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CHECK report for BUSpaRse on malbec1

This page was generated on 2021-05-06 12:27:03 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the BUSpaRse package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 221/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BUSpaRse 1.4.2  (landing page)
Lambda Moses
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/BUSpaRse
Branch: RELEASE_3_12
Last Commit: ac591a3
Last Changed Date: 2021-03-01 14:55:24 -0400 (Mon, 01 Mar 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: BUSpaRse
Version: 1.4.2
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BUSpaRse_1.4.2.tar.gz
StartedAt: 2021-05-05 23:39:48 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 23:49:26 -0400 (Wed, 05 May 2021)
EllapsedTime: 577.9 seconds
RetCode: 0
Status:   OK  
CheckDir: BUSpaRse.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BUSpaRse_1.4.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BUSpaRse.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.4.2’
* 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 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
tr2g_TxDb        38.864  1.880  45.783
knee_plot        38.196  1.940  53.734
dl_transcriptome 18.616  0.312  33.890
transcript2gene   9.900  0.064  21.270
tr2g_EnsDb        5.044  0.804   6.211
tr2g_ensembl      5.024  0.028  17.696
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/BUSpaRse.Rcheck/00check.log’
for details.



Installation output

BUSpaRse.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BUSpaRse
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘BUSpaRse’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppProgress/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/RcppProgress/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fill_cell_gene.cpp -o fill_cell_gene.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o BUSpaRse.so RcppExports.o fill_cell_gene.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-BUSpaRse/00new/BUSpaRse/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 (BUSpaRse)

Tests output

BUSpaRse.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 104 ]
> 
> proc.time()
   user  system elapsed 
 59.884   0.776  76.734 

Example timings

BUSpaRse.Rcheck/BUSpaRse-Ex.timings

nameusersystemelapsed
EC2gene0.1600.0040.214
annots_from_fa_df0.2840.0000.326
dl_transcriptome18.616 0.31233.890
get_velocity_files2.2320.0282.425
knee_plot38.196 1.94053.734
make_sparse_matrix0.0000.0000.014
read_count_output0.0080.0040.019
read_velocity_output0.0000.0040.006
save_tr2g_bustools0.6640.0000.670
sort_tr2g0.5080.0000.512
species2dataset000
subset_annot1.9600.1362.455
tr2g_EnsDb5.0440.8046.211
tr2g_TxDb38.864 1.88045.783
tr2g_ensembl 5.024 0.02817.696
tr2g_fasta0.0360.0000.034
tr2g_gff32.5840.0082.615
tr2g_gtf0.7760.0240.803
transcript2gene 9.900 0.06421.270