Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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

Package 188/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocHail 1.8.0  (landing page)
Vincent Carey
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/BiocHail
git_branch: RELEASE_3_21
git_last_commit: 747e24e
git_last_commit_date: 2025-04-15 13:15:00 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
merida1macOS 12.7.6 Monterey / x86_64... NOT SUPPORTED ...
kjohnson1macOS 13.7.5 Ventura / arm64... NOT SUPPORTED ...
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for BiocHail on kunpeng2

To the developers/maintainers of the BiocHail package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocHail.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: BiocHail
Version: 1.8.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BiocHail.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BiocHail_1.8.0.tar.gz
StartedAt: 2025-10-14 06:41:16 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 06:56:40 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 924.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: BiocHail.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:BiocHail.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BiocHail_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BiocHail.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocHail/DESCRIPTION’ ... OK
* this is package ‘BiocHail’ version ‘1.8.0’
* 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 ... 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 ‘BiocHail’ can be installed ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
get_ukbb_sumstat_10kloci_mt 34.478  9.896  54.871
as.data.frame               10.845  1.228  40.634
get_1kg                      0.851  0.109   5.107
filter                       0.148  0.004   6.418
filter.hail.table.Table      0.145  0.005   5.006
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
 ERROR
Running the tests in ‘tests/test.R’ failed.
Last 13 lines of output:
   3.     └─BiocHail (local) fun(...)
   4.       └─hl$read_matrix_table(paste0(folder, "/1kg.mt"))
   5.         └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
  ── Error ('test_ukbb.R:8:1'): basic matrix_table operations succeed ────────────
  <requests.exceptions.ConnectionError/requests.exceptions.RequestException/python.builtin.OSError/python.builtin.Exception/python.builtin.BaseException/python.builtin.object/error/condition>
  Error in `py_call_impl(callable, call_args$unnamed, call_args$named)`: requests.exceptions.ConnectionError: HTTPConnectionPool(host='localhost', port=39187): Max retries exceeded with url: /references/load (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0xffff789552b0>: Failed to establish a new connection: [Errno 111] Connection refused'))
  Run `reticulate::py_last_error()` for details.
  Backtrace:
      ▆
   1. └─hl$read_matrix_table(paste0(td, "/myss2.mt")) at test_ukbb.R:8:1
   2.   └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 2 ]
  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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/BiocHail.Rcheck/00check.log’
for details.


Installation output

BiocHail.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL BiocHail
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘BiocHail’ ...
** this is package ‘BiocHail’ version ‘1.8.0’
** using staged installation
** R
** data
** 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 (BiocHail)

Tests output

BiocHail.Rcheck/tests/test.Rout.fail


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(BiocHail)

Attaching package: 'BiocHail'

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

    filter

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

    as.data.frame

> 
> test_check("BiocHail")
/home/biocbuild/.cache/R/basilisk/1.20.0/BiocHail/1.8.0/bsklenv/lib/python3.12/site-packages/hail/context.py:352: UserWarning: Using hl.init with a default_reference argument is deprecated. To set a default reference genome after initializing hail, call `hl.default_reference` with an argument to set the default reference genome.
  warnings.warn(
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
Running on Apache Spark version 3.5.6
SparkUI available at http://kunpeng2:4040
Welcome to
     __  __     <>__
    / /_/ /__  __/ /
   / __  / _ `/ / /
  /_/ /_/\_,_/_/_/   version 0.2.133-4c60fddb171a
LOGGING: writing to /home/biocbuild/tmp/Rtmpv9VjBc/file3de01b6365f527
SLF4J: Failed to load class "org.slf4j.impl.StaticMDCBinder".
SLF4J: Defaulting to no-operation MDCAdapter implementation.
SLF4J: See http://www.slf4j.org/codes.html#no_static_mdc_binder for further details.
NULL
+---------------+------------+
| locus         | alleles    |
+---------------+------------+
| locus<GRCh37> | array<str> |
+---------------+------------+
| 1:904165      | ["G","A"]  |
| 1:909917      | ["G","A"]  |
| 1:986963      | ["C","T"]  |
| 1:1563691     | ["T","G"]  |
| 1:1707740     | ["T","G"]  |
+---------------+------------+
showing top 5 rows

2025-10-14 06:45:48.417 Hail: INFO: Reading table to impute column types
2025-10-14 06:45:53.488 Hail: INFO: Finished type imputation
  Loading field 'Sample' as type str (imputed)
  Loading field 'Population' as type str (imputed)
  Loading field 'SuperPopulation' as type str (imputed)
  Loading field 'isFemale' as type bool (imputed)
  Loading field 'PurpleHair' as type bool (imputed)
  Loading field 'CaffeineConsumption' as type int32 (imputed)
----------------------------------------
Global fields:
    None
----------------------------------------
Row fields:
    'Sample': str 
    'Population': str 
    'SuperPopulation': str 
    'isFemale': bool 
    'PurpleHair': bool 
    'CaffeineConsumption': int32 
----------------------------------------
Key: ['Sample']
----------------------------------------
2025-10-14 06:46:00.468 Hail: WARN: aggregate_cols(): Aggregates over cols ordered by 'col_key'.
    To preserve matrix table column order, first unkey columns with 'key_cols_by()'
+-----------+------------+-----------------+----------+------------+---------------------+
| Sample    | Population | SuperPopulation | isFemale | PurpleHair | CaffeineConsumption |
+-----------+------------+-----------------+----------+------------+---------------------+
| str       | str        | str             |     bool |       bool |               int32 |
+-----------+------------+-----------------+----------+------------+---------------------+
| "HG00096" | "GBR"      | "EUR"           |    False |      False |                   4 |
| "HG00097" | "GBR"      | "EUR"           |     True |       True |                   4 |
| "HG00098" | "GBR"      | "EUR"           |    False |      False |                   5 |
| "HG00099" | "GBR"      | "EUR"           |     True |      False |                   4 |
| "HG00100" | "GBR"      | "EUR"           |     True |      False |                   5 |
| "HG00101" | "GBR"      | "EUR"           |    False |       True |                   1 |
| "HG00102" | "GBR"      | "EUR"           |     True |       True |                   6 |
| "HG00103" | "GBR"      | "EUR"           |    False |       True |                   5 |
| "HG00104" | "GBR"      | "EUR"           |     True |      False |                   5 |
| "HG00105" | "GBR"      | "EUR"           |    False |      False |                   4 |
+-----------+------------+-----------------+----------+------------+---------------------+
showing top 10 rows

--------------------------------------------------------
Type:
        struct {
        s: str, 
        pheno: struct {
            Population: str, 
            SuperPopulation: str, 
            isFemale: bool, 
            PurpleHair: bool, 
            CaffeineConsumption: int32
        }
    }
--------------------------------------------------------
Source:
    <hail.matrixtable.MatrixTable object at 0xffff7aeba1e0>
Index:
    ['column']
--------------------------------------------------------

[Stage 9:>                                                          (0 + 2) / 2]

[Stage 9:=============================>                             (1 + 1) / 2]

[Stage 10:>                                                         (0 + 2) / 2]
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 2 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_gwas.R:117:1'): gwas can be conducted ──────────────────────────
<requests.exceptions.ConnectionError/requests.exceptions.RequestException/python.builtin.OSError/python.builtin.Exception/python.builtin.BaseException/python.builtin.object/error/condition>
Error in `py_call_impl(callable, call_args$unnamed, call_args$named)`: requests.exceptions.ConnectionError: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))
Run `reticulate::py_last_error()` for details.
Backtrace:
    ▆
 1. └─mt$count_cols() at test_gwas.R:117:1
 2.   └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
── Error ('test_tutorial.R:7:3'): get_1kg succeeds ─────────────────────────────
<requests.exceptions.ConnectionError/requests.exceptions.RequestException/python.builtin.OSError/python.builtin.Exception/python.builtin.BaseException/python.builtin.object/error/condition>
Error in `py_call_impl(callable, call_args$unnamed, call_args$named)`: requests.exceptions.ConnectionError: HTTPConnectionPool(host='localhost', port=39187): Max retries exceeded with url: /references/load (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0xffff7aed5ca0>: Failed to establish a new connection: [Errno 111] Connection refused'))
Run `reticulate::py_last_error()` for details.
Backtrace:
    ▆
 1. └─BiocHail::get_1kg(hl) at test_tutorial.R:7:3
 2.   └─basilisk::basiliskRun(...)
 3.     └─BiocHail (local) fun(...)
 4.       └─hl$read_matrix_table(paste0(folder, "/1kg.mt"))
 5.         └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
── Error ('test_ukbb.R:8:1'): basic matrix_table operations succeed ────────────
<requests.exceptions.ConnectionError/requests.exceptions.RequestException/python.builtin.OSError/python.builtin.Exception/python.builtin.BaseException/python.builtin.object/error/condition>
Error in `py_call_impl(callable, call_args$unnamed, call_args$named)`: requests.exceptions.ConnectionError: HTTPConnectionPool(host='localhost', port=39187): Max retries exceeded with url: /references/load (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0xffff789552b0>: Failed to establish a new connection: [Errno 111] Connection refused'))
Run `reticulate::py_last_error()` for details.
Backtrace:
    ▆
 1. └─hl$read_matrix_table(paste0(td, "/myss2.mt")) at test_ukbb.R:8:1
 2.   └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 2 ]
Error: Test failures
Execution halted

Example timings

BiocHail.Rcheck/BiocHail-Ex.timings

nameusersystemelapsed
as.data.frame10.845 1.22840.634
as.data.frame.default0.0990.0044.652
as.data.frame.hail.table.Table0.0890.0083.587
bare_hail0.0010.0000.000
colnames-hail.table.Table-method0.0760.0011.958
filter0.1480.0046.418
filter.hail.table.Table0.1450.0055.006
get_1kg0.8510.1095.107
get_key0.0890.0082.103
get_key.hail.table.Table0.0760.0161.419
get_ukbb_sumstat_10kloci_mt34.478 9.89654.871
hail_init0.0010.0000.001
hail_init_simple0.0090.0070.026
hail_stop0.0000.0000.001
kg_32020.0880.0080.097
multipop_df1.0290.0382.336
osn_1kg_path000
osn_ukbb_sumst10k_path000
path_1kg_annotations0.0010.0010.001
pcs_191k0.010.000.01
pcs_38k0.0110.0030.014
rg_update0.0100.0040.024
rownames-hail.table.Table-method0.1030.0022.930
ukbb_init0.0200.0120.058