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This page was generated on 2021-12-06 13:05:49 -0500 (Mon, 06 Dec 2021).

CHECK results for AffiXcan on machv2

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? here 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 21/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AffiXcan 1.12.0  (landing page)
Alessandro Lussana
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/AffiXcan
git_branch: RELEASE_3_14
git_last_commit: 61ecd22
git_last_commit_date: 2021-10-26 12:47:11 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: AffiXcan
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AffiXcan.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AffiXcan_1.12.0.tar.gz
StartedAt: 2021-12-05 11:36:27 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 11:40:10 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 222.6 seconds
RetCode: 0
Status:   OK  
CheckDir: AffiXcan.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AffiXcan.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AffiXcan_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/AffiXcan.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AffiXcan/DESCRIPTION’ ... OK
* this is package ‘AffiXcan’ version ‘1.12.0’
* 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 for sufficient/correct file permissions ... 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 5.236  1.537   4.231
affiXcanImpute   3.543  1.857   2.565
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/AffiXcan.Rcheck/00check.log’
for details.



Installation output

AffiXcan.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AffiXcan
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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-package5.2361.5374.231
affiXcanBs0.0020.0010.003
affiXcanGReX0.0020.0010.003
affiXcanImpute3.5431.8572.565
affiXcanPca0.0010.0010.002
affiXcanPcs0.0010.0000.001
affiXcanTrain0.0010.0000.001
assoc2list0.0010.0010.000
computeBs0.0050.0010.006
computeCorrelation0.0030.0010.003
computeExpr0.0020.0010.004
computePca0.0030.0010.003
computePcs0.0020.0000.002
computeRSquared0.0020.0010.003
exprMatrix0.0180.0050.023
overlookRegions0.0010.0010.000
regionAssoc0.0080.0040.011
subsetKFold0.0010.0000.001
trainingCovariates0.0020.0020.005