Multiple platform build/check report for BioC 3.21 - CHECK results for rhdf5client on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4824
palomino7	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4566
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4604
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4545
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4579
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for rhdf5client on palomino7

To the developers/maintainers of the rhdf5client package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rhdf5client.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: rhdf5client

Version: 1.30.0

Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rhdf5client.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings rhdf5client_1.30.0.tar.gz

StartedAt: 2025-08-15 06:06:36 -0400 (Fri, 15 Aug 2025)

EndedAt: 2025-08-15 06:08:54 -0400 (Fri, 15 Aug 2025)

EllapsedTime: 138.3 seconds

RetCode: 1

Status: ERROR

CheckDir: rhdf5client.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rhdf5client.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings rhdf5client_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/rhdf5client.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'rhdf5client/DESCRIPTION' ... OK
* this is package 'rhdf5client' version '1.30.0'
* 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 'rhdf5client' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* 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 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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/rhdf5client/libs/x64/rhdf5client.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
* 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:
  <head><title>503 Service Temporarily Unavailable</title></head>
  <body>
  <center><h1>503 Service Temporarily Unavailable</h1></center>
  <hr><center>nginx</center>
  </body>
  </html>
  
  Backtrace:
      ▆
   1. └─rhdf5client::HSDSFile(src.hsds, "/shared/bioconductor/test_numbers.h5") at test.R:183:3
   2.   └─rhdf5client:::submitRequest(request)
  
  [ FAIL 4 | WARN 0 | SKIP 8 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  'E:/biocbuild/bbs-3.21-bioc/meat/rhdf5client.Rcheck/00check.log'
for details.

Installation output

rhdf5client.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL rhdf5client
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'rhdf5client' ...
** this is package 'rhdf5client' version '1.30.0'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c extract.c -o extract.o
extract.c: In function 'extractBin':
extract.c:101:52: warning: 'rip' may be used uninitialized [-Wmaybe-uninitialized]
  101 |     A[ia] = (Rf_isReal(resvec_sexp) ? rdp[ib] : rip[ib]);
      |                                                    ^
extract.c:89:8: note: 'rip' was declared here
   89 |   int *rip;
      |        ^~~
extract.c:101:42: warning: 'rdp' may be used uninitialized [-Wmaybe-uninitialized]
  101 |     A[ia] = (Rf_isReal(resvec_sexp) ? rdp[ib] : rip[ib]);
      |                                          ^
extract.c:90:11: note: 'rdp' was declared here
   90 |   double *rdp;
      |           ^~~
gcc -shared -s -static-libgcc -o rhdf5client.dll tmp.def extract.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-rhdf5client/00new/rhdf5client/libs/x64
** 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 (rhdf5client)

Tests output

rhdf5client.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

Attaching package: 'IRanges'

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

    windows

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 4 | WARN 0 | SKIP 8 | PASS 0 ]

══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• empty test (8): 'test.R:4:1', 'test.R:26:1', 'test.R:38:1', 'test.R:50:1',
  'test.R:61:1', 'test.R:78:1', 'test.R:105:1', 'test.R:204:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test.R:123:5'): Basic string support ────────────────────────────────
Error in `submitRequest(request)`: Request failed:
request: https://hsdsdev.bioconductor.org?domain=/shared/bioconductor/test_string.h5
error message: <html>

<head><title>503 Service Temporarily Unavailable</title></head>

<body>

<center><h1>503 Service Temporarily Unavailable</h1></center>

<hr><center>nginx</center>

</body>

</html>


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)`: Request failed:
request: https://hsdsdev.bioconductor.org?domain=/shared/bioconductor/test_compound.h5
error message: <html>

<head><title>503 Service Temporarily Unavailable</title></head>

<body>

<center><h1>503 Service Temporarily Unavailable</h1></center>

<hr><center>nginx</center>

</body>

</html>


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)`: Request failed:
request: https://hsdsdev.bioconductor.org?domain=/shared/bioconductor/test_scalar.h5
error message: <html>

<head><title>503 Service Temporarily Unavailable</title></head>

<body>

<center><h1>503 Service Temporarily Unavailable</h1></center>

<hr><center>nginx</center>

</body>

</html>


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)`: Request failed:
request: https://hsdsdev.bioconductor.org?domain=/shared/bioconductor/test_numbers.h5
error message: <html>

<head><title>503 Service Temporarily Unavailable</title></head>

<body>

<center><h1>503 Service Temporarily Unavailable</h1></center>

<hr><center>nginx</center>

</body>

</html>


Backtrace:
    ▆
 1. └─rhdf5client::HSDSFile(src.hsds, "/shared/bioconductor/test_numbers.h5") at test.R:183:3
 2.   └─rhdf5client:::submitRequest(request)

[ FAIL 4 | WARN 0 | SKIP 8 | PASS 0 ]
Error: Test failures
Execution halted

Example timings

rhdf5client.Rcheck/rhdf5client-Ex.timings

name	user	system	elapsed
HSDSArray	0.04	0.03	0.17
HSDSDataset	0.01	0.00	0.03
HSDSFile	0.03	0.00	0.04
HSDSSource	0.00	0.00	0.04
URL_hsds	0	0	0
check_hsds	0.03	0.00	0.04
getData-methods	0.00	0.00	0.03
listDatasets	0.00	0.00	0.04
listDomains-methods	0.02	0.00	0.04
sproc	0	0	0