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CHECK report for alpine on tokay1

This page was generated on 2020-09-27 10:17:41 -0400 (Sun, 27 Sep 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE alpine PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 44/1923HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alpine 1.15.0
Michael Love
Snapshot Date: 2020-09-26 14:42:06 -0400 (Sat, 26 Sep 2020)
URL: https://git.bioconductor.org/packages/alpine
Branch: master
Last Commit: ba310e3
Last Changed Date: 2020-04-27 15:00:57 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: alpine
Version: 1.15.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:alpine.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings alpine_1.15.0.tar.gz
StartedAt: 2020-09-27 04:02:49 -0400 (Sun, 27 Sep 2020)
EndedAt: 2020-09-27 04:12:45 -0400 (Sun, 27 Sep 2020)
EllapsedTime: 595.6 seconds
RetCode: 0
Status:  OK  
CheckDir: alpine.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:alpine.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings alpine_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/alpine.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'alpine/DESCRIPTION' ... OK
* this is package 'alpine' version '1.15.0'
* 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 'alpine' 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 ... NOTE
Unexported object imported by a ':::' call: 'S4Vectors:::fancy_mseq'
  See the note in ?`:::` about the use of this operator.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
fitBiasModels     17.53   1.47   26.93
estimateAbundance 14.23   1.90   17.19
predictCoverage    9.45   0.75   10.34
getFragmentWidths  5.74   0.36    6.31
getReadLength      4.76   0.25    5.97
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
fitBiasModels     19.14   1.27   20.58
estimateAbundance 17.61   1.58   19.63
predictCoverage   10.19   0.75   11.24
getFragmentWidths  4.98   0.17    5.39
* 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-3.12-bioc/meat/alpine.Rcheck/00check.log'
for details.



Installation output

alpine.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/alpine_1.15.0.tar.gz && rm -rf alpine.buildbin-libdir && mkdir alpine.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=alpine.buildbin-libdir alpine_1.15.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL alpine_1.15.0.zip && rm alpine_1.15.0.tar.gz alpine_1.15.0.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
100  194k  100  194k    0     0  3552k      0 --:--:-- --:--:-- --:--:-- 3816k

install for i386

* installing *source* package 'alpine' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'alpine'
    finding HTML links ... done
    alpine-package                          html  
    buildFragtypes                          html  
    estimateAbundance                       html  
    extractAlpine                           html  
    fitBiasModels                           html  
    getFragmentWidths                       html  
    getReadLength                           html  
    mergeGenes                              html  
    normalizeDESeq                          html  
    plotFragLen                             html  
    plotGC                                  html  
    plotGRL                                 html  
    plotOrder0                              html  
    plotRelPos                              html  
    predictCoverage                         html  
    preprocessedData                        html  
    splitGenesAcrossChroms                  html  
    splitLongGenes                          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 'alpine' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'alpine' as alpine_1.15.0.zip
* DONE (alpine)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'alpine' successfully unpacked and MD5 sums checked

Tests output

alpine.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(alpine)
> test_check("alpine")
== testthat results  ===========================================================
[ OK: 1 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   61.9     5.7    68.7 

alpine.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(alpine)
> test_check("alpine")
== testthat results  ===========================================================
[ OK: 1 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  51.65    4.37   56.56 

Example timings

alpine.Rcheck/examples_i386/alpine-Ex.timings

nameusersystemelapsed
buildFragtypes2.850.354.94
estimateAbundance14.23 1.9017.19
extractAlpine0.030.000.03
fitBiasModels17.53 1.4726.93
getFragmentWidths5.740.366.31
getReadLength4.760.255.97
mergeGenes0.330.000.33
normalizeDESeq000
plotFragLen0.030.020.04
plotGC0.050.000.05
plotGRL0.180.000.19
plotOrder00.080.010.09
plotRelPos0.050.000.05
predictCoverage 9.45 0.7510.34
splitGenesAcrossChroms0.390.020.40
splitLongGenes0.480.030.52

alpine.Rcheck/examples_x64/alpine-Ex.timings

nameusersystemelapsed
buildFragtypes4.260.154.42
estimateAbundance17.61 1.5819.63
extractAlpine0.020.000.01
fitBiasModels19.14 1.2720.58
getFragmentWidths4.980.175.39
getReadLength4.490.264.89
mergeGenes0.30.00.3
normalizeDESeq000
plotFragLen0.030.000.03
plotGC0.050.000.04
plotGRL0.200.020.22
plotOrder00.060.000.06
plotRelPos0.030.000.03
predictCoverage10.19 0.7511.24
splitGenesAcrossChroms0.530.030.56
splitLongGenes0.920.000.92