Back to Multiple platform build/check report for BioC 3.16:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-04-12 11:05:24 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for AffiXcan on palomino4


To the developers/maintainers of the AffiXcan package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AffiXcan.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 20/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AffiXcan 1.16.0  (landing page)
Alessandro Lussana
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/AffiXcan
git_branch: RELEASE_3_16
git_last_commit: 13cd956
git_last_commit_date: 2022-11-01 11:18:33 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: AffiXcan
Version: 1.16.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AffiXcan.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings AffiXcan_1.16.0.tar.gz
StartedAt: 2023-04-10 22:43:59 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 22:48:28 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 269.7 seconds
RetCode: 0
Status:   OK  
CheckDir: AffiXcan.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AffiXcan.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings AffiXcan_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/AffiXcan.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'AffiXcan/DESCRIPTION' ... OK
* this is package 'AffiXcan' version '1.16.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'AffiXcan' 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 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
computeBs: no visible binding for global variable 'V1'
computeRSquared: no visible binding for global variable 'exprMatrix'
Undefined global functions or variables:
  V1 exprMatrix
* 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
AffiXcan-package 3.57   0.10   62.91
affiXcanImpute   2.89   0.07   60.44
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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
  'F:/biocbuild/bbs-3.16-bioc/meat/AffiXcan.Rcheck/00check.log'
for details.



Installation output

AffiXcan.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL AffiXcan
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'AffiXcan' ...
** 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 (AffiXcan)

Tests output


Example timings

AffiXcan.Rcheck/AffiXcan-Ex.timings

nameusersystemelapsed
AffiXcan-package 3.57 0.1062.91
affiXcanBs000
affiXcanGReX000
affiXcanImpute 2.89 0.0760.44
affiXcanPca000
affiXcanPcs000
affiXcanTrain000
assoc2list000
computeBs0.000.020.01
computeCorrelation000
computeExpr000
computePca0.000.020.02
computePcs000
computeRSquared000
exprMatrix0.000.010.02
overlookRegions000
regionAssoc0.000.020.01
subsetKFold000
trainingCovariates0.000.010.02