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CHECK report for BANDITS on tokay1

This page was generated on 2020-04-15 12:32:16 -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: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BANDITS.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings BANDITS_1.2.3.tar.gz
StartedAt: 2020-04-15 01:24:12 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:28:21 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 248.3 seconds
RetCode: 0
Status:  OK  
CheckDir: BANDITS.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:BANDITS.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings BANDITS_1.2.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/BANDITS.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 '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 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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
create_data 0.75   0.03   12.28
test_DTU    0.10   0.03   15.32
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
prior_precision 6.91   0.01    6.92
create_data     1.05   0.05   14.14
test_DTU        0.17   0.02   14.05
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/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:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/BANDITS_1.2.3.tar.gz && rm -rf BANDITS.buildbin-libdir && mkdir BANDITS.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BANDITS.buildbin-libdir BANDITS_1.2.3.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL BANDITS_1.2.3.zip && rm BANDITS_1.2.3.tar.gz BANDITS_1.2.3.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  785k  100  785k    0     0  14.9M      0 --:--:-- --:--:-- --:--:-- 16.3M

install for i386

* installing *source* package 'BANDITS' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Rcpp_Together.cpp -o Rcpp_Together.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Rcpp_Together_MultiGroup.cpp -o Rcpp_Together_MultiGroup.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Rcpp_Unique.cpp -o Rcpp_Unique.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Rcpp_Unique_MultiGroup.cpp -o Rcpp_Unique_MultiGroup.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o BANDITS.dll tmp.def RcppExports.o Rcpp_Together.o Rcpp_Together_MultiGroup.o Rcpp_Unique.o Rcpp_Unique_MultiGroup.o -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/BANDITS.buildbin-libdir/00LOCK-BANDITS/00new/BANDITS/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BANDITS'
    finding HTML links ... done
    BANDITS-package                         html  
    BANDITS_data-class                      html  
    BANDITS_test-class                      html  
    create_data                             html  
    eff_len_compute                         html  
    filter_genes                            html  
    filter_transcripts                      html  
    gene_tr_id                              html  
    input_data                              html  
    plot_precision                          html  
    precision                               html  
    prior_precision                         html  
    results                                 html  
    test_DTU                                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 'BANDITS' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Rcpp_Together.cpp -o Rcpp_Together.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Rcpp_Together_MultiGroup.cpp -o Rcpp_Together_MultiGroup.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Rcpp_Unique.cpp -o Rcpp_Unique.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c Rcpp_Unique_MultiGroup.cpp -o Rcpp_Unique_MultiGroup.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o BANDITS.dll tmp.def RcppExports.o Rcpp_Together.o Rcpp_Together_MultiGroup.o Rcpp_Unique.o Rcpp_Unique_MultiGroup.o -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/BANDITS.buildbin-libdir/BANDITS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BANDITS' as BANDITS_1.2.3.zip
* DONE (BANDITS)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'BANDITS' successfully unpacked and MD5 sums checked

Tests output

BANDITS.Rcheck/tests_i386/testthat.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.

> library(testthat)
> library(BANDITS)
> test_check("BANDITS")
== testthat results  ===========================================================
[ OK: 34 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   6.59    0.62   12.89 

BANDITS.Rcheck/tests_x64/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-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.

> library(testthat)
> library(BANDITS)
> test_check("BANDITS")
== testthat results  ===========================================================
[ OK: 34 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   7.03    0.35   13.29 

Example timings

BANDITS.Rcheck/examples_i386/BANDITS-Ex.timings

nameusersystemelapsed
BANDITS_data-class000
BANDITS_test-class0.340.000.35
create_data 0.75 0.0312.28
eff_len_compute0.140.010.16
filter_genes0.020.000.01
filter_transcripts0.400.000.41
gene_tr_id000
input_data000
plot_precision000
precision000
prior_precision4.220.024.23
results0.010.000.02
test_DTU 0.10 0.0315.32

BANDITS.Rcheck/examples_x64/BANDITS-Ex.timings

nameusersystemelapsed
BANDITS_data-class000
BANDITS_test-class0.440.000.44
create_data 1.05 0.0514.14
eff_len_compute0.140.010.16
filter_genes0.020.000.01
filter_transcripts0.570.020.61
gene_tr_id0.020.000.02
input_data000
plot_precision0.010.000.02
precision000
prior_precision6.910.016.92
results0.020.000.01
test_DTU 0.17 0.0214.05