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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:HDF5Array.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings HDF5Array_1.35.16.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/HDF5Array.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 ‘HDF5Array/DESCRIPTION’ ... OK
* this is package ‘HDF5Array’ version ‘1.35.16’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HDF5Array’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  8.7Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
* 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 whether startup messages can be suppressed ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  H5SparseMatrix-class.Rd: h5ls
  H5SparseMatrixSeed-class.Rd: h5ls
  HDF5Array-class.Rd: H5File, h5ls
  HDF5ArraySeed-class.Rd: h5ls
  ReshapedHDF5Array-class.Rd: h5ls
  ReshapedHDF5ArraySeed-class.Rd: h5ls
  TENxMatrix-class.Rd: h5ls
  TENxMatrixSeed-class.Rd: h5ls
  dump-management.Rd: h5createDataset, h5ls
  writeHDF5Array.Rd: DelayedArray, h5writeDimnames, h5ls
  writeTENxMatrix.Rd: DelayedMatrix, h5ls
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
TENxMatrix-class 61.441 17.088  41.127
writeTENxMatrix  15.920  1.597  17.746
HDF5Array-class   2.160  0.228   5.185
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 ERROR
Running the tests in ‘tests/run_unitTests.R’ failed.
Last 13 lines of output:
  HDF5Array RUnit Tests - 5 test functions, 2 errors, 0 failures
  ERROR in test_CSR_H5ADMatrixSeed: Error : Error installing package(s): "'anndata==0.10.9'", "'h5py==3.12.1'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.1.2'", "'packaging==24.1'", "'pandas==2.2.3'", "'python==3.12.7'", "'scipy==1.14.1'"
  ERROR in test_Dense_H5ADMatrixSeed: Error : Error installing package(s): "'anndata==0.10.9'", "'h5py==3.12.1'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.1.2'", "'packaging==24.1'", "'pandas==2.2.3'", "'python==3.12.7'", "'scipy==1.14.1'"
  
  Test files with failing tests
  
     test_H5ADMatrixSeed-class.R 
       test_CSR_H5ADMatrixSeed 
       test_Dense_H5ADMatrixSeed 
  
  
  Error in BiocGenerics:::testPackage("HDF5Array") : 
    unit tests failed for package HDF5Array
  Calls: <Anonymous> -> <Anonymous>
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/HDF5Array.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL HDF5Array
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘HDF5Array’ ...
** this is package ‘HDF5Array’ version ‘1.35.16’
** 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 (HDF5Array)

R Under development (unstable) (2025-03-13 r87965) -- "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.

> require("HDF5Array") || stop("unable to load HDF5Array package")
Loading required package: HDF5Array
Loading required package: SparseArray
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
Loading required package: stats4

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

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

Loading required package: DelayedArray

Attaching package: 'DelayedArray'

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

    apply, scale, sweep

Loading required package: h5mread
Loading required package: rhdf5

Attaching package: 'h5mread'

The following object is masked from 'package:rhdf5':

    h5ls

[1] TRUE
> HDF5Array:::.test()
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    rowMedians

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

    anyMissing, rowMedians

Using Python: /home/biocbuild/.pyenv/versions/3.12.7/bin/python3.12
Creating virtual environment '/home/biocbuild/.cache/R/basilisk/1.19.2/zellkonverter/1.17.1/zellkonverterAnnDataEnv-0.10.9' ... 
+ /home/biocbuild/.pyenv/versions/3.12.7/bin/python3.12 -m venv /home/biocbuild/.cache/R/basilisk/1.19.2/zellkonverter/1.17.1/zellkonverterAnnDataEnv-0.10.9
Done!
Installing packages: pip, wheel, setuptools
+ /home/biocbuild/.cache/R/basilisk/1.19.2/zellkonverter/1.17.1/zellkonverterAnnDataEnv-0.10.9/bin/python -m pip install --upgrade pip wheel setuptools
Requirement already satisfied: pip in /home/biocbuild/.cache/R/basilisk/1.19.2/zellkonverter/1.17.1/zellkonverterAnnDataEnv-0.10.9/lib/python3.12/site-packages (24.2)
Collecting pip
  Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 kB)
Collecting wheel
  Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
  Using cached setuptools-77.0.3-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-77.0.3-py3-none-any.whl (1.3 MB)
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: pip
    Found existing installation: pip 24.2
    Uninstalling pip-24.2:
      Successfully uninstalled pip-24.2
Successfully installed pip-25.0.1 setuptools-77.0.3 wheel-0.45.1
Virtual environment '/home/biocbuild/.cache/R/basilisk/1.19.2/zellkonverter/1.17.1/zellkonverterAnnDataEnv-0.10.9' successfully created.
Using virtual environment '/home/biocbuild/.cache/R/basilisk/1.19.2/zellkonverter/1.17.1/zellkonverterAnnDataEnv-0.10.9' ...
+ /home/biocbuild/.cache/R/basilisk/1.19.2/zellkonverter/1.17.1/zellkonverterAnnDataEnv-0.10.9/bin/python -m pip install --upgrade --no-user 'anndata==0.10.9' 'h5py==3.12.1' 'hdf5==1.14.3' 'natsort==8.4.0' 'numpy==2.1.2' 'packaging==24.1' 'pandas==2.2.3' 'python==3.12.7' 'scipy==1.14.1'
Collecting anndata==0.10.9
  Using cached anndata-0.10.9-py3-none-any.whl.metadata (6.9 kB)
Collecting h5py==3.12.1
  Using cached h5py-3.12.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Timing stopped at: 7.511 1.273 9.183
Error : Error installing package(s): "'anndata==0.10.9'", "'h5py==3.12.1'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.1.2'", "'packaging==24.1'", "'pandas==2.2.3'", "'python==3.12.7'", "'scipy==1.14.1'"
Using Python: /home/biocbuild/.pyenv/versions/3.12.7/bin/python3.12
Creating virtual environment '/home/biocbuild/.cache/R/basilisk/1.19.2/zellkonverter/1.17.1/zellkonverterAnnDataEnv-0.10.9' ... 
+ /home/biocbuild/.pyenv/versions/3.12.7/bin/python3.12 -m venv /home/biocbuild/.cache/R/basilisk/1.19.2/zellkonverter/1.17.1/zellkonverterAnnDataEnv-0.10.9
Done!
Installing packages: pip, wheel, setuptools
+ /home/biocbuild/.cache/R/basilisk/1.19.2/zellkonverter/1.17.1/zellkonverterAnnDataEnv-0.10.9/bin/python -m pip install --upgrade pip wheel setuptools
Requirement already satisfied: pip in /home/biocbuild/.cache/R/basilisk/1.19.2/zellkonverter/1.17.1/zellkonverterAnnDataEnv-0.10.9/lib/python3.12/site-packages (24.2)
Collecting pip
  Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 kB)
Collecting wheel
  Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
  Using cached setuptools-77.0.3-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-77.0.3-py3-none-any.whl (1.3 MB)
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: pip
    Found existing installation: pip 24.2
    Uninstalling pip-24.2:
      Successfully uninstalled pip-24.2
Successfully installed pip-25.0.1 setuptools-77.0.3 wheel-0.45.1
Virtual environment '/home/biocbuild/.cache/R/basilisk/1.19.2/zellkonverter/1.17.1/zellkonverterAnnDataEnv-0.10.9' successfully created.
Using virtual environment '/home/biocbuild/.cache/R/basilisk/1.19.2/zellkonverter/1.17.1/zellkonverterAnnDataEnv-0.10.9' ...
+ /home/biocbuild/.cache/R/basilisk/1.19.2/zellkonverter/1.17.1/zellkonverterAnnDataEnv-0.10.9/bin/python -m pip install --upgrade --no-user 'anndata==0.10.9' 'h5py==3.12.1' 'hdf5==1.14.3' 'natsort==8.4.0' 'numpy==2.1.2' 'packaging==24.1' 'pandas==2.2.3' 'python==3.12.7' 'scipy==1.14.1'
Collecting anndata==0.10.9
  Using cached anndata-0.10.9-py3-none-any.whl.metadata (6.9 kB)
Collecting h5py==3.12.1
  Using cached h5py-3.12.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
ERROR: Could not find a version that satisfies the requirement hdf5==1.14.3 (from versions: none)
ERROR: No matching distribution found for hdf5==1.14.3
Timing stopped at: 7.307 1.152 8.742
Error : Error installing package(s): "'anndata==0.10.9'", "'h5py==3.12.1'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.1.2'", "'packaging==24.1'", "'pandas==2.2.3'", "'python==3.12.7'", "'scipy==1.14.1'"
automatic block size set to 77 bytes (was 1e+08)
automatic block size set to 1e+08 bytes (was 77)
automatic block size set to 77 bytes (was 1e+08)
automatic block size set to 1e+08 bytes (was 77)


RUNIT TEST PROTOCOL -- Thu Mar 20 22:58:43 2025 
*********************************************** 
Number of test functions: 5 
Number of errors: 2 
Number of failures: 0 

 
1 Test Suite : 
HDF5Array RUnit Tests - 5 test functions, 2 errors, 0 failures
ERROR in test_CSR_H5ADMatrixSeed: Error : Error installing package(s): "'anndata==0.10.9'", "'h5py==3.12.1'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.1.2'", "'packaging==24.1'", "'pandas==2.2.3'", "'python==3.12.7'", "'scipy==1.14.1'"
ERROR in test_Dense_H5ADMatrixSeed: Error : Error installing package(s): "'anndata==0.10.9'", "'h5py==3.12.1'", "'hdf5==1.14.3'", "'natsort==8.4.0'", "'numpy==2.1.2'", "'packaging==24.1'", "'pandas==2.2.3'", "'python==3.12.7'", "'scipy==1.14.1'"

Test files with failing tests

   test_H5ADMatrixSeed-class.R 
     test_CSR_H5ADMatrixSeed 
     test_Dense_H5ADMatrixSeed 


Error in BiocGenerics:::testPackage("HDF5Array") : 
  unit tests failed for package HDF5Array
Calls: <Anonymous> -> <Anonymous>
Execution halted