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CHECK report for clonotypeR on tokay1

This page was generated on 2020-04-15 12:21:40 -0400 (Wed, 15 Apr 2020).

Package 303/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clonotypeR 1.24.0
Charles Plessy
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/clonotypeR
Branch: RELEASE_3_10
Last Commit: a749642
Last Changed Date: 2019-10-29 13:08:40 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 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  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: clonotypeR
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clonotypeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings clonotypeR_1.24.0.tar.gz
StartedAt: 2020-04-15 02:07:15 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:07:42 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 26.8 seconds
RetCode: 0
Status:  OK  
CheckDir: clonotypeR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clonotypeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings clonotypeR_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/clonotypeR.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clonotypeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'clonotypeR' version '1.24.0'
* 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 'clonotypeR' 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 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 '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

clonotypeR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/clonotypeR_1.24.0.tar.gz && rm -rf clonotypeR.buildbin-libdir && mkdir clonotypeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clonotypeR.buildbin-libdir clonotypeR_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL clonotypeR_1.24.0.zip && rm clonotypeR_1.24.0.tar.gz clonotypeR_1.24.0.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  103k  100  103k    0     0  1443k      0 --:--:-- --:--:-- --:--:-- 1526k

install for i386

* installing *source* package 'clonotypeR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'clonotypeR'
    finding HTML links ... done
    clonotypeR                              html  
    clonotype_table                         html  
    clonotyper_extdata                      html  
    common_clonotypes                       html  
    is_unproductive                         html  
    private_clonotypes                      html  
    read_clonotypes                         html  
    unique_clonotypes                       html  
    yassai_identifier                       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 'clonotypeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clonotypeR' as clonotypeR_1.24.0.zip
* DONE (clonotypeR)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'clonotypeR' successfully unpacked and MD5 sums checked

Tests output

clonotypeR.Rcheck/tests_i386/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.

> BiocGenerics:::testPackage("clonotypeR")


RUNIT TEST PROTOCOL -- Wed Apr 15 02:07:34 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
clonotypeR RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   0.48    0.03    0.51 

clonotypeR.Rcheck/tests_x64/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.

> BiocGenerics:::testPackage("clonotypeR")


RUNIT TEST PROTOCOL -- Wed Apr 15 02:07:35 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
clonotypeR RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   0.48    0.04    0.51 

Example timings

clonotypeR.Rcheck/examples_i386/clonotypeR-Ex.timings

nameusersystemelapsed
clonotype_table0.020.000.03
clonotyper_extdata0.000.000.02
common_clonotypes0.030.000.03
is_unproductive000
private_clonotypes000
read_clonotypes0.010.000.02
unique_clonotypes0.020.000.01
yassai_identifier0.080.000.08

clonotypeR.Rcheck/examples_x64/clonotypeR-Ex.timings

nameusersystemelapsed
clonotype_table0.030.000.03
clonotyper_extdata000
common_clonotypes0.060.000.06
is_unproductive000
private_clonotypes0.010.000.02
read_clonotypes000
unique_clonotypes0.020.000.01
yassai_identifier0.090.000.10