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CHECK report for recount3 on malbec1

This page was generated on 2021-05-06 12:28:47 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the recount3 package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1490/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
recount3 1.0.7  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/recount3
Branch: RELEASE_3_12
Last Commit: 66048cf
Last Changed Date: 2021-02-10 16:20:59 -0400 (Wed, 10 Feb 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    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: recount3
Version: 1.0.7
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:recount3.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings recount3_1.0.7.tar.gz
StartedAt: 2021-05-06 05:05:05 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:30:24 -0400 (Thu, 06 May 2021)
EllapsedTime: 1519.2 seconds
RetCode: 0
Status:   OK  
CheckDir: recount3.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:recount3.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings recount3_1.0.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/recount3.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 ‘recount3/DESCRIPTION’ ... OK
* this is package ‘recount3’ version ‘1.0.7’
* 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 ‘recount3’ 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 ... NOTE
expand_sra_attributes: no visible global function definition for
  ‘colData<-’
Undefined global functions or variables:
  colData<-
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
create_rse            140.516  2.344 257.799
create_rse_manual      25.948  0.568  46.142
available_projects     22.616  0.280  30.845
compute_read_counts    21.756  0.380 346.263
read_counts            20.208  0.188  22.979
read_metadata          15.288  0.156 329.428
expand_sra_attributes  14.360  0.116  22.764
available_samples      10.924  0.220  14.501
transform_counts        7.104  0.100  14.752
compute_scale_factors   7.000  0.124  13.143
is_paired_end           6.508  0.080  12.375
file_retrieve           4.540  0.060   8.673
locate_url              2.424  0.060   8.670
* 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/recount3.Rcheck/00check.log’
for details.



Installation output

recount3.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL recount3
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘recount3’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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
* DONE (recount3)

Tests output

recount3.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(recount3)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> 
> test_check("recount3")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 57 ]
> 
> proc.time()
   user  system elapsed 
 78.312   1.488 158.144 

Example timings

recount3.Rcheck/recount3-Ex.timings

nameusersystemelapsed
annotation_ext0.0000.0000.001
annotation_options000
available_projects22.616 0.28030.845
available_samples10.924 0.22014.501
compute_read_counts 21.756 0.380346.263
compute_scale_factors 7.000 0.12413.143
create_rse140.516 2.344257.799
create_rse_manual25.948 0.56846.142
expand_sra_attributes14.360 0.11622.764
file_retrieve4.5400.0608.673
is_paired_end 6.508 0.08012.375
locate_url2.4240.0608.670
locate_url_ann0.0000.0000.001
project_homes0.3200.0122.633
read_counts20.208 0.18822.979
read_metadata 15.288 0.156329.428
recount3_cache0.2880.0000.288
recount3_cache_files0.2000.0000.201
recount3_cache_rm0.2560.0040.260
transform_counts 7.104 0.10014.752