##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:rhdf5client.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings rhdf5client_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/rhdf5client.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘rhdf5client/DESCRIPTION’ ... OK
* this is package ‘rhdf5client’ version ‘1.29.0’
* 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 ‘rhdf5client’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 code 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 loading without being on the library search path ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘rhdf5client-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HSDSArray
> ### Title: A DelayedArray backend for accessing a remote HDF5 server.
> ### Aliases: HSDSArray HSDSArray-class
> 
> ### ** Examples
> 
> if (check_hsds()) {
+  HSDSArray(URL_hsds(), 
+     "hsds", "/shared/bioconductor/darmgcls.h5", "/assay001")
+ }
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [hsdsdev.bioconductor.org]: SSL connection timeout
Calls: check_hsds ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
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:
  <curl_error_operation_timedout/curl_error/error/condition>
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [hsdsdev.bioconductor.org]: SSL connection timeout
  Backtrace:
      ▆
   1. ├─rhdf5client::check_hsds() at test.R:205:3
   2. │ └─httr::GET(tst)
   3. │   └─httr:::request_perform(req, hu$handle$handle)
   4. │     ├─httr:::request_fetch(req$output, req$url, handle)
   5. │     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   6. │       └─curl::curl_fetch_memory(url, handle = handle)
   7. └─curl:::raise_libcurl_error(...)
  
  [ FAIL 12 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘delayed-array.Rmd’ using rmarkdown

Quitting from lines 33-38 [lkdela3] (delayed-array.Rmd)
Error: processing vignette 'delayed-array.Rmd' failed with diagnostics:
Timeout was reached [hsdsdev.bioconductor.org]: SSL connection timeout
--- failed re-building ‘delayed-array.Rmd’

SUMMARY: processing the following file failed:
  ‘delayed-array.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/rhdf5client.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL rhdf5client
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘rhdf5client’ ...
** this is package ‘rhdf5client’ version ‘1.29.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c extract.c -o extract.o
gcc -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o rhdf5client.so extract.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-rhdf5client/00new/rhdf5client/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rhdf5client)

R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(rhdf5client)
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

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: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    expand, unname

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

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

The following objects are masked from 'package:base':

    apply, scale, sweep

> 
> test_check("rhdf5client")
[ FAIL 12 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test.R:5:2'): sproc/isplit work ─────────────────────────────────────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [hsdsdev.bioconductor.org]: SSL connection timeout
Backtrace:
    ▆
 1. ├─rhdf5client::check_hsds() at test.R:5:2
 2. │ └─httr::GET(tst)
 3. │   └─httr:::request_perform(req, hu$handle$handle)
 4. │     ├─httr:::request_fetch(req$output, req$url, handle)
 5. │     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 6. │       └─curl::curl_fetch_memory(url, handle = handle)
 7. └─curl:::raise_libcurl_error(...)
── Error ('test.R:27:2'): Server found ─────────────────────────────────────────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [hsdsdev.bioconductor.org]: SSL connection timeout
Backtrace:
    ▆
 1. ├─rhdf5client::check_hsds() at test.R:27:2
 2. │ └─httr::GET(tst)
 3. │   └─httr:::request_perform(req, hu$handle$handle)
 4. │     ├─httr:::request_fetch(req$output, req$url, handle)
 5. │     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 6. │       └─curl::curl_fetch_memory(url, handle = handle)
 7. └─curl:::raise_libcurl_error(...)
── Error ('test.R:39:2'): Files can be opened for reading ──────────────────────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [hsdsdev.bioconductor.org]: SSL connection timeout
Backtrace:
    ▆
 1. ├─rhdf5client::check_hsds() at test.R:39:2
 2. │ └─httr::GET(tst)
 3. │   └─httr:::request_perform(req, hu$handle$handle)
 4. │     ├─httr:::request_fetch(req$output, req$url, handle)
 5. │     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 6. │       └─curl::curl_fetch_memory(url, handle = handle)
 7. └─curl:::raise_libcurl_error(...)
── Error ('test.R:51:3'): HSDSFile can be a directory ──────────────────────────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [hsdsdev.bioconductor.org]: SSL connection timeout
Backtrace:
    ▆
 1. ├─rhdf5client::check_hsds() at test.R:51:3
 2. │ └─httr::GET(tst)
 3. │   └─httr:::request_perform(req, hu$handle$handle)
 4. │     ├─httr:::request_fetch(req$output, req$url, handle)
 5. │     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 6. │       └─curl::curl_fetch_memory(url, handle = handle)
 7. └─curl:::raise_libcurl_error(...)
── Error ('test.R:62:2'): Data can be retrieved from Datasets ──────────────────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [hsdsdev.bioconductor.org]: SSL connection timeout
Backtrace:
    ▆
 1. ├─rhdf5client::check_hsds() at test.R:62:2
 2. │ └─httr::GET(tst)
 3. │   └─httr:::request_perform(req, hu$handle$handle)
 4. │     ├─httr:::request_fetch(req$output, req$url, handle)
 5. │     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 6. │       └─curl::curl_fetch_memory(url, handle = handle)
 7. └─curl:::raise_libcurl_error(...)
── Error ('test.R:79:2'): DelayedArray can be instantiated and accessed ────────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [hsdsdev.bioconductor.org]: SSL connection timeout
Backtrace:
    ▆
 1. ├─rhdf5client::check_hsds() at test.R:79:2
 2. │ └─httr::GET(tst)
 3. │   └─httr:::request_perform(req, hu$handle$handle)
 4. │     ├─httr:::request_fetch(req$output, req$url, handle)
 5. │     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 6. │       └─curl::curl_fetch_memory(url, handle = handle)
 7. └─curl:::raise_libcurl_error(...)
── Error ('test.R:106:2'): Bad slices rejected ─────────────────────────────────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [hsdsdev.bioconductor.org]: SSL connection timeout
Backtrace:
    ▆
 1. ├─rhdf5client::check_hsds() at test.R:106:2
 2. │ └─httr::GET(tst)
 3. │   └─httr:::request_perform(req, hu$handle$handle)
 4. │     ├─httr:::request_fetch(req$output, req$url, handle)
 5. │     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 6. │       └─curl::curl_fetch_memory(url, handle = handle)
 7. └─curl:::raise_libcurl_error(...)
── Error ('test.R:123:5'): Basic string support ────────────────────────────────
Error in `submitRequest(request)`: Bad request (no response)
Backtrace:
    ▆
 1. └─rhdf5client::HSDSFile(src.hsds, "/shared/bioconductor/test_string.h5") at test.R:123:5
 2.   └─rhdf5client:::submitRequest(request)
── Error ('test.R:138:3'): Basic compound support ──────────────────────────────
Error in `submitRequest(request)`: Bad request (no response)
Backtrace:
    ▆
 1. └─rhdf5client::HSDSFile(src.hsds, "/shared/bioconductor/test_compound.h5") at test.R:138:3
 2.   └─rhdf5client:::submitRequest(request)
── Error ('test.R:173:3'): Support of scalar values ────────────────────────────
Error in `submitRequest(request)`: Bad request (no response)
Backtrace:
    ▆
 1. └─rhdf5client::HSDSFile(src.hsds, "/shared/bioconductor/test_scalar.h5") at test.R:173:3
 2.   └─rhdf5client:::submitRequest(request)
── Error ('test.R:183:3'): Integer types are supported properly ────────────────
Error in `submitRequest(request)`: Bad request (no response)
Backtrace:
    ▆
 1. └─rhdf5client::HSDSFile(src.hsds, "/shared/bioconductor/test_numbers.h5") at test.R:183:3
 2.   └─rhdf5client:::submitRequest(request)
── Error ('test.R:205:3'): Request errors are reported ─────────────────────────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [hsdsdev.bioconductor.org]: SSL connection timeout
Backtrace:
    ▆
 1. ├─rhdf5client::check_hsds() at test.R:205:3
 2. │ └─httr::GET(tst)
 3. │   └─httr:::request_perform(req, hu$handle$handle)
 4. │     ├─httr:::request_fetch(req$output, req$url, handle)
 5. │     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 6. │       └─curl::curl_fetch_memory(url, handle = handle)
 7. └─curl:::raise_libcurl_error(...)

[ FAIL 12 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted