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This page was generated on 2021-10-18 12:04:19 -0400 (Mon, 18 Oct 2021).

CHECK results for ROSeq on riesling1

To the developers/maintainers of the ROSeq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ROSeq.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 1628/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ROSeq 1.5.0  (landing page)
Krishan Gupta
Snapshot Date: 2021-10-17 14:50:03 -0400 (Sun, 17 Oct 2021)
git_url: https://git.bioconductor.org/packages/ROSeq
git_branch: master
git_last_commit: a291781
git_last_commit_date: 2021-05-19 12:51:57 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    NA  

Summary

Package: ROSeq
Version: 1.5.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ROSeq.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ROSeq_1.5.0.tar.gz
StartedAt: 2021-10-18 02:50:47 -0400 (Mon, 18 Oct 2021)
EndedAt: 2021-10-18 02:57:18 -0400 (Mon, 18 Oct 2021)
EllapsedTime: 391.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ROSeq.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ROSeq.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ROSeq_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/ROSeq.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ROSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ROSeq' version '1.5.0'
* 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 'ROSeq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... 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 ... WARNING
  LazyData DB of 7.2 MB without LazyDataCompression set
  See ยง1.1.6 of 'Writing R Extensions'
* 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
ROSeq            116.48   0.59  117.16
TMMnormalization   5.87   0.47    6.34
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
ROSeq            127.45   0.75  128.27
TMMnormalization   5.03   0.52    5.54
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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, 2 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/ROSeq.Rcheck/00check.log'
for details.



Installation output

ROSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ROSeq_1.5.0.tar.gz && rm -rf ROSeq.buildbin-libdir && mkdir ROSeq.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ROSeq.buildbin-libdir ROSeq_1.5.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ROSeq_1.5.0.zip && rm ROSeq_1.5.0.tar.gz ROSeq_1.5.0.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 4286k  100 4286k    0     0  8731k      0 --:--:-- --:--:-- --:--:-- 8731k

install for i386

* installing *source* package 'ROSeq' ...
** 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 'ROSeq'
    finding HTML links ... done
    L_Tung_single                           html  
    ROSeq                                   html  
    TMMnormalization                        html  
    computeDEG                              html  
    findParams                              html  
    getDataStatistics                       html  
    getI                                    html  
    getd                                    html  
    getdu1da                                html  
    getdu1db                                html  
    getdu2da                                html  
    getdu2db                                html  
    getdvda                                 html  
    getdvdb                                 html  
    getu1                                   html  
    getu2                                   html  
    getv                                    html  
    initiateAnalysis                        html  
    minimizeNLL                             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 'ROSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ROSeq' as ROSeq_1.5.0.zip
* DONE (ROSeq)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'ROSeq' successfully unpacked and MD5 sums checked

Tests output

ROSeq.Rcheck/tests_i386/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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.

> BiocGenerics:::testPackage("ROSeq")


RUNIT TEST PROTOCOL -- Mon Oct 18 02:55:29 2021 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ROSeq RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   0.62    0.06    0.65 

ROSeq.Rcheck/tests_x64/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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.

> BiocGenerics:::testPackage("ROSeq")


RUNIT TEST PROTOCOL -- Mon Oct 18 02:55:30 2021 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ROSeq RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   0.67    0.01    0.67 

Example timings

ROSeq.Rcheck/examples_i386/ROSeq-Ex.timings

nameusersystemelapsed
L_Tung_single000
ROSeq116.48 0.59117.16
TMMnormalization5.870.476.34

ROSeq.Rcheck/examples_x64/ROSeq-Ex.timings

nameusersystemelapsed
L_Tung_single0.020.000.01
ROSeq127.45 0.75128.27
TMMnormalization5.030.525.54