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CHECK report for powerTCR on tokay2

This page was generated on 2018-10-17 08:45:16 -0400 (Wed, 17 Oct 2018).

Package 1116/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
powerTCR 1.0.0
Hillary Koch
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/powerTCR
Branch: RELEASE_3_7
Last Commit: 33507f4
Last Changed Date: 2018-09-20 13:38:13 -0400 (Thu, 20 Sep 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: powerTCR
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:powerTCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings powerTCR_1.0.0.tar.gz
StartedAt: 2018-10-17 04:02:49 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:05:56 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 187.3 seconds
RetCode: 0
Status:  OK  
CheckDir: powerTCR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:powerTCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings powerTCR_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/powerTCR.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 'powerTCR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'powerTCR' version '1.0.0'
* package encoding: UTF-8
* 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 '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 22.93   0.02   22.96
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
get_bootstraps 28.97      0      29
* 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://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/powerTCR_1.0.0.tar.gz && rm -rf powerTCR.buildbin-libdir && mkdir powerTCR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=powerTCR.buildbin-libdir powerTCR_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL powerTCR_1.0.0.zip && rm powerTCR_1.0.0.tar.gz powerTCR_1.0.0.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 30119  100 30119    0     0   467k      0 --:--:-- --:--:-- --:--:--  525k

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_1.0.0.zip
* DONE (powerTCR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-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 3.5.1 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("powerTCR")


RUNIT TEST PROTOCOL -- Wed Oct 17 04:05:44 2018 
*********************************************** 
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 
   5.20    0.50    5.73 

powerTCR.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("powerTCR")


RUNIT TEST PROTOCOL -- Wed Oct 17 04:05:51 2018 
*********************************************** 
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 
   6.28    0.48    6.75 

Example timings

powerTCR.Rcheck/examples_i386/powerTCR-Ex.timings

nameusersystemelapsed
Accessors2.110.112.22
JS_desponds0.500.030.53
JS_dist0.780.000.78
JS_spliced0.760.000.77
clusterPlot1.040.001.03
discgammagpd1.450.001.45
fdesponds0.330.020.35
fdiscgammagpd2.180.002.18
get_bootstraps22.93 0.0222.96
get_distances101
repertoires000

powerTCR.Rcheck/examples_x64/powerTCR-Ex.timings

nameusersystemelapsed
Accessors3.270.003.27
JS_desponds1.010.001.03
JS_dist1.270.021.28
JS_spliced1.030.001.03
clusterPlot1.720.011.73
discgammagpd1.810.001.81
fdesponds0.690.000.69
fdiscgammagpd2.680.002.69
get_bootstraps28.97 0.0029.00
get_distances1.040.001.05
repertoires0.020.000.01