Multiple platform build/check report for BioC 3.14 - CHECK results for miRcomp on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (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*

Package: miRcomp

Version: 1.24.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:miRcomp.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings miRcomp_1.24.0.tar.gz

StartedAt: 2022-04-12 22:58:32 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 22:59:44 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 71.3 seconds

RetCode: 0

Status: WARNINGS

CheckDir: miRcomp.Rcheck

Warnings: 1

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:miRcomp.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings miRcomp_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/miRcomp.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 'miRcomp/DESCRIPTION' ... OK
* this is package 'miRcomp' version '1.24.0'
* 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 'miRcomp' 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                  old_size new_size compress
  lifetech.rda       350Kb    276Kb       xz
  qpcRb4.rda         290Kb    244Kb       xz
  qpcRb5.rda         288Kb    242Kb       xz
  qpcRdefault.rda    290Kb    242Kb       xz
  qpcRl5.rda         287Kb    239Kb       xz
  qpcRlinexp.rda     235Kb    199Kb       xz
* 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/miRcomp.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/miRcomp_1.24.0.tar.gz && rm -rf miRcomp.buildbin-libdir && mkdir miRcomp.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=miRcomp.buildbin-libdir miRcomp_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL miRcomp_1.24.0.zip && rm miRcomp_1.24.0.tar.gz miRcomp_1.24.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  4 1802k    4 80787    0     0   298k      0  0:00:06 --:--:--  0:00:06  297k
 55 1802k   55  992k    0     0   785k      0  0:00:02  0:00:01  0:00:01  785k
100 1802k  100 1802k    0     0  1026k      0  0:00:01  0:00:01 --:--:-- 1026k

install for i386

* installing *source* package 'miRcomp' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'miRcomp'
    finding HTML links ... done
    accuracy                                html  
    completeFeatures                        html  
    expressionComp                          html  
    lifetech                                html  
    limitOfDetection                        html  
    miRcompShinyApp                         html  
    precision                               html  
    qpcRb4                                  html  
    qpcRb5                                  html  
    qpcRdefault                             html  
    qpcRl5                                  html  
    qpcRlinexp                              html  
    qualityAssessment                       html  
    titrationResponse                       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 'miRcomp' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'miRcomp' as miRcomp_1.24.0.zip
* DONE (miRcomp)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'miRcomp' successfully unpacked and MD5 sums checked


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.

> BiocGenerics:::testPackage("miRcomp")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.



RUNIT TEST PROTOCOL -- Tue Apr 12 22:59:33 2022 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
miRcomp RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   2.54    0.12    2.65


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.

> BiocGenerics:::testPackage("miRcomp")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.



RUNIT TEST PROTOCOL -- Tue Apr 12 22:59:36 2022 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
miRcomp RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   2.46    0.06    2.51

name	user	system	elapsed
accuracy	1.16	0.02	1.17
completeFeatures	0.04	0.00	0.05
expressionComp	0.14	0.00	0.14
lifetech	0.02	0.00	0.01
limitOfDetection	0.57	0.03	0.61
miRcompShinyApp	0	0	0
precision	0.77	0.01	0.78
qpcRb4	0	0	0
qpcRb5	0.01	0.00	0.01
qpcRdefault	0	0	0
qpcRl5	0.02	0.00	0.02
qpcRlinexp	0	0	0
qualityAssessment	0.17	0.02	0.19
titrationResponse	0.61	0.00	0.61

name	user	system	elapsed
accuracy	1.52	0.00	1.56
completeFeatures	0.04	0.00	0.04
expressionComp	0.16	0.00	0.16
lifetech	0	0	0
limitOfDetection	0.68	0.02	0.70
miRcompShinyApp	0	0	0
precision	0.91	0.02	0.92
qpcRb4	0.01	0.00	0.02
qpcRb5	0	0	0
qpcRdefault	0.02	0.00	0.01
qpcRl5	0	0	0
qpcRlinexp	0.02	0.00	0.02
qualityAssessment	0.15	0.01	0.17
titrationResponse	0.71	0.02	0.72

CHECK results for miRcomp on tokay2

Summary

Command output

Installation output

Tests output

Example timings