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CHECK report for gwascat on malbec2

This page was generated on 2020-10-17 11:54:55 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE gwascat PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 796/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gwascat 2.20.1
VJ Carey
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/gwascat
Branch: RELEASE_3_11
Last Commit: 97258a1
Last Changed Date: 2020-05-02 10:36:06 -0400 (Sat, 02 May 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gwascat
Version: 2.20.1
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:gwascat.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings gwascat_2.20.1.tar.gz
StartedAt: 2020-10-17 02:04:55 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:12:19 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 443.6 seconds
RetCode: 0
Status:  OK 
CheckDir: gwascat.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:gwascat.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings gwascat_2.20.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/gwascat.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gwascat/DESCRIPTION’ ... OK
* this is package ‘gwascat’ version ‘2.20.1’
* 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 53.0Mb
  sub-directories of 1Mb or more:
    data     45.0Mb
    obo       3.1Mb
    olddata   2.2Mb
    tab       1.1Mb
* 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 ... NOTE
Namespace in Imports field not imported from: 'BiocGenerics'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
chklocs: no visible binding for global variable ‘gwrngs19’
chklocs: no visible global function definition for ‘snpsBySeqname’
chklocs: no visible global function definition for ‘start’
gwdf2GRanges: no visible global function definition for ‘new’
lo38to19: no visible global function definition for ‘liftOver’
lo38to19: no visible global function definition for ‘sessionInfo’
lo38to19: no visible binding for global variable ‘si.hs.37’
lo38to19: no visible global function definition for ‘new’
locs4trait: no visible global function definition for ‘new’
makeCurrentGwascat: no visible binding for global variable ‘si.hs.38’
makeCurrentGwascat: no visible global function definition for
  ‘sessionInfo’
makeCurrentGwascat.legacy: no visible binding for global variable
  ‘si.hs.38’
obo2graphNEL: no visible global function definition for ‘new’
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 binding for global variable ‘PVALUE_MLOG’
variantProps: no visible binding for global variable ‘gwrngs’
[,gwaswloc-ANY-ANY-ANY: no visible global function definition for ‘new’
show,gwaswloc: no visible global function definition for ‘show’
Undefined global functions or variables:
  PVALUE_MLOG getSNPlocs gwrngs gwrngs19 liftOver new phr sessionInfo
  show si.hs.37 si.hs.38 snpsBySeqname start
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "start")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 6 marked Latin-1 strings
  Note: found 53 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
gwcex2gviz       10.236  0.160  10.396
riskyAlleleCount  5.681  0.108   5.790
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.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
  ‘/home/biocbuild/bbs-3.11-bioc/meat/gwascat.Rcheck/00check.log’
for details.



Installation output

gwascat.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL gwascat
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘gwascat’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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/test-all.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> BiocGenerics:::testPackage("gwascat")
gwascat loaded.  Use makeCurrentGwascat() to extract current image.
 from EBI.  The data folder of this package has some legacy extracts.


RUNIT TEST PROTOCOL -- Sat Oct 17 02:12:15 2020 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
gwascat RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 14.808   0.421  18.100 

Example timings

gwascat.Rcheck/gwascat-Ex.timings

nameusersystemelapsed
bindcadd_snv0.0000.0000.001
gwascat-package1.1060.0201.126
gwastagger1.3370.0561.393
gwaswloc-class0.0010.0000.002
gwcex2gviz10.236 0.16010.396
gwdf_2012_02_02000
ldtagr3.2260.1163.359
locon60.0120.0000.012
makeCurrentGwascat0.0010.0000.000
obo2graphNEL0.1540.0040.157
riskyAlleleCount5.6810.1085.790
si.hs.370.0110.0000.010
topTraits0.3600.0200.381
traitsManh000