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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:recountmethylation.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings recountmethylation_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/recountmethylation.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 ‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
gds_idat2rg   24.296  0.524  32.386
getdb          0.924  0.196   8.324
gds_idatquery  0.844  0.148  21.153
servermatrix   0.912  0.052   6.662
* 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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL recountmethylation
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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)

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.

> 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/RtmpMlgIP8/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/RtmpMlgIP8/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/RtmpMlgIP8/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/RtmpMlgIP8/GSM2814572_9992576177_R05C01_Red.idat
Test passed 🎉
> 
> proc.time()
   user  system elapsed 
 24.056   0.712  37.680 

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.

> 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
 38  246k   38 98304    0     0   106k      0  0:00:02 --:--:--  0:00:02  106k
100  246k  100  246k    0     0   249k      0 --:--:-- --:--:-- --:--:--  248k
Test passed 🥇
> 
> 
> proc.time()
   user  system elapsed 
  2.680   0.344   9.527 

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.

> 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
 24  129k   24 32768    0     0  54072      0  0:00:02 --:--:--  0:00:02 53983
100  129k  100  129k    0     0   187k      0 --:--:-- --:--:-- --:--:--  186k
  % 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 68522  100 68522    0     0   116k      0 --:--:-- --:--:-- --:--:--  116k
Test passed 🥇
> 
> 
> proc.time()
   user  system elapsed 
 36.400   1.160  46.446 

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.

> 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 
  2.868   0.252   8.772