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CHECK report for miRcomp on tokay2

This page was generated on 2018-10-17 08:41:18 -0400 (Wed, 17 Oct 2018).

Package 915/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miRcomp 1.10.0
Matthew N. McCall
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/miRcomp
Branch: RELEASE_3_7
Last Commit: 243196c
Last Changed Date: 2018-04-30 10:35:38 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: miRcomp
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:miRcomp.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings miRcomp_1.10.0.tar.gz
StartedAt: 2018-10-17 03:23:59 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 03:25:07 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 67.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: miRcomp.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:miRcomp.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings miRcomp_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/miRcomp.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.10.0'
* 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    243Kb       xz
  qpcRb5.rda         288Kb    242Kb       xz
  qpcRdefault.rda    290Kb    242Kb       xz
  qpcRl5.rda         287Kb    239Kb       xz
  qpcRlinexp.rda     235Kb    205Kb       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-3.7-bioc/meat/miRcomp.Rcheck/00check.log'
for details.



Installation output

miRcomp.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/miRcomp_1.10.0.tar.gz && rm -rf miRcomp.buildbin-libdir && mkdir miRcomp.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=miRcomp.buildbin-libdir miRcomp_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL miRcomp_1.10.0.zip && rm miRcomp_1.10.0.tar.gz miRcomp_1.10.0.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 1800k  100 1800k    0     0  21.8M      0 --:--:-- --:--:-- --:--:-- 23.7M

install for i386

* installing *source* package 'miRcomp' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'miRcomp' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'miRcomp' as miRcomp_1.10.0.zip
* DONE (miRcomp)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'miRcomp' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

miRcomp.Rcheck/tests_i386/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, 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 -- Wed Oct 17 03:24:59 2018 
*********************************************** 
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 
   2.82    0.12    2.93 

miRcomp.Rcheck/tests_x64/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, 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 -- Wed Oct 17 03:25:02 2018 
*********************************************** 
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    0.14    2.67 

Example timings

miRcomp.Rcheck/examples_i386/miRcomp-Ex.timings

nameusersystemelapsed
accuracy1.420.021.45
completeFeatures0.050.010.06
expressionComp0.170.020.19
lifetech0.020.000.01
limitOfDetection0.770.030.80
miRcompShinyApp0.010.000.02
precision1.080.001.07
qpcRb4000
qpcRb50.020.000.01
qpcRdefault0.000.010.02
qpcRl5000
qpcRlinexp0.000.020.02
qualityAssessment0.230.000.23
titrationResponse0.800.000.79

miRcomp.Rcheck/examples_x64/miRcomp-Ex.timings

nameusersystemelapsed
accuracy1.560.041.61
completeFeatures0.050.000.04
expressionComp0.120.020.14
lifetech0.020.000.01
limitOfDetection0.650.010.68
miRcompShinyApp000
precision1.20.01.2
qpcRb4000
qpcRb50.000.020.02
qpcRdefault0.020.000.02
qpcRl5000
qpcRlinexp0.010.000.01
qualityAssessment0.140.020.16
titrationResponse0.800.010.81