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CHECK report for powerTCR on tokay1

This page was generated on 2019-04-13 11:28:50 -0400 (Sat, 13 Apr 2019).

Package 1180/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
powerTCR 1.2.0
Hillary Koch
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/powerTCR
Branch: RELEASE_3_8
Last Commit: 9895403
Last Changed Date: 2018-10-30 11:42:07 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  ERROR  ERROR  skipped  skipped 

Summary

Package: powerTCR
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:powerTCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings powerTCR_1.2.0.tar.gz
StartedAt: 2019-04-13 04:37:44 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:41:18 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 213.6 seconds
RetCode: 0
Status:  OK  
CheckDir: powerTCR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:powerTCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings powerTCR_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/powerTCR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'powerTCR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'powerTCR' version '1.2.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'powerTCR' 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 ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
get_bootstraps 20.95      0   20.95
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
get_bootstraps 21.43      0   21.44
* 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: OK


Installation output

powerTCR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/powerTCR_1.2.0.tar.gz && rm -rf powerTCR.buildbin-libdir && mkdir powerTCR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=powerTCR.buildbin-libdir powerTCR_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL powerTCR_1.2.0.zip && rm powerTCR_1.2.0.tar.gz powerTCR_1.2.0.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 29437  100 29437    0     0   815k      0 --:--:-- --:--:-- --:--:--  898k

install for i386

* installing *source* package 'powerTCR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'powerTCR'
    finding HTML links ... done
    Accessors                               html  
    JS_desponds                             html  
    JS_dist                                 html  
    JS_spliced                              html  
    clusterPlot                             html  
    discgammagpd                            html  
    fdesponds                               html  
    fdiscgammagpd                           html  
    get_bootstraps                          html  
    get_distances                           html  
    parse                                   html  
    repertoires                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'powerTCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'powerTCR' as powerTCR_1.2.0.zip
* DONE (powerTCR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'powerTCR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

powerTCR.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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("powerTCR")


RUNIT TEST PROTOCOL -- Sat Apr 13 04:41:09 2019 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
powerTCR RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
Warning message:
In c("min.KS", "Cmin", "powerlaw.exponent", "pareto.alpha") == names(fit1) :
  longer object length is not a multiple of shorter object length
> 
> proc.time()
   user  system elapsed 
   4.17    0.54    4.70 

powerTCR.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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("powerTCR")


RUNIT TEST PROTOCOL -- Sat Apr 13 04:41:14 2019 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
powerTCR RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
Warning message:
In c("min.KS", "Cmin", "powerlaw.exponent", "pareto.alpha") == names(fit1) :
  longer object length is not a multiple of shorter object length
> 
> proc.time()
   user  system elapsed 
   4.67    0.35    5.03 

Example timings

powerTCR.Rcheck/examples_i386/powerTCR-Ex.timings

nameusersystemelapsed
Accessors2.860.112.97
JS_desponds0.450.050.50
JS_dist0.840.000.85
JS_spliced0.970.000.97
clusterPlot1.260.031.29
discgammagpd1.190.021.21
fdesponds0.310.010.33
fdiscgammagpd2.180.032.20
get_bootstraps20.95 0.0020.95
get_distances1.000.021.02
repertoires0.000.010.01

powerTCR.Rcheck/examples_x64/powerTCR-Ex.timings

nameusersystemelapsed
Accessors2.200.022.22
JS_desponds0.600.010.66
JS_dist0.870.020.89
JS_spliced0.880.000.87
clusterPlot1.110.001.11
discgammagpd1.170.001.17
fdesponds0.360.000.36
fdiscgammagpd2.330.002.33
get_bootstraps21.43 0.0021.44
get_distances1.130.001.12
repertoires0.020.000.02