Multiple platform build/check report for BioC 3.21 - BUILD results for HiCool on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4742
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4545
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4459
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*

BUILD results for HiCool on kunpeng2

To the developers/maintainers of the HiCool package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiCool.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: HiCool

Version: 1.7.1

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data HiCool

StartedAt: 2025-03-18 23:38:20 -0000 (Tue, 18 Mar 2025)

EndedAt: 2025-03-18 23:41:47 -0000 (Tue, 18 Mar 2025)

EllapsedTime: 207.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data HiCool
###
##############################################################################
##############################################################################


* checking for file ‘HiCool/DESCRIPTION’ ... OK
* preparing ‘HiCool’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘HiCool.Rmd’ using rmarkdown
Channels:
 - conda-forge
 - bioconda
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.19.1/HiCool/1.7.1/env

  added / updated specs:
    - python=3.7.12


The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu 
  ca-certificates    conda-forge/linux-aarch64::ca-certificates-2025.1.31-hcefe29a_0 
  ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.43-h80caac9_4 
  libffi             conda-forge/linux-aarch64::libffi-3.4.6-he21f813_0 
  libgcc             conda-forge/linux-aarch64::libgcc-14.2.0-he277a41_2 
  libgcc-ng          conda-forge/linux-aarch64::libgcc-ng-14.2.0-he9431aa_2 
  libgomp            conda-forge/linux-aarch64::libgomp-14.2.0-he277a41_2 
  liblzma            conda-forge/linux-aarch64::liblzma-5.6.4-h86ecc28_0 
  liblzma-devel      conda-forge/linux-aarch64::liblzma-devel-5.6.4-h86ecc28_0 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.49.1-h5eb1b54_2 
  libstdcxx          conda-forge/linux-aarch64::libstdcxx-14.2.0-h3f4de04_2 
  libstdcxx-ng       conda-forge/linux-aarch64::libstdcxx-ng-14.2.0-hf1166c9_2 
  libzlib            conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2 
  ncurses            conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_3 
  openssl            conda-forge/linux-aarch64::openssl-3.4.1-hd08dc88_0 
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 
  python             conda-forge/linux-aarch64::python-3.7.12-h47f6e27_100_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8382b9d_2 
  setuptools         conda-forge/noarch::setuptools-69.0.3-pyhd8ed1ab_0 
  sqlite             conda-forge/linux-aarch64::sqlite-3.49.1-h578a6b9_2 
  tk                 conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0 
  wheel              conda-forge/noarch::wheel-0.42.0-pyhd8ed1ab_0 
  xz                 conda-forge/linux-aarch64::xz-5.6.4-h2dbfc1b_0 
  xz-gpl-tools       conda-forge/linux-aarch64::xz-gpl-tools-5.6.4-h2dbfc1b_0 
  xz-tools           conda-forge/linux-aarch64::xz-tools-5.6.4-h86ecc28_0 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
 - bioconda
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
    current version: 24.11.3
    latest version: 25.1.1

Please update conda by running

    $ conda update -n base -c conda-forge conda



# All requested packages already installed.

Channels:
 - conda-forge
 - bioconda
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides requested samtools 1.16.1**
  - nothing provides requested bowtie2 2.5.0**
  - package hicstuff-3.1.5-pyhdfd78af_0 requires pysam, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ bowtie2 2.5.0**  does not exist (perhaps a typo or a missing channel);
├─ hicstuff 3.1.5**  is installable and it requires
│  └─ pysam with the potential options
│     ├─ pysam [0.22.0|0.22.1|0.23.0] would require
│     │  ├─ python >=3.10,<3.11.0a0 , which can be installed;
│     │  └─ python_abi 3.10.* *_cp310, which can be installed;
│     ├─ pysam [0.22.0|0.22.1] would require
│     │  ├─ python >=3.8,<3.9.0a0 , which can be installed;
│     │  └─ python_abi 3.8.* *_cp38, which can be installed;
│     ├─ pysam [0.22.0|0.22.1|0.23.0] would require
│     │  ├─ python >=3.9,<3.10.0a0 , which can be installed;
│     │  └─ python_abi 3.9.* *_cp39, which can be installed;
│     ├─ pysam [0.22.1|0.23.0] would require
│     │  ├─ python >=3.11,<3.12.0a0 , which can be installed;
│     │  └─ python_abi 3.11.* *_cp311, which can be installed;
│     └─ pysam [0.22.1|0.23.0] would require
│        └─ python_abi 3.12.* *_cp312, which can be installed;
├─ python 3.7.12.*,3.7.12.*  is not installable because there are no viable options
│  ├─ python 3.7.12 conflicts with any installable versions previously reported;
│  └─ python 3.7.12 would require
│     └─ python_abi 3.7.* *_cp37m, which conflicts with any installable versions previously reported;
└─ samtools 1.16.1**  does not exist (perhaps a typo or a missing channel).


Quitting from HiCool.Rmd:70-80 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! one or more Python packages failed to install [error code 1]
---
Backtrace:
    ▆
 1. └─HiCool::HiCool(...)
 2.   └─basilisk::basiliskStart(env_HiCool)
 3.     └─basilisk::obtainEnvironmentPath(env)
 4.       └─basilisk::setupBasiliskEnv(...)
 5.         └─reticulate::conda_install(...)
 6.           └─reticulate:::stopf(fmt, result)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'HiCool.Rmd' failed with diagnostics:
one or more Python packages failed to install [error code 1]
--- failed re-building ‘HiCool.Rmd’

SUMMARY: processing the following file failed:
  ‘HiCool.Rmd’

Error: Vignette re-building failed.
Execution halted