Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:07:03 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 scanMiR on tokay2


To the developers/maintainers of the scanMiR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scanMiR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 1704/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scanMiR 1.0.0  (landing page)
Fridolin Gross
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/scanMiR
git_branch: RELEASE_3_14
git_last_commit: 91f9c75
git_last_commit_date: 2021-10-26 13:11:11 -0500 (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: scanMiR
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scanMiR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings scanMiR_1.0.0.tar.gz
StartedAt: 2022-01-21 02:14:28 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 02:17:16 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 168.3 seconds
RetCode: 0
Status:   OK  
CheckDir: scanMiR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scanMiR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings scanMiR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/scanMiR.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scanMiR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scanMiR' version '1.0.0'
* 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 'scanMiR' 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 ... NOTE
.aggregateSiteInfo: no visible binding for global variable 'ORF'
.aggregateSiteInfo: no visible global function definition for '.'
.aggregateSiteInfo: no visible binding for global variable
  'ORF.canonical'
.aggregateSiteInfo: no visible binding for global variable '..cols'
.aggregate_miRNA: no visible binding for global variable 'ORF'
.aggregate_miRNA: no visible binding for global variable 'log_kd'
.aggregate_miRNA: no visible binding for global variable 'orf.length'
.aggregate_miRNA: no visible binding for global variable 'utr.length'
.aggregate_miRNA: no visible binding for global variable 'utr_score'
.aggregate_miRNA: no visible binding for global variable 'orf_score'
dummyKdData: no visible binding for global variable 'SampleKdModel'
plotKdModel: no visible binding for global variable 'seed'
plotKdModel: no visible binding for global variable 'log_kd'
viewTargetAlignment: no visible binding for global variable 'x'
viewTargetAlignment: no visible binding for global variable 'y'
viewTargetAlignment: no visible binding for global variable 'label'
Undefined global functions or variables:
  . ..cols ORF ORF.canonical SampleKdModel label log_kd orf.length
  orf_score seed utr.length utr_score x y
* 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 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 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/scanMiR.Rcheck/00check.log'
for details.



Installation output

scanMiR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/scanMiR_1.0.0.tar.gz && rm -rf scanMiR.buildbin-libdir && mkdir scanMiR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scanMiR.buildbin-libdir scanMiR_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL scanMiR_1.0.0.zip && rm scanMiR_1.0.0.tar.gz scanMiR_1.0.0.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
 34 47663   34 16229    0     0   138k      0 --:--:-- --:--:-- --:--:--  139k
100 47663  100 47663    0     0   308k      0 --:--:-- --:--:-- --:--:--  308k

install for i386

* installing *source* package 'scanMiR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'scanMiR'
    finding HTML links ... done
    KdModel                                 html  
    KdModelList-methods                     html  
    KdModelList                             html  
    SampleKdModel                           html  
    SampleTranscript                        html  
    aggregateMatches                        html  
    finding level-2 HTML links ... done

    assignKdType                            html  
    conservation                            html  
    dummyKdData                             html  
    findSeedMatches                         html  
    get3pAlignment                          html  
    get8merRange                            html  
    getKdModel                              html  
    getKmers                                html  
    getMatchTypes                           html  
    getRandomSeq                            html  
    getSeed8mers                            html  
    plotKdModel                             html  
    removeOverlappingRanges                 html  
    viewTargetAlignment                     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 'scanMiR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scanMiR' as scanMiR_1.0.0.zip
* DONE (scanMiR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'scanMiR' successfully unpacked and MD5 sums checked

Tests output

scanMiR.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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(scanMiR)
> 
> test_check("scanMiR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 76 ]
> 
> proc.time()
   user  system elapsed 
  11.71    0.29   12.00 

scanMiR.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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(scanMiR)
> 
> test_check("scanMiR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 76 ]
> 
> proc.time()
   user  system elapsed 
  11.75    0.29   12.03 

Example timings

scanMiR.Rcheck/examples_i386/scanMiR-Ex.timings

nameusersystemelapsed
KdModel000
KdModelList-methods000
KdModelList000
SampleKdModel0.000.020.01
aggregateMatches0.690.000.69
assignKdType0.060.000.06
conservation0.020.000.02
dummyKdData000
findSeedMatches0.50.00.5
get3pAlignment0.010.000.01
get8merRange000
getKdModel0.080.000.08
getKmers000
getMatchTypes000
getRandomSeq000
getSeed8mers000
plotKdModel0.270.010.28
removeOverlappingRanges0.310.000.31
viewTargetAlignment0.610.000.61

scanMiR.Rcheck/examples_x64/scanMiR-Ex.timings

nameusersystemelapsed
KdModel000
KdModelList-methods0.020.000.02
KdModelList000
SampleKdModel000
aggregateMatches0.630.010.64
assignKdType0.040.000.04
conservation000
dummyKdData000
findSeedMatches0.50.00.5
get3pAlignment0.010.000.01
get8merRange000
getKdModel0.070.020.08
getKmers000
getMatchTypes000
getRandomSeq000
getSeed8mers000
plotKdModel0.380.000.37
removeOverlappingRanges0.230.000.24
viewTargetAlignment0.710.000.70