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CHECK report for BANDITS on merida1

This page was generated on 2020-04-15 12:49:10 -0400 (Wed, 15 Apr 2020).

Package 109/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BANDITS 1.2.3
Simone Tiberi
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/BANDITS
Branch: RELEASE_3_10
Last Commit: fe1f6bb
Last Changed Date: 2020-04-14 04:46:32 -0400 (Tue, 14 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK YES, new version is higher than in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK YES, new version is higher than in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK YES, new version is higher than in internal repository

Summary

Package: BANDITS
Version: 1.2.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BANDITS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BANDITS_1.2.3.tar.gz
StartedAt: 2020-04-15 00:32:19 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:35:33 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 193.6 seconds
RetCode: 0
Status:  OK 
CheckDir: BANDITS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BANDITS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BANDITS_1.2.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/BANDITS.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BANDITS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BANDITS’ version ‘1.2.3’
* 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 ‘BANDITS’ 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
* 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
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
infer_one_group: no visible binding for global variable ‘p’
plot_precision: no visible binding for global variable ‘x’
test_DTU: no visible binding for global variable ‘p’
test_DTU_multi_group: no visible binding for global variable ‘p’
Undefined global functions or variables:
  p x
* 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 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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
prior_precision 10.923  7.849  12.511
create_data      1.227  0.032  14.772
test_DTU         0.192  0.034  14.792
* 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
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/BANDITS.Rcheck/00check.log’
for details.



Installation output

BANDITS.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BANDITS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘BANDITS’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Rcpp_Together.cpp -o Rcpp_Together.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Rcpp_Together_MultiGroup.cpp -o Rcpp_Together_MultiGroup.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Rcpp_Unique.cpp -o Rcpp_Unique.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Rcpp_Unique_MultiGroup.cpp -o Rcpp_Unique_MultiGroup.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BANDITS.so RcppExports.o Rcpp_Together.o Rcpp_Together_MultiGroup.o Rcpp_Unique.o Rcpp_Unique_MultiGroup.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-BANDITS/00new/BANDITS/libs
** R
** data
** 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 (BANDITS)

Tests output

BANDITS.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(BANDITS)
> test_check("BANDITS")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 34 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  9.032   2.641  17.295 

Example timings

BANDITS.Rcheck/BANDITS-Ex.timings

nameusersystemelapsed
BANDITS_data-class0.0060.0010.006
BANDITS_test-class0.5180.0090.530
create_data 1.227 0.03214.772
eff_len_compute0.1260.0020.128
filter_genes0.0090.0000.010
filter_transcripts0.3930.0030.397
gene_tr_id0.0050.0010.007
input_data0.0030.0010.004
plot_precision0.0080.0010.008
precision0.0020.0010.002
prior_precision10.923 7.84912.511
results0.0030.0010.004
test_DTU 0.192 0.03414.792