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CHECK report for RSeqAn on malbec2

This page was generated on 2019-04-09 11:50:31 -0400 (Tue, 09 Apr 2019).

Package 1396/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RSeqAn 1.3.2
August Guang
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/RSeqAn
Branch: master
Last Commit: 11e6bb6
Last Changed Date: 2019-02-14 18:19:24 -0400 (Thu, 14 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  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 

Summary

Package: RSeqAn
Version: 1.3.2
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RSeqAn.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RSeqAn_1.3.2.tar.gz
StartedAt: 2019-04-09 03:21:42 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:22:05 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 22.4 seconds
RetCode: 0
Status:  OK 
CheckDir: RSeqAn.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RSeqAn.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RSeqAn_1.3.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/RSeqAn.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RSeqAn/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RSeqAn’ version ‘1.3.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘RSeqAn’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 13.9Mb
  sub-directories of 1Mb or more:
    include  13.7Mb
* 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
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/RSeqAn.Rcheck/00check.log’
for details.



Installation output

RSeqAn.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL RSeqAn
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘RSeqAn’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I../inst/include -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O3 -march=native -mtune=native -fPIC -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I../inst/include -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include  -fpic  -O3 -march=native -mtune=native -fPIC -c charstring.cpp -o charstring.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o RSeqAn.so RcppExports.o charstring.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-RSeqAn/00new/RSeqAn/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RSeqAn)

Tests output

RSeqAn.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(RSeqAn)
> 
> test_check("RSeqAn")
Converting from SEXP to CharString
Running output test with toCString(CharString)
ACTG
Converting from CharString to Rcpp::String
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 1 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  0.571   0.042   0.603 

Example timings