Package: BUSpaRse

Version: 1.0.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings BUSpaRse_1.0.0.tar.gz

StartedAt: 2020-04-15 06:50:08 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:56:27 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 379.1 seconds

RetCode: 0

Status:  OK

CheckDir: BUSpaRse.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings BUSpaRse_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/BUSpaRse.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BUSpaRse/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BUSpaRse’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BUSpaRse’ 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 ... 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 ... NOTE
GNU make is a SystemRequirements.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
transcript2gene 12.804  0.828  20.310
tr2g_EnsDb       7.868  0.856   9.619
tr2g_TxDb        7.312  0.376   7.694
tr2g_ensembl     2.444  0.032  13.961
* 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-3.10-bioc/meat/BUSpaRse.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL BUSpaRse
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘BUSpaRse’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppProgress/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I/usr/local/include -fopenmp  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppProgress/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I/usr/local/include -fopenmp  -fpic  -g -O2  -Wall -c fill_cell_gene.cpp -o fill_cell_gene.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o BUSpaRse.so RcppExports.o fill_cell_gene.o -fopenmp -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-BUSpaRse/00new/BUSpaRse/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 (BUSpaRse)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(BUSpaRse)
> 
> test_check("BUSpaRse")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 109 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 47.612   0.712  59.697 

name	user	system	elapsed
EC2gene	0.100	0.000	0.146
get_velocity_files	2.144	0.040	2.219
make_sparse_matrix	0.008	0.000	0.018
read_count_output	0.016	0.000	0.189
read_velocity_output	0.008	0.000	0.009
save_tr2g_bustools	0.124	0.000	0.171
sort_tr2g	0.432	0.004	0.186
species2dataset	0.004	0.000	0.001
tr2g_EnsDb	7.868	0.856	9.619
tr2g_TxDb	7.312	0.376	7.694
tr2g_ensembl	2.444	0.032	13.961
tr2g_fasta	0.012	0.000	0.021
tr2g_gff3	0.256	0.000	0.258
tr2g_gtf	0.12	0.00	0.12
transcript2gene	12.804	0.828	20.310