Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-03 13:05:17 -0500 (Fri, 03 Dec 2021).

CHECK results for gwascat on tokay2

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: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gwascat.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings gwascat_2.26.0.tar.gz
StartedAt: 2021-12-02 21:41:37 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 21:54:13 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 756.0 seconds
RetCode: 0
Status:   OK  
CheckDir: gwascat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gwascat.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings gwascat_2.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/gwascat.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'gwascat' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 34.2Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 2 marked Latin-1 strings
  Note: found 2075 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
gwascat_from_AHub 52.28   1.45   54.81
gwcat_snapshot    47.82   1.49   50.00
gg17N             10.87   0.11   10.98
gwcex2gviz        10.07   0.14   10.36
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
gwascat_from_AHub 51.57   0.97   54.75
gwcat_snapshot    48.00   0.87   50.63
gwcex2gviz        10.68   0.21   10.89
gg17N              8.39   0.09    8.49
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/gwascat.Rcheck/00check.log'
for details.



Installation output

gwascat.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/gwascat_2.26.0.tar.gz && rm -rf gwascat.buildbin-libdir && mkdir gwascat.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gwascat.buildbin-libdir gwascat_2.26.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL gwascat_2.26.0.zip && rm gwascat_2.26.0.tar.gz gwascat_2.26.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  4 32.8M    4 1540k    0     0  1749k      0  0:00:19 --:--:--  0:00:19 1749k
 13 32.8M   13 4499k    0     0  2369k      0  0:00:14  0:00:01  0:00:13 2369k
 24 32.8M   24 8290k    0     0  2876k      0  0:00:11  0:00:02  0:00:09 2876k
 39 32.8M   39 12.8M    0     0  3403k      0  0:00:09  0:00:03  0:00:06 3403k
 56 32.8M   56 18.4M    0     0  3856k      0  0:00:08  0:00:04  0:00:04 3856k
 69 32.8M   69 22.8M    0     0  3968k      0  0:00:08  0:00:05  0:00:03 4357k
 72 32.8M   72 23.8M    0     0  3546k      0  0:00:09  0:00:06  0:00:03 3994k
 84 32.8M   84 27.7M    0     0  3602k      0  0:00:09  0:00:07  0:00:02 4021k
 99 32.8M   99 32.5M    0     0  3750k      0  0:00:08  0:00:08 --:--:-- 4018k
100 32.8M  100 32.8M    0     0  3762k      0  0:00:08  0:00:08 --:--:-- 3647k

install for i386

* installing *source* package 'gwascat' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gwascat'
    finding HTML links ... done
    bindcadd_snv                            html  
    chklocs                                 html  
    ebicat_2020_04_30                       html  
    g17SM                                   html  
    getRsids-gwaswloc-method                html  
    getRsids                                html  
    getTraits-gwaswloc-method               html  
    getTraits                               html  
    get_cached_gwascat                      html  
    gg17N                                   html  
    gr6.0_hg38                              html  
    gw6.rs_17                               html  
    gwascat_from_AHub                       html  
    gwastagger                              html  
    gwaswloc-class                          html  
    gwcat_snapshot                          html  
    gwcex2gviz                              html  
    ldtagr                                  html  
    locon6                                  html  
    locs4trait                              html  
    low17                                   html  
    makeCurrentGwascat                      html  
    obo2graphNEL                            html  
    process_gwas_dataframe                  html  
    riskyAlleleCount                        html  
    si.hs.37                                html  
    si.hs.38                                html  
    sub-gwaswloc-ANY-ANY-ANY-method         html  
    subsetByChromosome-gwaswloc-method      html  
    subsetByChromosome                      html  
    subsetByTraits-gwaswloc-method          html  
    subsetByTraits                          html  
    topTraits                               html  
    traitsManh                              html  
** 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

install for x64

* installing *source* package 'gwascat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gwascat' as gwascat_2.26.0.zip
* DONE (gwascat)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'gwascat' successfully unpacked and MD5 sums checked

Tests output

gwascat.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  11.28    1.20   12.46 

gwascat.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  12.54    0.46   13.04 

Example timings

gwascat.Rcheck/examples_i386/gwascat-Ex.timings

nameusersystemelapsed
bindcadd_snv000
gg17N10.87 0.1110.98
gwascat_from_AHub52.28 1.4554.81
gwcat_snapshot47.82 1.4950.00
gwcex2gviz10.07 0.1410.36
ldtagr0.580.000.58
makeCurrentGwascat000
obo2graphNEL0.310.030.35
riskyAlleleCount000
topTraits1.250.011.26
traitsManh000

gwascat.Rcheck/examples_x64/gwascat-Ex.timings

nameusersystemelapsed
bindcadd_snv000
gg17N8.390.098.49
gwascat_from_AHub51.57 0.9754.75
gwcat_snapshot48.00 0.8750.63
gwcex2gviz10.68 0.2110.89
ldtagr0.640.000.64
makeCurrentGwascat000
obo2graphNEL0.320.020.33
riskyAlleleCount000
topTraits1.060.001.08
traitsManh000