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This page was generated on 2021-11-26 15:05:52 -0500 (Fri, 26 Nov 2021).

CHECK results for gwascat on machv2

To the developers/maintainers of the gwascat package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gwascat.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 846/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gwascat 2.26.0  (landing page)
VJ Carey
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/gwascat
git_branch: RELEASE_3_14
git_last_commit: 4098842
git_last_commit_date: 2021-10-26 12:02:07 -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: gwascat
Version: 2.26.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gwascat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gwascat_2.26.0.tar.gz
StartedAt: 2021-11-25 17:26:55 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 17:37:10 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 614.6 seconds
RetCode: 0
Status:   OK  
CheckDir: gwascat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gwascat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gwascat_2.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/gwascat.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 ‘gwascat/DESCRIPTION’ ... OK
* this is package ‘gwascat’ version ‘2.26.0’
* 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 ‘gwascat’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 34.0Mb
  sub-directories of 1Mb or more:
    data     10.1Mb
    legacy   15.6Mb
    obo       3.0Mb
    olddata   2.2Mb
    tab       1.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘IRanges’
A package should be listed in only one of these fields.
* 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
addSeqlengths: no visible global function definition for ‘seqlengths’
addSeqlengths: no visible global function definition for ‘seqlengths<-’
bindcadd_snv: no visible global function definition for ‘TabixFile’
bindcadd_snv: no visible global function definition for ‘findOverlaps’
buildq: no visible global function definition for ‘read.delim’
chklocs: no visible binding for global variable ‘gwrngs19’
chklocs: no visible global function definition for ‘snpsBySeqname’
gwascat_from_AHub: no visible global function definition for ‘data’
gwascat_from_AHub: no visible binding for global variable ‘si.hs.38’
gwascat_from_AHub: no visible global function definition for
  ‘sessionInfo’
gwcat_snapshot: no visible global function definition for ‘data’
gwcat_snapshot: no visible binding for global variable ‘si.hs.38’
gwcat_snapshot: no visible global function definition for ‘sessionInfo’
lo38to19: no visible global function definition for ‘liftOver’
lo38to19: no visible global function definition for ‘sessionInfo’
lo38to19: no visible global function definition for ‘data’
lo38to19: no visible binding for global variable ‘si.hs.37’
makeCurrentGwascat: no visible global function definition for
  ‘download.file’
makeCurrentGwascat: no visible global function definition for ‘data’
makeCurrentGwascat: no visible binding for global variable ‘si.hs.38’
makeCurrentGwascat: no visible global function definition for
  ‘sessionInfo’
process_gwas_dataframe: no visible global function definition for
  ‘data’
process_gwas_dataframe: no visible binding for global variable
  ‘si.hs.38’
process_gwas_dataframe: no visible global function definition for
  ‘sessionInfo’
snpGenos: no visible global function definition for ‘getSNPlocs’
tfilt: no visible binding for global variable ‘phr’
tpad: no visible binding for global variable ‘phr’
traitsManh: no visible global function definition for ‘aes’
traitsManh: no visible binding for global variable ‘PVALUE_MLOG’
variantProps: no visible binding for global variable ‘gwrngs’
Undefined global functions or variables:
  PVALUE_MLOG TabixFile aes data download.file findOverlaps getSNPlocs
  gwrngs gwrngs19 liftOver phr read.delim seqlengths seqlengths<-
  sessionInfo si.hs.37 si.hs.38 snpsBySeqname
Consider adding
  importFrom("utils", "data", "download.file", "read.delim",
             "sessionInfo")
to your NAMESPACE file.
* 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 ... NOTE
  Note: found 2077 marked UTF-8 strings
* 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
gwascat_from_AHub 35.372  1.190  44.829
gwcat_snapshot    33.427  0.893  39.577
gg17N             14.757  0.114  14.940
gwcex2gviz        13.383  0.470  15.011
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/gwascat.Rcheck/00check.log’
for details.



Installation output

gwascat.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘gwascat’ ...
** 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 (gwascat)

Tests output

gwascat.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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)
> 
> test_check("gwascat")
Loading required package: gwascat
gwascat loaded.  Use makeCurrentGwascat() to extract current image.
 from EBI.  The data folder of this package has some legacy extracts.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> 
> proc.time()
   user  system elapsed 
 17.786   0.810  20.243 

Example timings

gwascat.Rcheck/gwascat-Ex.timings

nameusersystemelapsed
bindcadd_snv0.0010.0010.001
gg17N14.757 0.11414.940
gwascat_from_AHub35.372 1.19044.829
gwcat_snapshot33.427 0.89339.577
gwcex2gviz13.383 0.47015.011
ldtagr1.0550.0121.385
makeCurrentGwascat0.0000.0010.000
obo2graphNEL0.5200.0330.764
riskyAlleleCount0.0000.0000.001
topTraits1.3300.0301.374
traitsManh0.0000.0000.001