Vincent Carey
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/BiocHail |
| git_branch: RELEASE_3_17 |
| git_last_commit: f0ee4b7 |
| git_last_commit_date: 2023-08-22 00:36:52 -0400 (Tue, 22 Aug 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:12 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 178/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocHail 1.0.1 (landing page) Vincent Carey
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | ... NOT SUPPORTED ... | ||||||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 1.0.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BiocHail.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BiocHail_1.0.1.tar.gz |
| StartedAt: 2023-10-15 19:32:42 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 19:39:27 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 405.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BiocHail.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BiocHail.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BiocHail_1.0.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BiocHail.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BiocHail/DESCRIPTION’ ... OK
* this is package ‘BiocHail’ version ‘1.0.1’
* 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 R 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 36.199 14.097 51.043
as.data.frame 5.968 1.271 20.684
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘gwas_tut.Rmd’ using ‘UTF-8’... OK
‘large_t2t.Rmd’ using ‘UTF-8’... OK
‘ukbb.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/BiocHail.Rcheck/00check.log’
for details.
BiocHail.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BiocHail ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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")
2023-10-15 19:35:28.187 WARN Utils:69 - Your hostname, nebbiolo1 resolves to a loopback address: 127.0.1.1; using 155.52.47.135 instead (on interface enp175s0f1np1)
2023-10-15 19:35:28.191 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:/home/biocbuild/.cache/R/basilisk/1.12.1/BiocHail/1.0.1/bsklenv/lib/python3.8/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
2023-10-15 19:35:28.558 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/RtmpgOF69N/file36135353fbe0d
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
2023-10-15 19:35:39.098 Hail: INFO: wrote table with 3501 rows in 1 partition to /tmp/persist_table8yPkgmg1x2
2023-10-15 19:35:39.645 Hail: INFO: Reading table to impute column types
----------------------------------------
Global fields:
None
----------------------------------------
Row fields:
'Sample': str
'Population': str
'SuperPopulation': str
'isFemale': bool
'PurpleHair': bool
'CaffeineConsumption': int32
----------------------------------------
Key: ['Sample']
----------------------------------------
2023-10-15 19:35:40.608 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)
+-----------+------------+-----------------+----------+------------+---------------------+
| 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 0x7f0fe14e72e0>
Index:
['column']
--------------------------------------------------------
[Stage 11:> (0 + 2) / 2]
[Stage 19:> (0 + 2) / 2]
2023-10-15 19:35:55.867 Hail: INFO: linear_regression_rows: running on 250 samples for 1 response variable y,
with input variable x, and 1 additional covariate...
2023-10-15 19:35:57.703 Hail: INFO: wrote table with 10961 rows in 2 partitions to /tmp/persist_table6nHxBMPqEg
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)
----------------------------------------
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']
----------------------------------------
2023-10-15 19:36:47.382 Hail: WARN: cols(): Resulting column table is sorted by 'col_key'.
To preserve matrix table column order, first unkey columns with 'key_cols_by()'
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2023-10-15 19:37:09.006 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
55.452 13.845 137.794
BiocHail.Rcheck/BiocHail-Ex.timings
| name | user | system | elapsed | |
| as.data.frame | 5.968 | 1.271 | 20.684 | |
| as.data.frame.default | 0.102 | 0.008 | 2.770 | |
| as.data.frame.hail.table.Table | 0.114 | 0.004 | 2.246 | |
| bare_hail | 0.001 | 0.000 | 0.001 | |
| colnames-hail.table.Table-method | 0.115 | 0.004 | 1.706 | |
| filter | 0.184 | 0.027 | 4.226 | |
| filter.hail.table.Table | 0.195 | 0.006 | 3.283 | |
| get_1kg | 0.529 | 0.086 | 3.065 | |
| get_key | 0.096 | 0.024 | 1.367 | |
| get_key.hail.table.Table | 0.101 | 0.027 | 1.253 | |
| get_ukbb_sumstat_10kloci_mt | 36.199 | 14.097 | 51.043 | |
| hail_init | 0.000 | 0.001 | 0.000 | |
| hail_init_simple | 0.021 | 0.002 | 0.021 | |
| hail_stop | 0.001 | 0.000 | 0.000 | |
| kg_3202 | 0.103 | 0.006 | 0.110 | |
| multipop_df | 3.422 | 0.102 | 4.000 | |
| osn_1kg_path | 0.001 | 0.000 | 0.000 | |
| osn_ukbb_sumst10k_path | 0 | 0 | 0 | |
| path_1kg_annotations | 0.000 | 0.000 | 0.001 | |
| pcs_191k | 0.012 | 0.000 | 0.011 | |
| pcs_38k | 0.018 | 0.000 | 0.018 | |
| rg_update | 0.004 | 0.005 | 0.014 | |
| rownames-hail.table.Table-method | 0.096 | 0.005 | 1.759 | |
| ukbb_init | 0.015 | 0.009 | 0.028 | |