Multiple platform build/check report for BioC 3.12 - CHECK report for getDEE2 on tokay1

Package: getDEE2

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:getDEE2.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings getDEE2_1.0.0.tar.gz

StartedAt: 2021-05-06 03:10:48 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 03:16:25 -0400 (Thu, 06 May 2021)

EllapsedTime: 337.1 seconds

RetCode: 0

Status: OK

CheckDir: getDEE2.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:getDEE2.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings getDEE2_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/getDEE2.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'getDEE2/DESCRIPTION' ... OK
* this is package 'getDEE2' 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 whether package 'getDEE2' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
srx_agg: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
getDEE2_bundle 2.32   0.11    8.97
getDEE2        0.97   0.07    5.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
getDEE2_bundle 2.79   0.14    9.07
getDEE2        0.67   0.06    7.61
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-getDEE2.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-getDEE2.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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/getDEE2.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/getDEE2_1.0.0.tar.gz && rm -rf getDEE2.buildbin-libdir && mkdir getDEE2.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=getDEE2.buildbin-libdir getDEE2_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL getDEE2_1.0.0.zip && rm getDEE2_1.0.0.tar.gz getDEE2_1.0.0.zip
###
##############################################################################
##############################################################################


  % 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 11135  100 11135    0     0   280k      0 --:--:-- --:--:-- --:--:--  286k

install for i386

* installing *source* package 'getDEE2' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'getDEE2'
    finding HTML links ... done
    Tx2Gene                                 html  
    getDEE2                                 html  
    getDEE2Metadata                         html  
    getDEE2_bundle                          html  
    list_bundles                            html  
    loadFullMeta                            html  
    loadGeneCounts                          html  
    loadGeneInfo                            html  
    loadQcMx                                html  
    loadSummaryMeta                         html  
    loadTxCounts                            html  
    loadTxInfo                              html  
    queryDEE2                               html  
    query_bundles                           html  
    se                                      html  
    srx_agg                                 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 'getDEE2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'getDEE2' as getDEE2_1.0.0.zip
* DONE (getDEE2)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'getDEE2' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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("getDEE2")
> library("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

Attaching package: 'IRanges'

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

    windows

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

> library("testthat")
> 
> # E. coli 
> x<-getDEE2("ecoli",c("SRR1613487","SRR1613488"),legacy=TRUE)
trying URL 'http://dee2.io/metadata/ecoli_metadata.tsv.cut'
Content type 'text/tab-separated-values' length 697430 bytes (681 KB)
==================================================
downloaded 681 KB

trying URL 'http://dee2.io/cgi-bin/request.sh?org=ecoli&x=SRR1613487&x=SRR1613488'
Content type 'application/zip' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.....
downloaded 155 KB

For more information about DEE2 QC metrics, visit
    https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
> 
> test_that("eco works", {
+     expect_equal( sum(x$GeneCounts) , 20624168 )
+ })
Test passed 
> 
> 
> # A. thaliana bundle
> x <- getDEE2_bundle("athaliana", "SRP058781",col="SRP_accession")
trying URL 'http://dee2.io/huge/athaliana/'
Content type 'text/html;charset=UTF-8' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... .........
downloaded 449 KB

trying URL 'http://dee2.io/huge/athaliana/SRP058781_NA.zip'
Content type 'application/zip' length 4214382 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

For more information about DEE2 QC metrics, visit
    https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
> 
> test_that("ath bundles work", {
+     expect_equal( nrow(assays(x)[[1]]) , 32833 )
+     expect_equal( ncol(assays(x)[[1]]) , 32 )
+ })
Test passed 
> 
> 
> # check absent present
> dat <- query_bundles("drerio",c("SRP131781","SRP055996","SRXXX"),col="SRP_accession")
trying URL 'http://dee2.io/huge/drerio/'
Content type 'text/html;charset=UTF-8' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... ..
downloaded 172 KB

> 
> test_that("dre bundle query", {
+     expect_equal( length(dat$absent) , 1 )
+     expect_equal( length(dat$present) , 2 )
+ })
Test passed 
> 
> proc.time()
   user  system elapsed 
  14.76    1.00   29.09


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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("getDEE2")
> library("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

Attaching package: 'IRanges'

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

    windows

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

> library("testthat")
> 
> # E. coli 
> x<-getDEE2("ecoli",c("SRR1613487","SRR1613488"),legacy=TRUE)
trying URL 'http://dee2.io/metadata/ecoli_metadata.tsv.cut'
Content type 'text/tab-separated-values' length 697430 bytes (681 KB)
==================================================
downloaded 681 KB

trying URL 'http://dee2.io/cgi-bin/request.sh?org=ecoli&x=SRR1613487&x=SRR1613488'
Content type 'application/zip' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.....
downloaded 155 KB

For more information about DEE2 QC metrics, visit
    https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
> 
> test_that("eco works", {
+     expect_equal( sum(x$GeneCounts) , 20624168 )
+ })
Test passed 
> 
> 
> # A. thaliana bundle
> x <- getDEE2_bundle("athaliana", "SRP058781",col="SRP_accession")
trying URL 'http://dee2.io/huge/athaliana/'
Content type 'text/html;charset=UTF-8' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... .........
downloaded 449 KB

trying URL 'http://dee2.io/huge/athaliana/SRP058781_NA.zip'
Content type 'application/zip' length 4214382 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

For more information about DEE2 QC metrics, visit
    https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.md
> 
> test_that("ath bundles work", {
+     expect_equal( nrow(assays(x)[[1]]) , 32833 )
+     expect_equal( ncol(assays(x)[[1]]) , 32 )
+ })
Test passed 
> 
> 
> # check absent present
> dat <- query_bundles("drerio",c("SRP131781","SRP055996","SRXXX"),col="SRP_accession")
trying URL 'http://dee2.io/huge/drerio/'
Content type 'text/html;charset=UTF-8' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... ..
downloaded 172 KB

> 
> test_that("dre bundle query", {
+     expect_equal( length(dat$absent) , 1 )
+     expect_equal( length(dat$present) , 2 )
+ })
Test passed 
> 
> proc.time()
   user  system elapsed 
  14.76    0.48   30.21

name	user	system	elapsed
Tx2Gene	0.43	0.11	4.08
getDEE2	0.97	0.07	5.53
getDEE2Metadata	0.09	0.01	1.05
getDEE2_bundle	2.32	0.11	8.97
list_bundles	1.12	0.00	2.45
loadFullMeta	0.10	0.06	2.86
loadGeneCounts	0.15	0.03	1.91
loadGeneInfo	0.13	0.05	2.39
loadQcMx	0.12	0.08	3.70
loadSummaryMeta	0.14	0.03	2.58
loadTxCounts	0.14	0.05	3.05
loadTxInfo	0.19	0.03	3.11
queryDEE2	0.03	0.00	1.91
query_bundles	0.39	0.00	0.87
se	0.14	0.01	3.31
srx_agg	0.12	0.04	3.29

name	user	system	elapsed
Tx2Gene	0.83	0.05	4.27
getDEE2	0.67	0.06	7.61
getDEE2Metadata	0.06	0.02	1.43
getDEE2_bundle	2.79	0.14	9.07
list_bundles	0.35	0.00	1.28
loadFullMeta	0.09	0.03	3.19
loadGeneCounts	0.10	0.02	3.17
loadGeneInfo	0.07	0.03	3.39
loadQcMx	0.16	0.01	3.52
loadSummaryMeta	0.09	0.02	3.43
loadTxCounts	0.09	0.01	3.39
loadTxInfo	0.13	0.00	3.46
queryDEE2	0.05	0.00	2.11
query_bundles	0.29	0.00	0.76
se	0.13	0.00	3.25
srx_agg	0.15	0.05	3.50

CHECK report for getDEE2 on tokay1

Summary

Command output

Installation output

Tests output

Example timings