Sean K Maden
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/recountmethylation |
| Branch: RELEASE_3_12 |
| Last Commit: 8c2ff8d |
| Last Changed Date: 2020-10-27 12:00:30 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:36:21 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the recountmethylation package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1491/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| recountmethylation 1.0.0 (landing page) Sean K Maden
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: recountmethylation |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:recountmethylation.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings recountmethylation_1.0.0.tar.gz |
| StartedAt: 2021-05-06 05:17:10 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 05:20:08 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 177.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: recountmethylation.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:recountmethylation.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings recountmethylation_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/recountmethylation.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recountmethylation/DESCRIPTION’ ... OK
* this is package ‘recountmethylation’ 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 for sufficient/correct file permissions ... OK
* checking whether package ‘recountmethylation’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
gds_idat2rg 22.212 1.192 28.784
gds_idatquery 0.691 0.408 5.295
getdb 0.225 0.043 5.455
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-gds.R’
Running ‘test-getdb_h5_test.R’
Running ‘test-getdb_h5se_test.R’
Running ‘test-servermatrix.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: OK
recountmethylation.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL recountmethylation ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘recountmethylation’ ... ** using staged installation ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (recountmethylation)
recountmethylation.Rcheck/tests/test-gds.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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.
> testthat::context("GEO validate SummarizedExperiment")
>
> testthat::test_that("Download and object properties", {
+ dldn <- tempdir()
+ gsmv <- c("GSM2465267", "GSM2814572")
+ gdq <- recountmethylation::gds_idatquery(gsmv, dfp = dldn)
+ # ids in query
+ idmatch <- grepl(paste(gsmv, collapse = "|"), gdq$basenames)
+ testthat::expect_equal(length(idmatch[idmatch]), 2)
+ # idat downloads
+ gds.se <- recountmethylation::gds_idat2rg(gsmv, dfp = dldn)
+ testthat::expect_that(gds.se, testthat::is_a("RGChannelSet"))
+ })
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2465nnn/GSM2465267/suppl/GSM2465267_9285451205_R03C02_Grn.idat.gz'
Content type 'unknown' length 4265261 bytes (4.1 MB)
==================================================
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2465nnn/GSM2465267/suppl/GSM2465267_9285451205_R03C02_Red.idat.gz'
Content type 'unknown' length 4361480 bytes (4.2 MB)
==================================================
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2814nnn/GSM2814572/suppl/GSM2814572_9992576177_R05C01_Grn.idat.gz'
Content type 'unknown' length 4313778 bytes (4.1 MB)
==================================================
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2814nnn/GSM2814572/suppl/GSM2814572_9992576177_R05C01_Red.idat.gz'
Content type 'unknown' length 4322593 bytes (4.1 MB)
==================================================
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2465nnn/GSM2465267/suppl/GSM2465267_9285451205_R03C02_Grn.idat.gz'
Content type 'unknown' length 4265261 bytes (4.1 MB)
==================================================
Error in decompressFile.default(filename = filename, ..., ext = ext, FUN = FUN) :
File already exists: /tmp/RtmpNyYDx8/GSM2465267_9285451205_R03C02_Grn.idat
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2465nnn/GSM2465267/suppl/GSM2465267_9285451205_R03C02_Red.idat.gz'
Content type 'unknown' length 4361480 bytes (4.2 MB)
==================================================
Error in decompressFile.default(filename = filename, ..., ext = ext, FUN = FUN) :
File already exists: /tmp/RtmpNyYDx8/GSM2465267_9285451205_R03C02_Red.idat
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2814nnn/GSM2814572/suppl/GSM2814572_9992576177_R05C01_Grn.idat.gz'
Content type 'unknown' length 4313778 bytes (4.1 MB)
==================================================
Error in decompressFile.default(filename = filename, ..., ext = ext, FUN = FUN) :
File already exists: /tmp/RtmpNyYDx8/GSM2814572_9992576177_R05C01_Grn.idat
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2814nnn/GSM2814572/suppl/GSM2814572_9992576177_R05C01_Red.idat.gz'
Content type 'unknown' length 4322593 bytes (4.1 MB)
==================================================
Error in decompressFile.default(filename = filename, ..., ext = ext, FUN = FUN) :
File already exists: /tmp/RtmpNyYDx8/GSM2814572_9992576177_R05C01_Red.idat
Test passed 🌈
>
> proc.time()
user system elapsed
21.797 1.524 33.306
recountmethylation.Rcheck/tests/test-getdb_h5_test.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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.
> testthat::context("Test HDF5 dataset download")
>
> testthat::test_that("HDF5 database properties", {
+ # database download
+ dldn <- tempdir()
+ h5path <- recountmethylation::getdb_h5_test(dfp = dldn)
+ testthat::expect_true(file.exists(h5path))
+ # database properties
+ h5dat <- rhdf5::h5ls(h5path)
+ testthat::expect_true(is.data.frame(h5dat))
+ testthat::expect_equal(nrow(h5dat[h5dat$name == "greensignal",]), 1)
+ testthat::expect_equal(nrow(h5dat[h5dat$name == "greensignal",]), 1)
+ testthat::expect_equal(nrow(h5dat[h5dat$name == "redsignal",]), 1)
+ testthat::expect_equal(nrow(h5dat[h5dat$name == "mdpost",]), 1)
+ testthat::expect_equal(nrow(h5dat[h5dat$name == "greensignal.colnames",]), 1)
+ testthat::expect_equal(nrow(h5dat[h5dat$name == "greensignal.rownames",]), 1)
+ testthat::expect_equal(nrow(h5dat[h5dat$name == "redsignal.colnames",]), 1)
+ testthat::expect_equal(nrow(h5dat[h5dat$name == "redsignal.rownames",]), 1)
+ testthat::expect_equal(nrow(h5dat[h5dat$name == "mdpost.colnames",]), 1)
+ })
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 246k 100 246k 0 0 409k 0 --:--:-- --:--:-- --:--:-- 410k
Test passed 😸
>
>
> proc.time()
user system elapsed
1.889 0.183 6.974
recountmethylation.Rcheck/tests/test-getdb_h5se_test.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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.
> testthat::context("Test HDF5-SummarizedExperiment download")
>
> testthat::test_that("Database download and object properties", {
+ dldn <- tempdir()
+ h5se.dat <- recountmethylation::getdb_h5se_test(dfp = dldn)
+ testthat::expect_that(h5se.dat, testthat::is_a("GenomicRatioSet"))
+ testthat::expect_that(minfi::pData(h5se.dat),
+ testthat::is_a("DFrame"))
+ testthat::expect_that(minfi::getAnnotation(h5se.dat),
+ testthat::is_a("DFrame"))
+ testthat::expect_equal(nrow(minfi::pData(h5se.dat)), ncol(h5se.dat))
+ testthat::expect_equal(nrow(minfi::getAnnotation(h5se.dat)),
+ nrow(h5se.dat))
+ })
% 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 129k 100 129k 0 0 232k 0 --:--:-- --:--:-- --:--:-- 232k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 68522 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 68522 100 68522 0 0 138k 0 --:--:-- --:--:-- --:--:-- 137k
Test passed 🎉
>
>
> proc.time()
user system elapsed
33.232 1.363 41.170
recountmethylation.Rcheck/tests/test-servermatrix.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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.
> testthat::context("Servermatrix properties")
>
> testthat::test_that("Properties of server matrix returned from get_rmdl
+ and servermatrix", {
+ url = "https://recount.bio/data/"
+ show.files = FALSE
+ sslver = FALSE
+ ftpuseopt <- dirlistopt <- ifelse(show.files, FALSE, TRUE) # rcurl setup
+ dn <- RCurl::getURL(url, ftp.use.epsv = ftpuseopt, dirlistonly = dirlistopt,
+ .opts = list(ssl.verifypeer = sslver))
+ sm <- recountmethylation::servermatrix(dn = dn, sslver = sslver)
+ testthat::expect_true(is.matrix(sm))
+ testthat::expect_equal(ncol(sm), 4)
+ testthat::expect_true(is.character(sm[,1]))
+ })
Test passed 🥇
>
> proc.time()
user system elapsed
1.911 0.160 6.756
recountmethylation.Rcheck/recountmethylation-Ex.timings
| name | user | system | elapsed | |
| data_mdpost | 0.091 | 0.010 | 0.102 | |
| gds_idat2rg | 22.212 | 1.192 | 28.784 | |
| gds_idatquery | 0.691 | 0.408 | 5.295 | |
| getdb | 0.225 | 0.043 | 5.455 | |
| getrg | 0.217 | 0.012 | 0.229 | |
| hread | 0.010 | 0.001 | 0.011 | |
| matchds_1to2 | 0.002 | 0.001 | 0.003 | |
| rgse | 0.136 | 0.018 | 0.155 | |
| servermatrix | 0.205 | 0.018 | 4.516 | |