Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:44 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for muscat on tokay2


To the developers/maintainers of the muscat package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/muscat.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 1253/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
muscat 1.8.1  (landing page)
Helena L. Crowell
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/muscat
git_branch: RELEASE_3_14
git_last_commit: 06006c2
git_last_commit_date: 2022-01-14 03:51:16 -0500 (Fri, 14 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  YES
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: muscat
Version: 1.8.1
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:muscat.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings muscat_1.8.1.tar.gz
StartedAt: 2022-01-20 23:35:39 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 23:49:37 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 839.0 seconds
RetCode: 0
Status:   OK  
CheckDir: muscat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:muscat.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings muscat_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/muscat.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'muscat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'muscat' version '1.8.1'
* 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 'muscat' 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
* 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 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
simData   19.03   0.22   28.15
prepSim   14.51   0.14   14.66
mmDS      11.03   0.36   11.43
pbHeatmap  8.66   0.22    8.88
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
simData   16.36   0.09   16.46
prepSim   12.76   0.17   12.94
mmDS      10.47   0.16   12.08
pbHeatmap  7.86   0.03    7.89
* 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: OK


Installation output

muscat.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/muscat_1.8.1.tar.gz && rm -rf muscat.buildbin-libdir && mkdir muscat.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=muscat.buildbin-libdir muscat_1.8.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL muscat_1.8.1.zip && rm muscat_1.8.1.tar.gz muscat_1.8.1.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
 60 2034k   60 1239k    0     0  2241k      0 --:--:-- --:--:-- --:--:-- 2241k
100 2034k  100 2034k    0     0  2633k      0 --:--:-- --:--:-- --:--:-- 2632k

install for i386

* installing *source* package 'muscat' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning in checkMatrixPackageVersion() :
  Package version inconsistency detected.
TMB was built with Matrix version 1.3.4
Current Matrix version is 1.4.0
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
** help
*** installing help indices
  converting help for package 'muscat'
    finding HTML links ... done
    aggregateData                           html  
    calcExprFreqs                           html  
    data                                    html  
    mmDS                                    html  
    pbDS                                    html  
    pbFlatten                               html  
    pbHeatmap                               html  
    finding level-2 HTML links ... done

    pbMDS                                   html  
    prepSCE                                 html  
    prepSim                                 html  
    resDS                                   html  
    simData                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in checkMatrixPackageVersion() :
  Package version inconsistency detected.
TMB was built with Matrix version 1.3.4
Current Matrix version is 1.4.0
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
** testing if installed package can be loaded from final location
Warning in checkMatrixPackageVersion() :
  Package version inconsistency detected.
TMB was built with Matrix version 1.3.4
Current Matrix version is 1.4.0
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'muscat' ...
** testing if installed package can be loaded
Warning in checkMatrixPackageVersion() :
  Package version inconsistency detected.
TMB was built with Matrix version 1.3.4
Current Matrix version is 1.4.0
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
* MD5 sums
packaged installation of 'muscat' as muscat_1.8.1.zip
* DONE (muscat)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'muscat' successfully unpacked and MD5 sums checked

Tests output

muscat.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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(muscat)
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.3.4
Current Matrix version is 1.4.0
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
> 
> test_check("muscat")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 551 ]
> 
> proc.time()
   user  system elapsed 
 156.46    2.51  175.18 

muscat.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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(muscat)
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.3.4
Current Matrix version is 1.4.0
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
> 
> test_check("muscat")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 551 ]
> 
> proc.time()
   user  system elapsed 
 172.18    1.46  174.71 

Example timings

muscat.Rcheck/examples_i386/muscat-Ex.timings

nameusersystemelapsed
aggregateData4.650.134.78
calcExprFreqs1.260.091.36
data000
mmDS11.03 0.3611.43
pbDS2.570.042.61
pbFlatten1.670.051.72
pbHeatmap8.660.228.88
pbMDS1.280.001.28
prepSCE0.880.000.87
prepSim14.51 0.1414.66
resDS4.130.094.22
simData19.03 0.2228.15

muscat.Rcheck/examples_x64/muscat-Ex.timings

nameusersystemelapsed
aggregateData3.860.083.94
calcExprFreqs1.110.031.14
data000
mmDS10.47 0.1612.08
pbDS2.330.032.36
pbFlatten1.830.001.82
pbHeatmap7.860.037.89
pbMDS1.210.021.24
prepSCE0.880.000.87
prepSim12.76 0.1712.94
resDS3.850.053.89
simData16.36 0.0916.46