##############################################################################
##############################################################################
###
### 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BiocHail.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘BiocHail/DESCRIPTION’ ... OK
* this is package ‘BiocHail’ version ‘1.5.0’
* 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 35.833 11.593  49.904
as.data.frame                4.719  1.043  29.658
* 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-3.20-bioc/meat/BiocHail.Rcheck/00check.log’
for details.

##############################################################################
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###
### 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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")
2024-09-11 20:44:03.454 WARN  Utils:69 - Your hostname, nebbiolo2 resolves to a loopback address: 127.0.1.1; using 155.52.47.146 instead (on interface enp175s0f1np1)
2024-09-11 20:44:03.458 WARN  Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.spark.unsafe.Platform (file:/var/cache/basilisk/1.17.2/BiocHail/1.5.0/bsklenv/lib/python3.10/site-packages/pyspark/jars/spark-unsafe_2.12-3.1.3.jar) to constructor java.nio.DirectByteBuffer(long,int)
WARNING: Please consider reporting this to the maintainers of org.apache.spark.unsafe.Platform
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
2024-09-11 20:44:03.899 WARN  NativeCodeLoader:60 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
Running on Apache Spark version 3.1.3
SparkUI available at http://155.52.47.146:4040
Welcome to
     __  __     <>__
    / /_/ /__  __/ /
   / __  / _ `/ / /
  /_/ /_/\_,_/_/_/   version 0.2.108-fc03e9d5dc08
LOGGING: writing to /tmp/RtmpllBwyp/file206e9e37059a5a
NULL
2024-09-11 20:44:14.923 Hail: INFO: wrote table with 3501 rows in 1 partition to /tmp/persist_tableBKFv6eYiUR
+---------------+------------+
| 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

2024-09-11 20:44:15.429 Hail: INFO: Reading table to impute column types
2024-09-11 20:44:16.411 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']
----------------------------------------
+-----------+------------+-----------------+----------+------------+---------------------+
| 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 0x7efed2629e40>
Index:
    ['column']
--------------------------------------------------------

[Stage 11:>                                                         (0 + 2) / 2]
2024-09-11 20:44:31.441 Hail: INFO: linear_regression_rows: running on 250 samples for 1 response variable y,
    with input variable x, and 1 additional covariate...

[Stage 19:>                                                         (0 + 2) / 2]
2024-09-11 20:44:33.310 Hail: INFO: wrote table with 10961 rows in 2 partitions to /tmp/persist_tabley2h7IVC9lv
    Total size: 670.31 KiB
    * Rows: 670.30 KiB
    * Globals: 11.00 B
    * Smallest partition: 5460 rows (333.78 KiB)
    * Largest partition:  5501 rows (336.51 KiB)
2024-09-11 20:45:19.910 Hail: WARN: cols(): Resulting column table is sorted by 'col_key'.
    To preserve matrix table column order, first unkey columns with 'key_cols_by()'
----------------------------------------
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']
----------------------------------------

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2024-09-11 20:45:35.481 Hail: WARN: entries(): Resulting entries table is sorted by '(row_key, col_key)'.
    To preserve row-major matrix table order, first unkey columns with 'key_cols_by()'

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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
 46.546  10.714 124.100