue, 30 Nov 2021).

CHECK results for ASSIGN on riesling1

To the developers/maintainers of the ASSIGN package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ASSIGN.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.

raw results

Package 90/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASSIGN 1.31.0  (landing page)
Ying Shen , W. Evan Johnson
Snapshot Date: 2021-11-29 14:50:17 -0500 (Mon, 29 Nov 2021)
git_url: https://git.bioconductor.org/packages/ASSIGN
git_branch: master
git_last_commit: f1c4527
git_last_commit_date: 2021-10-26 12:12:42 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ASSIGN
Version: 1.31.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASSIGN.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ASSIGN_1.31.0.tar.gz
StartedAt: 2021-11-30 00:44:56 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 00:49:46 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 290.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ASSIGN.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ASSIGN.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ASSIGN_1.31.0.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ASSIGN.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ASSIGN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ASSIGN' version '1.31.0'
* 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:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'ASSIGN' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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 ... OK
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* 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 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/ASSIGN.Rcheck/00check.log'
for details.



Installation output

ASSIGN.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.15/bioc/src/contrib/ASSIGN_1.31.0.tar.gz && rm -rf ASSIGN.buildbin-libdir && mkdir ASSIGN.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ASSIGN.buildbin-libdir ASSIGN_1.31.0.tar.gz && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ASSIGN_1.31.0.zip && rm ASSIGN_1.31.0.tar.gz ASSIGN_1.31.0.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 1363k  100 1363k    0     0  2870k      0 --:--:-- --:--:-- --:--:-- 2870k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'ASSIGN' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ASSIGN'
    finding HTML links ... done
    ComBat.step2                            html  
    assign.convergence                      html  
    assign.cv.output                        html  
    assign.mcmc                             html  
    assign.output                           html  
    assign.preprocess                       html  
    assign.summary                          html  
    assign.wrapper                          html  
    excludegenes                            html  
    gather_assign_results                   html  
    geneList1                               html  
    gfrn_geneList                           html  
    merge_drop                              html  
    optimizeGFRN                            html  
    pcaplot                                 html  
    runassignGFRN                           html  
    testData1                               html  
    trainingData1                           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
* MD5 sums
packaged installation of 'ASSIGN' as ASSIGN_1.31.0.zip
* DONE (ASSIGN)
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
package 'ASSIGN' successfully unpacked and MD5 sums checked

Tests output

ASSIGN.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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(ASSIGN)
> 
> test_check("ASSIGN")
== Skipped tests ===============================================================
* On CRAN (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
   1.68    0.20    1.93 

Example timings

ASSIGN.Rcheck/ASSIGN-Ex.timings

nameusersystemelapsed
assign.convergence000
assign.cv.output1.170.161.35
assign.mcmc0.300.270.56
assign.output1.480.101.63
assign.preprocess0.000.020.01
assign.summary0.480.090.58
assign.wrapper1.690.191.87
merge_drop000
optimizeGFRN000
runassignGFRN000