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This page was generated on 2022-04-13 12:06:54 -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 miRNAmeConverter on tokay2


To the developers/maintainers of the miRNAmeConverter package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miRNAmeConverter.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 1167/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miRNAmeConverter 1.22.0  (landing page)
Stefan J. Haunsberger
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/miRNAmeConverter
git_branch: RELEASE_3_14
git_last_commit: ca6bcbb
git_last_commit_date: 2021-10-26 12:26:05 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: miRNAmeConverter
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:miRNAmeConverter.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings miRNAmeConverter_1.22.0.tar.gz
StartedAt: 2022-04-12 23:00:01 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 23:03:41 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 219.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: miRNAmeConverter.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:miRNAmeConverter.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings miRNAmeConverter_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/miRNAmeConverter.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 'miRNAmeConverter/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'miRNAmeConverter' version '1.22.0'
* 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 'miRNAmeConverter' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ...It is recommended to use 'given' instead of 'middle'.
 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 ... NOTE
MiRNANameConverter,ANY: no visible global function definition for 'new'
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'getMirnasForMirbaseVersion'
Undocumented S4 methods:
  generic 'getMirnasForMirbaseVersion' and siglist 'MiRNANameConverter'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
MiRNANameConverter-ANY-method  0.3   0.33   53.72
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/miRNAmeConverter.Rcheck/00check.log'
for details.



Installation output

miRNAmeConverter.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/miRNAmeConverter_1.22.0.tar.gz && rm -rf miRNAmeConverter.buildbin-libdir && mkdir miRNAmeConverter.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=miRNAmeConverter.buildbin-libdir miRNAmeConverter_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL miRNAmeConverter_1.22.0.zip && rm miRNAmeConverter_1.22.0.tar.gz miRNAmeConverter_1.22.0.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  313k  100  313k    0     0   762k      0 --:--:-- --:--:-- --:--:--  763k

install for i386

* installing *source* package 'miRNAmeConverter' ...
** using staged installation
It is recommended to use 'given' instead of 'middle'.
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function from function 'MiRNANameConverter' in package 'miRNAmeConverter'
** help
*** installing help indices
  converting help for package 'miRNAmeConverter'
    finding HTML links ... done
    MiRNANameConverter-ANY-method           html  
    MiRNANameConverter                      html  
    assessMiRNASwappingMIMAT                html  
    assessVersion                           html  
    checkMiRNAName                          html  
    currentVersion-set                      html  
    currentVersion                          html  
    example.miRNAs                          html  
    miRNAmeConverter                        html  
    nOrganisms-set                          html  
    nOrganisms                              html  
    nTotalEntries-set                       html  
    nTotalEntries                           html  
    saveResults                             html  
    show-MiRNANameConverter-method          html  
    translateMiRNAName                      html  
    validOrganisms-set                      html  
    validOrganisms                          html  
    validVersions-set                       html  
    validVersions                           html  
** building package indices
** 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 'miRNAmeConverter' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'miRNAmeConverter' as miRNAmeConverter_1.22.0.zip
* DONE (miRNAmeConverter)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'miRNAmeConverter' successfully unpacked and MD5 sums checked

Tests output

miRNAmeConverter.Rcheck/tests_i386/testthat.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.

> library(testthat)
> library(miRNAmeConverter)
Loading required package: miRBaseVersions.db
> 
> test_check("miRNAmeConverter")
	miRNA 'hsa-let-7a-3p' is the same as 'hsa-let-7a*'.
	->hsa-let-7a-3p is the most recent one and will be used. The other ones will be neglected.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
   9.59    0.40    9.98 

miRNAmeConverter.Rcheck/tests_x64/testthat.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.

> library(testthat)
> library(miRNAmeConverter)
Loading required package: miRBaseVersions.db
> 
> test_check("miRNAmeConverter")
	miRNA 'hsa-let-7a-3p' is the same as 'hsa-let-7a*'.
	->hsa-let-7a-3p is the most recent one and will be used. The other ones will be neglected.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
   8.64    0.29    8.92 

Example timings

miRNAmeConverter.Rcheck/examples_i386/miRNAmeConverter-Ex.timings

nameusersystemelapsed
MiRNANameConverter-ANY-method 0.30 0.3353.72
assessVersion0.490.000.49
checkMiRNAName0.250.000.25
currentVersion0.110.000.11
miRNAmeConverter0.790.000.80
nOrganisms0.110.000.11
nTotalEntries0.110.000.11
saveResults0.940.000.94
translateMiRNAName0.940.000.93
validOrganisms0.100.000.09
validVersions0.090.000.10

miRNAmeConverter.Rcheck/examples_x64/miRNAmeConverter-Ex.timings

nameusersystemelapsed
MiRNANameConverter-ANY-method0.060.080.14
assessVersion0.250.000.25
checkMiRNAName0.170.000.17
currentVersion0.080.000.08
miRNAmeConverter0.780.000.78
nOrganisms0.110.000.11
nTotalEntries0.090.000.09
saveResults0.920.000.95
translateMiRNAName1.050.001.05
validOrganisms0.080.000.07
validVersions0.090.000.10