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This page was generated on 2021-11-29 15:05:48 -0500 (Mon, 29 Nov 2021).

CHECK results for BUSpaRse on machv2

To the developers/maintainers of the BUSpaRse package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BUSpaRse.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 231/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BUSpaRse 1.8.0  (landing page)
Lambda Moses
Snapshot Date: 2021-11-28 04:15:06 -0500 (Sun, 28 Nov 2021)
git_url: https://git.bioconductor.org/packages/BUSpaRse
git_branch: RELEASE_3_14
git_last_commit: fa528cf
git_last_commit_date: 2021-10-26 12:53:45 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    ERROR  skipped
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BUSpaRse
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BUSpaRse_1.8.0.tar.gz
StartedAt: 2021-11-28 14:17:38 -0500 (Sun, 28 Nov 2021)
EndedAt: 2021-11-28 14:27:48 -0500 (Sun, 28 Nov 2021)
EllapsedTime: 609.9 seconds
RetCode: 0
Status:   OK  
CheckDir: BUSpaRse.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BUSpaRse.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BUSpaRse_1.8.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/BUSpaRse.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.8.0’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... 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        42.938  7.894  53.328
knee_plot        41.724  2.414  53.470
dl_transcriptome 14.842  0.893  30.984
transcript2gene  12.040  0.159  18.278
tr2g_EnsDb        5.687  1.892   7.936
tr2g_ensembl      4.732  0.043  21.536
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/BUSpaRse.Rcheck/00check.log’
for details.



Installation output

BUSpaRse.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BUSpaRse
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘BUSpaRse’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c fill_cell_gene.cpp -o fill_cell_gene.o
clang++ -mmacosx-version-min=10.13 -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 BUSpaRse.so RcppExports.o fill_cell_gene.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-darwin18/8.2.0 -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/4.1/Resources/library/00LOCK-BUSpaRse/00new/BUSpaRse/libs
** R
** data
*** moving datasets to lazyload DB
** 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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(BUSpaRse)
> 
> test_check("BUSpaRse")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 102 ]
> 
> proc.time()
   user  system elapsed 
 73.765   1.669  80.318 

Example timings

BUSpaRse.Rcheck/BUSpaRse-Ex.timings

nameusersystemelapsed
EC2gene0.1420.0050.149
annots_from_fa_df0.2730.0060.279
dl_transcriptome14.842 0.89330.984
get_velocity_files2.6440.2062.855
knee_plot41.724 2.41453.470
make_sparse_matrix0.0020.0010.003
read_count_output0.0130.0010.015
read_velocity_output0.0060.0010.007
save_tr2g_bustools0.7000.0290.731
sort_tr2g0.6170.0380.657
species2dataset0.0010.0000.001
subset_annot1.5850.1511.748
tr2g_EnsDb5.6871.8927.936
tr2g_TxDb42.938 7.89453.328
tr2g_ensembl 4.732 0.04321.536
tr2g_fasta0.0340.0040.037
tr2g_gff31.7450.0781.823
tr2g_gtf1.0670.0431.110
transcript2gene12.040 0.15918.278