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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:phantasus.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings phantasus_1.19.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/phantasus.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘phantasus/DESCRIPTION’ ... OK
* this is package ‘phantasus’ version ‘1.19.4’
* 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 ‘phantasus’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 28.9Mb
  sub-directories of 1Mb or more:
    testdata   5.0Mb
    www       23.4Mb
* checking package 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 ... NOTE
Unexported objects imported by ':::' calls:
  'GEOquery:::.parseGPLTxt' 'GEOquery:::getDirListing'
  'opencpu:::rookhandler' 'opencpu:::tmp_root' 'opencpu:::win_or_mac'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
generatePreloadedSession: no visible binding for global variable 'es'
generatePreloadedSession: no visible binding for global variable
  'heatmapJson'
getCountsMetaPart: no visible binding for global variable 'file_name'
loadCounts: no visible global function definition for '.'
loadCounts: no visible binding for global variable 'directory'
loadCounts: no visible binding for global variable 'DT_counts_meta'
loadCounts: no visible binding for global variable 'accession'
loadCounts: no visible binding for global variable 'collection_type'
loadCounts: no visible binding for global variable 'file_name'
loadSession: no visible binding for global variable 'es'
safeDownload: no visible binding for global variable 'tempDestFile'
validateCountsCollection: no visible binding for global variable
  'file_name'
Undefined global functions or variables:
  . DT_counts_meta accession collection_type directory es file_name
  heatmapJson tempDestFile
* checking Rd files ... NOTE
prepare_Rd: convertByAnnotationDB.Rd:36-41: Dropping empty section \examples
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘phantasus-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getGSE
> ### Title: Load ExpressionSet from GEO Series
> ### Aliases: getGSE
> 
> ### ** Examples
> 
> ## Not run: 
> ##D     getGSE('GSE14308', destdir = 'cache')
> ##D     getGSE('GSE27112')
> ## End(Not run)
> getGSE('GSE53986')
Trying www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53986&targ=self&form=text&view=brief
No encoding supplied: defaulting to UTF-8.
Stored brief data of GSE53986 at /tmp/Rtmp5SVzIE/geo/series/GSE53nnn/GSE53986/brief
Trying www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL1261&targ=self&form=text&view=brief
Error in curl::curl_fetch_memory(url, handle = handle) : 
  GnuTLS recv error (-9): Error decoding the received TLS packet.
Calls: getGSE ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. └─phantasus:::checkGSEType("GSE99709", tempdir())
    5.   └─base::sapply(...)
    6.     └─base::lapply(X = X, FUN = FUN, ...)
    7.       └─phantasus (local) FUN(X[[i]], ...)
    8.         └─phantasus:::getBriefData(gpl, destdir = destDir)
    9.           └─httr::GET(url)
   10.             └─httr:::request_perform(req, hu$handle$handle)
   11.               ├─httr:::request_fetch(req$output, req$url, handle)
   12.               └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   13.                 └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 7 | WARN 7 | SKIP 0 | PASS 98 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘phantasus-tutorial.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/phantasus.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL phantasus
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘phantasus’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (phantasus)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(phantasus)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading config from /home/biocbuild/bbs-3.17-bioc/R/library/opencpu/config/defaults.conf
Loading config from /home/biocbuild/.config/R/opencpu/user.conf
> 
> test_check("phantasus")
trying URL 'https://genome.ifmo.ru/files/software/phantasus/geo/series/GSE27nnn/GSE27112/matrix/GSE27112_series_matrix.txt.gz'
trying URL 'https://genome.ifmo.ru/files/software/phantasus/geo/series/GSE27nnn/GSE27112/matrix/GSE27112-GPL6103_series_matrix.txt.gz'
Content type 'application/x-gzip' length 596707 bytes (582 KB)
==================================================
downloaded 582 KB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL6nnn/GPL6103/annot/GPL6103.annot.gz'
Content type 'application/x-gzip' length 4652589 bytes (4.4 MB)
=====
downloaded 544 KB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/datasets/GDS4nnn/GDS4885/soft/GDS4885.soft.gz'
Content type 'application/x-gzip' length 1250109 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE53nnn/GSE53986/matrix/GSE53986_series_matrix.txt.gz'
Content type 'application/x-gzip' length 2848655 bytes (2.7 MB)
==
downloaded 128 KB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE14nnn/GSE14308/matrix/GSE14308_series_matrix.txt.gz'
Content type 'application/x-gzip' length 1807570 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL1nnn/GPL1261/annot/GPL1261.annot.gz'
Content type 'application/x-gzip' length 8389179 bytes (8.0 MB)
====
downloaded 768 KB

trying URL 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL17021&form=text&view=data'
downloaded 48 bytes

[ FAIL 7 | WARN 7 | SKIP 0 | PASS 98 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('testCollapse.R:64'): Collapse strip unannotated rows ────────────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: GnuTLS recv error (-9): Error decoding the received TLS packet.
Backtrace:
     ▆
  1. └─phantasus::getGSE("GSE53986") at testCollapse.R:64:4
  2.   └─phantasus:::checkGSEType(name, destdir)
  3.     └─base::sapply(...)
  4.       └─base::lapply(X = X, FUN = FUN, ...)
  5.         └─phantasus (local) FUN(X[[i]], ...)
  6.           └─phantasus:::getBriefData(gpl, destdir = destDir)
  7.             └─httr::GET(url)
  8.               └─httr:::request_perform(req, hu$handle$handle)
  9.                 ├─httr:::request_fetch(req$output, req$url, handle)
 10.                 └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 11.                   └─curl::curl_fetch_memory(url, handle = handle)
── Error ('testcounts.R:87'): loadCounts returns result ────────────────────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: Error in the HTTP2 framing layer
Backtrace:
     ▆
  1. └─phantasus::getGSE(test_gse, destdir = tmp_dir) at testcounts.R:87:4
  2.   └─phantasus:::checkGSEType(name, destdir)
  3.     └─base::sapply(...)
  4.       └─base::lapply(X = X, FUN = FUN, ...)
  5.         └─phantasus (local) FUN(X[[i]], ...)
  6.           └─phantasus:::getBriefData(gpl, destdir = destDir)
  7.             └─httr::GET(url)
  8.               └─httr:::request_perform(req, hu$handle$handle)
  9.                 ├─httr:::request_fetch(req$output, req$url, handle)
 10.                 └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 11.                   └─curl::curl_fetch_memory(url, handle = handle)
── Error ('testloadGEO.R:11'): loadGEO finishes with result ────────────────────
Error in `value[[3L]](cond)`: Could not download GPL GPL6103Error in download.file(annotURL, tmp): download from 'https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL6nnn/GPL6103/annot/GPL6103.annot.gz' failed

Backtrace:
     ▆
  1. └─phantasus:::loadGEO("GSE27112") at testloadGEO.R:11:4
  2.   └─phantasus::getES(name, type, destdir = cacheDir, mirrorPath = mirrorPath)
  3.     └─phantasus::getGSE(name, destdir, mirrorPath)
  4.       └─phantasus::getGSE(gpls[[i]], destdir = destdir, mirrorPath = mirrorPath)
  5.         └─phantasus:::annotateFeatureData(ess[[i]], destdir)
  6.           └─phantasus:::getGPLAnnotation(platform, destdir)
  7.             └─phantasus:::downloadGPL(GPL, destdir)
  8.               └─base::tryCatch(...)
  9.                 └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10.                   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11.                     └─value[[3L]](cond)
── Error ('testloadGEO.R:41'): filterPhenoAnnotations saves colnames ───────────
Error in `getGSE(name, destdir, mirrorPath)`: Can't download dataset  GSE53986
Backtrace:
    ▆
 1. └─phantasus::getES("GSE53986", destdir = cacheDir) at testloadGEO.R:41:4
 2.   └─phantasus::getGSE(name, destdir, mirrorPath)
── Error ('testloadGEO.R:47'): reparseCachedGSEs works ─────────────────────────
Error in `value[[3L]](cond)`: Could not download GPL GPL1261Error in download.file(annotURL, tmp): download from 'https://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL1nnn/GPL1261/annot/GPL1261.annot.gz' failed

Backtrace:
    ▆
 1. └─phantasus::getES("GSE14308", destdir = cacheDir) at testloadGEO.R:47:4
 2.   └─phantasus::getGSE(name, destdir, mirrorPath)
 3.     └─phantasus:::annotateFeatureData(ess[[i]], destdir)
 4.       └─phantasus:::getGPLAnnotation(platform, destdir)
 5.         └─phantasus:::downloadGPL(GPL, destdir)
 6.           └─base::tryCatch(...)
 7.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.                 └─value[[3L]](cond)
── Error ('testloadGEO.R:87'): getGSE works with ARCHS4 ────────────────────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: Error in the HTTP2 framing layer
Backtrace:
    ▆
 1. └─phantasus::getGSE(...) at testloadGEO.R:87:4
 2.   └─phantasus:::checkGSEType(name, destdir)
 3.     └─phantasus:::getBriefData(name, destDir)
 4.       └─httr::GET(url)
 5.         └─httr:::request_perform(req, hu$handle$handle)
 6.           ├─httr:::request_fetch(req$output, req$url, handle)
 7.           └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 8.             └─curl::curl_fetch_memory(url, handle = handle)
── Error ('testloadGEO.R:133'): getGSEType works ───────────────────────────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: Error in the HTTP2 framing layer
Backtrace:
     ▆
  1. ├─testthat::expect_true(checkGSEType("GSE99709", tempdir())) at testloadGEO.R:133:4
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. └─phantasus:::checkGSEType("GSE99709", tempdir())
  5.   └─base::sapply(...)
  6.     └─base::lapply(X = X, FUN = FUN, ...)
  7.       └─phantasus (local) FUN(X[[i]], ...)
  8.         └─phantasus:::getBriefData(gpl, destdir = destDir)
  9.           └─httr::GET(url)
 10.             └─httr:::request_perform(req, hu$handle$handle)
 11.               ├─httr:::request_fetch(req$output, req$url, handle)
 12.               └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 13.                 └─curl::curl_fetch_memory(url, handle = handle)

[ FAIL 7 | WARN 7 | SKIP 0 | PASS 98 ]
Error: Test failures
Execution halted