Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 106/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ASSET 2.24.0  (landing page)
Samsiddhi Bhattacharjee
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/ASSET
git_branch: RELEASE_3_20
git_last_commit: 19bb1f1
git_last_commit_date: 2024-10-29 09:47:35 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for ASSET on palomino8

To the developers/maintainers of the ASSET package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ASSET.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.

raw results


Summary

Package: ASSET
Version: 2.24.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ASSET.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ASSET_2.24.0.tar.gz
StartedAt: 2024-12-19 22:59:00 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 23:01:32 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 152.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ASSET.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ASSET.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ASSET_2.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ASSET.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ASSET/DESCRIPTION' ... OK
* this is package 'ASSET' version '2.24.0'
* 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 whether package 'ASSET' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL-2 + file LICENSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in 'NEWS':
  Cannot process chunk/lines:
    The stochastic p-value calculation with p-value screening appears to be unacceptably slow in many cases. 
  Cannot process chunk/lines:
    Reverting to older deterministic p-value calculation used till ASSET 1.8.0. P-value screening option 
  Cannot process chunk/lines:
    is not supported for now but may be included in future releases.
  Cannot process chunk/lines:
    A new p-value screening option p.bound introduced and stochastic p-value calculation incorporated to allow
  Cannot process chunk/lines:
    p-value screening.
* 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) fast_asset.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{cor}{A matrix of dimension k by k storing the correlation of z-statistics under the null hypothesis. It can be estimated using LD score regression (https://github.com/bulik/ldsc). For example, element \code{(j,k)} is the LD score regression intercept between traits \code{j} and {k}. Diagonal elements are equal to 1. Set to identity matrix if different studies do not have overlapping samples.}
       |                                                                                                                                                                                                                                                                                              ^
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
fast_asset 59.00   4.58   63.63
h.types     6.42   0.46    6.87
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/ASSET.Rcheck/00check.log'
for details.


Installation output

ASSET.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ASSET
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'ASSET' ...
** 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 (ASSET)

Tests output

ASSET.Rcheck/tests/runTests.Rout


R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> BiocGenerics:::testPackage("ASSET")


RUNIT TEST PROTOCOL -- Thu Dec 19 23:01:21 2024 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ASSET RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In formula.character(object, env = baseenv()) :
  Using formula(x) is deprecated when x is a character vector of length > 1.
  Consider formula(paste(x, collapse = " ")) instead.
2: In formula.character(object, env = baseenv()) :
  Using formula(x) is deprecated when x is a character vector of length > 1.
  Consider formula(paste(x, collapse = " ")) instead.
3: In formula.character(object, env = baseenv()) :
  Using formula(x) is deprecated when x is a character vector of length > 1.
  Consider formula(paste(x, collapse = " ")) instead.
4: In formula.character(object, env = baseenv()) :
  Using formula(x) is deprecated when x is a character vector of length > 1.
  Consider formula(paste(x, collapse = " ")) instead.
> 
> proc.time()
   user  system elapsed 
   7.76    0.42   12.12 

Example timings

ASSET.Rcheck/ASSET-Ex.timings

nameusersystemelapsed
create_blocks0.010.000.01
ex_fast_asset000
ex_trait000
ex_types0.020.000.01
fast_asset59.00 4.5863.63
h.forestPlot0.580.000.58
h.summary0.290.030.32
h.traits0.320.000.32
h.types6.420.466.87
p.dlm0.010.000.02
z.max0.020.000.01