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This page was generated on 2025-08-09 12:04 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 187/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocHail 1.9.4  (landing page)
Vincent Carey
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.7.1 Monterey / x86_64... NOT SUPPORTED ...
kjohnson3macOS 13.7.1 Ventura / arm64... NOT SUPPORTED ...


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: 2025-08-08 20:26:07 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 20:29:51 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 224.3 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 (2025-06-13)
* 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 ‘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 34.019  9.432  44.438
as.data.frame                6.308  0.787  19.228
* 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 (2025-06-13) -- "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/RtmpnBYI1i/file27453f8c59387
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

2025-08-08 20:28:47.350 Hail: INFO: Reading table to impute column types
2025-08-08 20:28:48.145 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']
----------------------------------------
2025-08-08 20:28:49.706 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 0x7170290dad30>
Index:
    ['column']
--------------------------------------------------------

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

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

[Stage 10:>                                                         (0 + 2) / 2]

[Stage 10:=============================>                            (1 + 1) / 2]

[Stage 11:>                                                         (0 + 2) / 2]

[Stage 11:=============================>                            (1 + 1) / 2]
2025-08-08 20:29:19.575 Hail: INFO: linear_regression_rows: running on 250 samples for 1 response variable y,
    with input variable x, and 1 additional covariate...

[Stage 23:>                                                         (0 + 2) / 2]
2025-08-08 20:29:22.577 Hail: INFO: wrote table with 10961 rows in 2 partitions to /tmp/persist_Table21Aa05xQUS
----------------------------------------
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 
 13.028   1.095  55.741 

Example timings

BiocHail.Rcheck/BiocHail-Ex.timings

nameusersystemelapsed
as.data.frame 6.308 0.78719.228
as.data.frame.default0.1110.0032.351
as.data.frame.hail.table.Table0.1120.0032.091
bare_hail0.0010.0000.001
colnames-hail.table.Table-method0.1050.0061.267
filter0.2230.0063.499
filter.hail.table.Table0.2190.0103.414
get_1kg0.7120.0932.888
get_key0.1360.0091.127
get_key.hail.table.Table0.0780.0060.990
get_ukbb_sumstat_10kloci_mt34.019 9.43244.438
hail_init000
hail_init_simple0.0070.0050.013
hail_stop000
kg_32020.0760.0050.081
multipop_df0.8010.0771.203
osn_1kg_path000
osn_ukbb_sumst10k_path000
path_1kg_annotations0.0010.0000.001
pcs_191k0.0110.0010.011
pcs_38k0.0170.0020.018
rg_update0.0070.0000.013
rownames-hail.table.Table-method0.0920.0031.328
ukbb_init0.0110.0060.018