##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BiocHail.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BiocHail_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BiocHail.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BiocHail/DESCRIPTION’ ... OK
* this is package ‘BiocHail’ version ‘1.6.1’
* 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 46.93 27.604 331.538
as.data.frame               10.27  1.562  35.102
* 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:
  	at java.base/java.lang.Thread.run(Thread.java:1583)
  
  
  
  Hail version: 0.2.133-4c60fddb171a
  Error summary: SparkException: Job 19 cancelled because SparkContext was shut down
  Run `reticulate::py_last_error()` for details.
  Backtrace:
      ▆
   1. └─sss$count() at test_ukbb.R:46:1
   2.   └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/BiocHail.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BiocHail
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘BiocHail’ ...
** 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)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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/1.18.0/BiocHail/1.6.1/bsklenv/lib/python3.10/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 3.5.4
SparkUI available at http://155.52.47.146:4040
Welcome to
     __  __     <>__
    / /_/ /__  __/ /
   / __  / _ `/ / /
  /_/ /_/\_,_/_/_/   version 0.2.133-4c60fddb171a
LOGGING: writing to /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpZxWUEn/file1ff8226f516a8a
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

2025-01-20 20:14:33.930 Hail: INFO: Reading table to impute column types
2025-01-20 20:14:34.705 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']
----------------------------------------
2025-01-20 20:14:36.133 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 0x75386abb3580>
Index:
    ['column']
--------------------------------------------------------

[Stage 9:>                                                          (0 + 2) / 2]
2025-01-20 20:14:47.624 Hail: INFO: linear_regression_rows: running on 250 samples for 1 response variable y,
    with input variable x, and 1 additional covariate...

[Stage 17:>                                                         (0 + 2) / 2]
2025-01-20 20:14:49.456 Hail: INFO: wrote table with 10961 rows in 2 partitions to /tmp/persist_TableRv7TD0wENj
----------------------------------------
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']
----------------------------------------

[Stage 19:>                                                    (0 + 19) / 20000]

[Stage 19:>                                                    (0 + 29) / 20000]

[Stage 19:>                                                    (0 + 39) / 20000]

[Stage 19:>                                                    (0 + 47) / 20000]

[Stage 19:>                                                    (0 + 55) / 20000]

[Stage 19:>                                                    (0 + 64) / 20000]

[Stage 19:>                                                    (0 + 72) / 20000]
Exception in thread "Executor task launch worker for task 58.0 in stage 19.0 (TID 87)" java.lang.OutOfMemoryError: Java heap space
Exception in thread "Spark Context Cleaner" java.lang.OutOfMemoryError: Java heap space
Exception in thread "Executor task launch worker for task 12.0 in stage 19.0 (TID 41)" java.lang.OutOfMemoryError: Java heap space
Exception in thread "Executor task launch worker for task 35.0 in stage 19.0 (TID 64)" java.lang.OutOfMemoryError: Java heap space
Exception in thread "RemoteBlock-temp-file-clean-thread" java.lang.OutOfMemoryError: Java heap space
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_ukbb.R:46:1'): ukbb code succeeds ──────────────────────────────
<hail.utils.java.FatalError/python.builtin.Exception/python.builtin.BaseException/python.builtin.object/error/condition>
Error in `py_call_impl(callable, call_args$unnamed, call_args$named)`: hail.utils.java.FatalError: SparkException: Job 19 cancelled because SparkContext was shut down

<...truncated...>hFilter.doFilter(AuthFilter.java:82)
	at jdk.httpserver/com.sun.net.httpserver.Filter$Chain.doFilter(Filter.java:101)
	at jdk.httpserver/sun.net.httpserver.ServerImpl$Exchange$LinkHandler.handle(ServerImpl.java:871)
	at jdk.httpserver/com.sun.net.httpserver.Filter$Chain.doFilter(Filter.java:98)
	at jdk.httpserver/sun.net.httpserver.ServerImpl$Exchange.run(ServerImpl.java:847)
	at jdk.httpserver/sun.net.httpserver.ServerImpl$DefaultExecutor.execute(ServerImpl.java:203)
	at jdk.httpserver/sun.net.httpserver.ServerImpl$Dispatcher.handle(ServerImpl.java:566)
	at jdk.httpserver/sun.net.httpserver.ServerImpl$Dispatcher.run(ServerImpl.java:531)
	at java.base/java.lang.Thread.run(Thread.java:1583)



Hail version: 0.2.133-4c60fddb171a
Error summary: SparkException: Job 19 cancelled because SparkContext was shut down
Run `reticulate::py_last_error()` for details.
Backtrace:
    ▆
 1. └─sss$count() at test_ukbb.R:46:1
 2.   └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]
Error: Test failures
Execution halted