Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:22 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 similaRpeak on tokay2


To the developers/maintainers of the similaRpeak package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/similaRpeak.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 1801/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
similaRpeak 1.26.0  (landing page)
Astrid Deschenes
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/similaRpeak
git_branch: RELEASE_3_14
git_last_commit: 9b96ea4
git_last_commit_date: 2021-10-26 12:20:36 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: similaRpeak
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:similaRpeak.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings similaRpeak_1.26.0.tar.gz
StartedAt: 2022-04-13 03:00:45 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 03:01:22 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 37.2 seconds
RetCode: 0
Status:   OK  
CheckDir: similaRpeak.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:similaRpeak.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings similaRpeak_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/similaRpeak.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'similaRpeak/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'similaRpeak' version '1.26.0'
* 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 'similaRpeak' 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: OK

Installation output

similaRpeak.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/similaRpeak_1.26.0.tar.gz && rm -rf similaRpeak.buildbin-libdir && mkdir similaRpeak.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=similaRpeak.buildbin-libdir similaRpeak_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL similaRpeak_1.26.0.zip && rm similaRpeak_1.26.0.tar.gz similaRpeak_1.26.0.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  220k  100  220k    0     0   590k      0 --:--:-- --:--:-- --:--:--  592k

install for i386

* installing *source* package 'similaRpeak' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'similaRpeak'
    finding HTML links ... done
    DiffPosMax                              html  
    Metric                                  html  
    MetricFactory                           html  
    RatioArea                               html  
    RatioIntersect                          html  
    RatioMaxMax                             html  
    RatioNormalizedIntersect                html  
    SpearmanCorrelation                     html  
    chr7Profiles                            html  
    demoProfiles                            html  
    diffPosMaxMethod                        html  
    ratioAreaMethod                         html  
    ratioIntersectMethod                    html  
    ratioMaxMaxMethod                       html  
    similaRpeak-package                     html  
    similarity                              html  
    spearmanCorrMethod                      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 'similaRpeak' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'similaRpeak' as similaRpeak_1.26.0.zip
* DONE (similaRpeak)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'similaRpeak' successfully unpacked and MD5 sums checked

Tests output

similaRpeak.Rcheck/tests_i386/runTests.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.

> ## Run all tests in the similaRpeak package
> BiocGenerics:::testPackage("similaRpeak")
Metric type: NA. Metric value: NA


RUNIT TEST PROTOCOL -- Wed Apr 13 03:01:11 2022 
*********************************************** 
Number of test functions: 84 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
similaRpeak RUnit Tests - 84 test functions, 0 errors, 0 failures
Number of test functions: 84 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In max(profile1, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
2: In max(profile2, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
> 
> 
> proc.time()
   user  system elapsed 
   0.64    0.04    0.68

similaRpeak.Rcheck/tests_x64/runTests.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
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.

> ## Run all tests in the similaRpeak package
> BiocGenerics:::testPackage("similaRpeak")
Metric type: NA. Metric value: NA


RUNIT TEST PROTOCOL -- Wed Apr 13 03:01:12 2022 
*********************************************** 
Number of test functions: 84 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
similaRpeak RUnit Tests - 84 test functions, 0 errors, 0 failures
Number of test functions: 84 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In max(profile1, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
2: In max(profile2, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
> 
> 
> proc.time()
   user  system elapsed 
   0.95    0.10    1.04

Example timings

similaRpeak.Rcheck/examples_i386/similaRpeak-Ex.timings

nameusersystemelapsed
MetricFactory0.140.000.14
chr7Profiles0.010.010.03
demoProfiles000
similarity0.030.000.03

similaRpeak.Rcheck/examples_x64/similaRpeak-Ex.timings

nameusersystemelapsed
MetricFactory0.120.000.12
chr7Profiles0.000.030.04
demoProfiles0.000.020.01
similarity0.000.010.02