Back to Multiple platform build/check report for BioC 3.16
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2022-08-18 11:06:53 -0400 (Thu, 18 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4379
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4161
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4169
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 palomino4


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? 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 1286/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
muscat 1.11.2  (landing page)
Helena L. Crowell
Snapshot Date: 2022-08-17 14:00:04 -0400 (Wed, 17 Aug 2022)
git_url: https://git.bioconductor.org/packages/muscat
git_branch: master
git_last_commit: fd893e8
git_last_commit_date: 2022-06-17 01:39:15 -0400 (Fri, 17 Jun 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: muscat
Version: 1.11.2
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:muscat.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings muscat_1.11.2.tar.gz
StartedAt: 2022-08-18 03:54:34 -0400 (Thu, 18 Aug 2022)
EndedAt: 2022-08-18 04:02:02 -0400 (Thu, 18 Aug 2022)
EllapsedTime: 447.2 seconds
RetCode: 0
Status:   OK  
CheckDir: muscat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:muscat.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings muscat_1.11.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/muscat.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'muscat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'muscat' version '1.11.2'
* 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
simData   13.27   0.09   13.38
prepSim   10.28   0.11   10.39
mmDS       8.20   0.19    8.39
pbHeatmap  7.08   0.11    7.18
* 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: OK


Installation output

muscat.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/muscat_1.11.2.tar.gz && rm -rf muscat.buildbin-libdir && mkdir muscat.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=muscat.buildbin-libdir muscat_1.11.2.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL muscat_1.11.2.zip && rm muscat_1.11.2.tar.gz muscat_1.11.2.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
 45 1620k   45  730k    0     0  2044k      0 --:--:-- --:--:-- --:--:-- 2045k
100 1620k  100 1620k    0     0  2637k      0 --:--:-- --:--:-- --:--:-- 2638k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'muscat' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning in checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.0
Current TMB version is 1.9.1
Please re-install glmmTMB from source or restore original 'TMB' package (see '?reinstalling' for more information)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.0
Current TMB version is 1.9.1
Please re-install glmmTMB from source or restore original 'TMB' package (see '?reinstalling' for more information)
** testing if installed package can be loaded from final location
Warning in checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.0
Current TMB version is 1.9.1
Please re-install glmmTMB from source or restore original 'TMB' package (see '?reinstalling' for more information)
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'muscat' as muscat_1.11.2.zip
* DONE (muscat)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'muscat' successfully unpacked and MD5 sums checked

Tests output

muscat.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 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 checkDepPackageVersion(dep_pkg = "TMB") :
  Package version inconsistency detected.
glmmTMB was built with TMB version 1.9.0
Current TMB version is 1.9.1
Please re-install glmmTMB from source or restore original 'TMB' package (see '?reinstalling' for more information)
> 
> test_check("muscat")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 551 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 551 ]
> 
> proc.time()
   user  system elapsed 
 119.15    2.12  121.26 

Example timings

muscat.Rcheck/muscat-Ex.timings

nameusersystemelapsed
aggregateData2.560.062.63
calcExprFreqs0.530.030.56
data000
mmDS8.200.198.39
pbDS2.500.022.52
pbFlatten0.970.121.09
pbHeatmap7.080.117.18
pbMDS0.820.030.85
prepSCE0.760.060.82
prepSim10.28 0.1110.39
resDS4.310.054.36
simData13.27 0.0913.38