Back to Multiple platform build/check report for BioC 3.22:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-09-24 12:03 -0400 (Wed, 24 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4827
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4614
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4558
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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 189/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocHail 1.9.4  (landing page)
Vincent Carey
Snapshot Date: 2025-09-23 13:45 -0400 (Tue, 23 Sep 2025)
git_url: https://git.bioconductor.org/packages/BiocHail
git_branch: devel
git_last_commit: 89db83f
git_last_commit_date: 2025-07-01 08:20:55 -0400 (Tue, 01 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64... NOT SUPPORTED ...
kjohnson3macOS 13.7.7 Ventura / arm64... NOT SUPPORTED ...
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for BiocHail on nebbiolo2

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.

raw results


Summary

Package: BiocHail
Version: 1.9.4
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BiocHail.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BiocHail_1.9.4.tar.gz
StartedAt: 2025-09-23 21:28:19 -0400 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 21:34:27 -0400 (Tue, 23 Sep 2025)
EllapsedTime: 367.7 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocHail.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BiocHail.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BiocHail_1.9.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BiocHail.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BiocHail/DESCRIPTION’ ... OK
* this is package ‘BiocHail’ version ‘1.9.4’
* 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 45.101 15.419  72.158
as.data.frame                8.388  0.766  43.083
get_1kg                      0.975  0.128   5.368
filter                       0.190  0.005   7.060
filter.hail.table.Table      0.180  0.007   6.083
as.data.frame.default        0.109  0.008   5.347
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
 OK
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/BiocHail.Rcheck/00check.log’
for details.


Installation output

BiocHail.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BiocHail
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BiocHail’ ...
** this is package ‘BiocHail’ version ‘1.9.4’
** 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


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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.

> 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/1.21.5/BiocHail/1.9.4/bsklenv/lib/python3.9/site-packages/hail/context.py:354: 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(
Running on Apache Spark version 3.5.6
SparkUI available at http://155.52.47.146:4040
Welcome to
     __  __     <>__
    / /_/ /__  __/ /
   / __  / _ `/ / /
  /_/ /_/\_,_/_/_/   version 0.2.135-034ef3e08116
LOGGING: writing to /tmp/RtmpWDwg9W/file3e9e7819c20725
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

2025-09-23 21:33:04.351 Hail: INFO: Reading table to impute column types
2025-09-23 21:33:06.205 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']
----------------------------------------
2025-09-23 21:33:09.800 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 0x7aa452af34c0>
Index:
    ['column']
--------------------------------------------------------

[Stage 9:>                                                          (0 + 2) / 2]
2025-09-23 21:33:33.844 Hail: INFO: linear_regression_rows: running on 250 samples for 1 response variable y,
    with input variable x, and 1 additional covariate...

[Stage 22:>                                                         (0 + 2) / 2]

[Stage 23:>                                                         (0 + 2) / 2]
2025-09-23 21:33:38.318 Hail: INFO: wrote table with 10961 rows in 2 partitions to /tmp/persist_TableKDLs3NE6aX
----------------------------------------
Global fields:
    None
----------------------------------------
Column fields:
    'trait_type': str
    'phenocode': str
    'pheno_sex': str
    'coding': str
    'modifier': str
    'pheno_data': array<struct {
        n_cases: int32, 
        n_controls: int32, 
        heritability: float64, 
        saige_version: str, 
        inv_normalized: bool, 
        pop: str
    }>
    'description': str
    'description_more': str
    'coding_description': str
    'category': str
    'n_cases_full_cohort_both_sexes': int64
    'n_cases_full_cohort_females': int64
    'n_cases_full_cohort_males': int64
----------------------------------------
Row fields:
    'locus': locus<GRCh37>
    'alleles': array<str>
    'gene': str
    'annotation': str
----------------------------------------
Entry fields:
    'summary_stats': array<struct {
        AF_Allele2: float64, 
        imputationInfo: float64, 
        BETA: float64, 
        SE: float64, 
        `p.value.NA`: float64, 
        `AF.Cases`: float64, 
        `AF.Controls`: float64, 
        Pvalue: float64, 
        low_confidence: bool
    }>
----------------------------------------
Column key: ['trait_type', 'phenocode', 'pheno_sex', 'coding', 'modifier']
Row key: ['locus', 'alleles']
----------------------------------------
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
> 
> proc.time()
   user  system elapsed 
 16.699   1.061  75.253 

Example timings

BiocHail.Rcheck/BiocHail-Ex.timings

nameusersystemelapsed
as.data.frame 8.388 0.76643.083
as.data.frame.default0.1090.0085.347
as.data.frame.hail.table.Table0.1110.0064.249
bare_hail0.0010.0000.000
colnames-hail.table.Table-method0.0830.0002.794
filter0.1900.0057.060
filter.hail.table.Table0.1800.0076.083
get_1kg0.9750.1285.368
get_key0.1040.0052.357
get_key.hail.table.Table0.0930.0052.141
get_ukbb_sumstat_10kloci_mt45.10115.41972.158
hail_init0.0010.0000.000
hail_init_simple0.0130.0020.016
hail_stop000
kg_32020.1150.0100.125
multipop_df1.2150.1163.044
osn_1kg_path0.0000.0000.001
osn_ukbb_sumst10k_path0.0000.0000.001
path_1kg_annotations0.0010.0000.002
pcs_191k0.0150.0020.017
pcs_38k0.0210.0020.024
rg_update0.0100.0030.044
rownames-hail.table.Table-method0.1510.0034.666
ukbb_init0.0260.0090.055