Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:07:11 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 scruff on palomino4


To the developers/maintainers of the scruff package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scruff.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 1771/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scruff 1.15.0  (landing page)
Zhe Wang
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/scruff
git_branch: master
git_last_commit: add27b1
git_last_commit_date: 2022-04-26 11:50:08 -0400 (Tue, 26 Apr 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: scruff
Version: 1.15.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scruff.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings scruff_1.15.0.tar.gz
StartedAt: 2022-06-24 05:37:50 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 05:45:05 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 435.5 seconds
RetCode: 0
Status:   OK  
CheckDir: scruff.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scruff.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings scruff_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/scruff.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'scruff/DESCRIPTION' ... OK
* this is package 'scruff' version '1.15.0'
* 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 'scruff' 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 ... NOTE
Unexported object imported by a ':::' call: 'ShortRead:::.set_omp_threads'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call(ShortRead:::.set_omp_threads, ...)
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* 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
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
tenxBamqc   6.84   0.22   42.87
rview       5.08   0.02    5.10
qcplots     4.87   0.14    5.01
demultiplex 2.41   0.19   33.75
* 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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/scruff.Rcheck/00check.log'
for details.



Installation output

scruff.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/scruff_1.15.0.tar.gz && rm -rf scruff.buildbin-libdir && mkdir scruff.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scruff.buildbin-libdir scruff_1.15.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL scruff_1.15.0.zip && rm scruff_1.15.0.tar.gz scruff_1.15.0.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 4408k  100 4408k    0     0  15.4M      0 --:--:-- --:--:-- --:--:-- 15.5M
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'scruff' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 'scruff' as scruff_1.15.0.zip
* DONE (scruff)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'scruff' successfully unpacked and MD5 sums checked

Tests output

scruff.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
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(scruff)
> 
> test_check("scruff")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  15.54    1.10   16.62 

Example timings

scruff.Rcheck/scruff-Ex.timings

nameusersystemelapsed
alignRsubread000
countUMI0.020.000.02
demultiplex 2.41 0.1933.75
gview1.110.061.17
qcplots4.870.145.01
rview5.080.025.10
scruff000
tenxBamqc 6.84 0.2242.87