Multiple platform build/check report for BioC 3.20 - BUILD results for HiCool on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4746
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4493
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4517
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4469
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4394
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 taishan

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: 1.6.0

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

StartedAt: 2025-01-21 00:35:49 -0000 (Tue, 21 Jan 2025)

EndedAt: 2025-01-21 00:39:41 -0000 (Tue, 21 Jan 2025)

EllapsedTime: 232.1 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/1.18.0/HiCool/1.6.0/env

  added / updated specs:
    - python=3.7.12


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    sqlite-3.48.0              |       h578a6b9_0         1.0 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         1.0 MB

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-2024.12.14-hcefe29a_0 
  ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.43-h80caac9_2 
  libffi             conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5 
  libgcc             conda-forge/linux-aarch64::libgcc-14.2.0-he277a41_1 
  libgcc-ng          conda-forge/linux-aarch64::libgcc-ng-14.2.0-he9431aa_1 
  libgomp            conda-forge/linux-aarch64::libgomp-14.2.0-he277a41_1 
  liblzma            conda-forge/linux-aarch64::liblzma-5.6.3-h86ecc28_1 
  liblzma-devel      conda-forge/linux-aarch64::liblzma-devel-5.6.3-h86ecc28_1 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.48.0-h5eb1b54_0 
  libstdcxx          conda-forge/linux-aarch64::libstdcxx-14.2.0-h3f4de04_1 
  libstdcxx-ng       conda-forge/linux-aarch64::libstdcxx-ng-14.2.0-hf1166c9_1 
  libzlib            conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2 
  ncurses            conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_2 
  openssl            conda-forge/linux-aarch64::openssl-3.4.0-hd08dc88_1 
  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-h8fc344f_1 
  setuptools         conda-forge/noarch::setuptools-69.0.3-pyhd8ed1ab_0 
  sqlite             conda-forge/linux-aarch64::sqlite-3.48.0-h578a6b9_0 
  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-5.6.3-h2dbfc1b_1 
  xz-gpl-tools       conda-forge/linux-aarch64::xz-gpl-tools-5.6.3-h2dbfc1b_1 
  xz-tools           conda-forge/linux-aarch64::xz-tools-5.6.3-h86ecc28_1 


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: 24.3.0
    latest version: 24.11.3

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] 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] 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 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 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 lines 71-80 [unnamed-chunk-3] (HiCool.Rmd)
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