Mark Ziemann
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/getDEE2 |
| git_branch: RELEASE_3_13 |
| git_last_commit: 2536232 |
| git_last_commit_date: 2021-05-19 12:53:03 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:06 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the getDEE2 package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/getDEE2.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. |
| Package 761/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| getDEE2 1.2.0 (landing page) Mark Ziemann
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: getDEE2 |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:getDEE2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings getDEE2_1.2.0.tar.gz |
| StartedAt: 2021-10-14 23:46:07 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 23:51:25 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 317.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: getDEE2.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:getDEE2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings getDEE2_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/getDEE2.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.2.0'
* 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 2.20 0.13 7.26
getDEE2 1.12 0.07 6.81
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getDEE2_bundle 2.95 0.11 11.19
getDEE2 1.64 0.05 7.44
* 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-3.13-bioc/meat/getDEE2.Rcheck/00check.log'
for details.
getDEE2.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/getDEE2_1.2.0.tar.gz && rm -rf getDEE2.buildbin-libdir && mkdir getDEE2.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=getDEE2.buildbin-libdir getDEE2_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL getDEE2_1.2.0.zip && rm getDEE2_1.2.0.tar.gz getDEE2_1.2.0.zip
###
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% 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 11023 100 11023 0 0 99k 0 --:--:-- --:--:-- --:--:-- 99k
100 11023 100 11023 0 0 99k 0 --:--:-- --:--:-- --:--:-- 98k
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_1.2.0.zip
* DONE (getDEE2)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'getDEE2' successfully unpacked and MD5 sums checked
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getDEE2.Rcheck/tests_i386/test-getDEE2.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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 objects are masked from 'package:base':
I, expand.grid, unname
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 700296 bytes (683 KB)
==================================================
downloaded 683 KB
trying URL 'http://dee2.io/cgi-bin/request.sh?org=ecoli&x=SRR1613487&x=SRR1613488'
Content type 'application/zip' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
....
downloaded 154 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
10.98 0.76 25.36
|
getDEE2.Rcheck/tests_x64/test-getDEE2.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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 objects are masked from 'package:base':
I, expand.grid, unname
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 700296 bytes (683 KB)
==================================================
downloaded 683 KB
trying URL 'http://dee2.io/cgi-bin/request.sh?org=ecoli&x=SRR1613487&x=SRR1613488'
Content type 'application/zip' length unknown
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
....
downloaded 154 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
11.45 0.46 25.39
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getDEE2.Rcheck/examples_i386/getDEE2-Ex.timings
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getDEE2.Rcheck/examples_x64/getDEE2-Ex.timings
|