Vincent Carey
| Snapshot Date: 2024-05-30 18:28:32 -0400 (Thu, 30 May 2024) |
| git_url: https://git.bioconductor.org/packages/BiocHail |
| git_branch: RELEASE_3_19 |
| git_last_commit: 9d40c00 |
| git_last_commit_date: 2024-04-30 11:49:16 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-31 17:02:50 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| 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 182/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocHail 1.4.0 (landing page) Vincent Carey
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | ... NOT SUPPORTED ... | ||||||||||||
|
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. |
| Package: BiocHail |
| Version: 1.4.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BiocHail.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BiocHail_1.4.0.tar.gz |
| StartedAt: 2024-05-31 01:37:52 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 01:43:06 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 314.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocHail.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BiocHail.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BiocHail_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BiocHail.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BiocHail/DESCRIPTION’ ... OK
* this is package ‘BiocHail’ version ‘1.4.0’
* 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 36.418 13.720 51.690
as.data.frame 8.481 1.181 26.599
* 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-3.19-bioc/meat/BiocHail.Rcheck/00check.log’
for details.
BiocHail.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BiocHail ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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)
BiocHail.Rcheck/tests/test.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
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")
2024-05-31 01:40:44.447 WARN Utils:69 - Your hostname, nebbiolo1 resolves to a loopback address: 127.0.1.1; using 155.52.47.135 instead (on interface enp175s0f1np1)
2024-05-31 01:40:44.452 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/1.16.0/BiocHail/1.4.0/bsklenv/lib/python3.9/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
2024-05-31 01:40:44.881 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://nebbiolo1.bioconductor.org:4040
Welcome to
__ __ <>__
/ /_/ /__ __/ /
/ __ / _ `/ / /
/_/ /_/\_,_/_/_/ version 0.2.108-fc03e9d5dc08
LOGGING: writing to /tmp/Rtmp4teAsz/file3eada13c0ed6e5
NULL
2024-05-31 01:40:55.319 Hail: INFO: wrote table with 3501 rows in 1 partition to /tmp/persist_tablejINhLWgIuz
+---------------+------------+
| 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
2024-05-31 01:40:55.890 Hail: INFO: Reading table to impute column types
2024-05-31 01:40:56.961 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 0x7ff0764db1f0>
Index:
['column']
--------------------------------------------------------
[Stage 11:> (0 + 2) / 2]
2024-05-31 01:41:11.542 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]
2024-05-31 01:41:13.300 Hail: INFO: wrote table with 10961 rows in 2 partitions to /tmp/persist_tablehdRcnPguc6
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)
2024-05-31 01:42:02.625 Hail: WARN: cols(): Resulting column table is sorted by 'col_key'.
----------------------------------------
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']
----------------------------------------
To preserve matrix table column order, first unkey columns with 'key_cols_by()'
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2024-05-31 01:42:17.278 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
48.051 13.306 125.128
BiocHail.Rcheck/BiocHail-Ex.timings
| name | user | system | elapsed | |
| as.data.frame | 8.481 | 1.181 | 26.599 | |
| as.data.frame.default | 0.098 | 0.000 | 2.595 | |
| as.data.frame.hail.table.Table | 0.147 | 0.004 | 2.411 | |
| bare_hail | 0.000 | 0.002 | 0.001 | |
| colnames-hail.table.Table-method | 0.091 | 0.005 | 1.490 | |
| filter | 0.149 | 0.004 | 3.914 | |
| filter.hail.table.Table | 0.174 | 0.015 | 3.290 | |
| get_1kg | 0.636 | 0.100 | 3.113 | |
| get_key | 0.066 | 0.036 | 1.293 | |
| get_key.hail.table.Table | 0.095 | 0.033 | 1.135 | |
| get_ukbb_sumstat_10kloci_mt | 36.418 | 13.720 | 51.690 | |
| hail_init | 0.000 | 0.000 | 0.001 | |
| hail_init_simple | 0.011 | 0.007 | 0.019 | |
| hail_stop | 0.000 | 0.001 | 0.000 | |
| kg_3202 | 0.075 | 0.014 | 0.089 | |
| multipop_df | 0.771 | 0.066 | 1.219 | |
| osn_1kg_path | 0.001 | 0.000 | 0.001 | |
| osn_ukbb_sumst10k_path | 0.000 | 0.000 | 0.001 | |
| path_1kg_annotations | 0.000 | 0.001 | 0.001 | |
| pcs_191k | 0.007 | 0.004 | 0.012 | |
| pcs_38k | 0.018 | 0.000 | 0.019 | |
| rg_update | 0.003 | 0.008 | 0.077 | |
| rownames-hail.table.Table-method | 0.145 | 0.007 | 1.969 | |
| ukbb_init | 0.007 | 0.021 | 0.148 | |