Hangjia Zhao
| Snapshot Date: 2024-05-11 09:00:03 -0400 (Sat, 11 May 2024) |
| git_url: https://git.bioconductor.org/packages/pgxRpi |
| git_branch: devel |
| git_last_commit: 833ff02 |
| git_last_commit_date: 2024-05-03 12:57:02 -0400 (Fri, 03 May 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-13 11:32:10 -0400 (Mon, 13 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
| 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 1498/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pgxRpi 1.1.2 (landing page) Hangjia Zhao
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the pgxRpi package: - 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: pgxRpi |
| Version: 1.1.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pgxRpi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pgxRpi_1.1.2.tar.gz |
| StartedAt: 2024-05-12 22:31:35 -0400 (Sun, 12 May 2024) |
| EndedAt: 2024-05-12 22:34:41 -0400 (Sun, 12 May 2024) |
| EllapsedTime: 185.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pgxRpi.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pgxRpi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pgxRpi_1.1.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/pgxRpi.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pgxRpi/DESCRIPTION’ ... OK
* this is package ‘pgxRpi’ version ‘1.1.2’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘pgxRpi’ 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 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 ... NOTE
pgxSegprocess: no visible binding for global variable
‘followup_state_id’
pgxSegprocess: no visible binding for global variable ‘followup_time’
Undefined global functions or variables:
followup_state_id followup_time
* 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
pgxFilter 8.022 0.062 9.325
pgxFreqplot 3.595 0.129 9.948
pgxLoader 1.534 0.103 14.867
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/pgxRpi.Rcheck/00check.log’
for details.
pgxRpi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pgxRpi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘pgxRpi’ ... ** 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 (pgxRpi)
pgxRpi.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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(pgxRpi)
>
> test_check("pgxRpi")
trying: http://www.progenetix.org/services/intervalFrequencies/?filters=NCIT:C4323,pgx:icdom-85003&output=pgxfreq&datasetIds=progenetix
trying: http://www.progenetix.org/services/intervalFrequencies/?output=pgxmatrix&filters=NCIT:C4323,pgx:icdom-85003&datasetIds=progenetix
trying: http://www.progenetix.org/services/intervalFrequencies/?output=pgxmatrix&filters=NCIT:C5228,pgx:icdom-87203&datasetIds=cellz
trying: http://progenetix.org/services/sampletable/?filters=NCIT:C3697&datasetIds=progenetix
trying: http://progenetix.org/services/sampletable/?biosampleIds=pgxbs-kftvh94d,pgxbs-kftvh94g&datasetIds=progenetix
trying: http://progenetix.org/services/sampletable/?biosampleIds=pgxbs-kftvh94d,pgxbs-kftvjji1&requestEntityPathId=individual&datasetIds=progenetix
trying: http://progenetix.org/services/sampletable/?individualIds=pgxind-kftx3565,pgxind-kftx5g4v&requestEntityPathId=individual&datasetIds=progenetix
trying: http://progenetix.org/services/sampletable/?filters=NCIT:C3512&requestEntityPathId=individual&limit=1000&datasetIds=progenetix
trying: http://progenetix.org/services/sampletable/?filters=NCIT:C7707&datasetIds=cellz
trying: http://progenetix.org/beacon/biosamples/pgxbs-kftvh94d/g_variants?datasetIds=progenetix
trying: https://progenetix.org/services/pgxsegvariants/?biosampleIds=pgxbs-kftvh94d,pgxbs-kftvh94g,pgxbs-kftvh972&datasetIds=progenetix
trying: https://progenetix.org/services/samplematrix/?biosampleIds=pgxbs-kftvh94d,pgxbs-kftvh94g,pgxbs-kftvh972&datasetIds=progenetix
trying: https://progenetix.org/services/samplematrix/?individualIds=pgxind-kftx3565,pgxind-kftx5g4v&datasetIds=progenetix
trying: https://progenetix.org/services/samplematrix/?filters=pgx:icdom-88503&datasetIds=progenetix
trying: https://progenetix.org/beacon/analyses/?output=cnvstats&biosampleIds=pgxbs-kftvh94d,pgxbs-kftvh94g,pgxbs-kftvh972&datasetIds=progenetix
trying: https://progenetix.org/beacon/analyses/?output=cnvstats&individualIds=pgxind-kftx3565,pgxind-kftx5g4v&datasetIds=progenetix
trying: https://progenetix.org/beacon/analyses/?output=cnvstats&filters=pgx:icdom-88503&datasetIds=progenetix
trying: http://progenetix.org/beacon/biosamples/cellzbs-0821E6df/g_variants?datasetIds=cellz
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 54 ]
>
> proc.time()
user system elapsed
20.802 0.367 103.244
pgxRpi.Rcheck/pgxRpi-Ex.timings
| name | user | system | elapsed | |
| pgxCount | 0.068 | 0.012 | 1.313 | |
| pgxFilter | 8.022 | 0.062 | 9.325 | |
| pgxFreqplot | 3.595 | 0.129 | 9.948 | |
| pgxLoader | 1.534 | 0.103 | 14.867 | |
| pgxSegprocess | 3.107 | 0.112 | 3.227 | |
| segtoFreq | 2.870 | 0.079 | 2.957 | |