Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-03 13:05:19 -0500 (Fri, 03 Dec 2021).

CHECK results for ipdDb on tokay2

To the developers/maintainers of the ipdDb package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ipdDb.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 952/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ipdDb 1.12.0  (landing page)
Steffen Klasberg
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/ipdDb
git_branch: RELEASE_3_14
git_last_commit: da8cb12
git_last_commit_date: 2021-10-26 12:45:35 -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: ipdDb
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ipdDb.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ipdDb_1.12.0.tar.gz
StartedAt: 2021-12-02 22:20:12 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 22:25:32 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 319.7 seconds
RetCode: 0
Status:   OK  
CheckDir: ipdDb.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ipdDb.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ipdDb_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ipdDb.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 'ipdDb/DESCRIPTION' ... OK
* this is package 'ipdDb' 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 whether package 'ipdDb' 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
* 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
IpdDb                           7.58   0.98   12.14
loadHlaData                     5.54   0.50    6.47
loadKirData                     4.88   0.31    5.67
getClosestComplete-IpdDb-method 4.74   0.43   10.38
getAlleles-IpdDb-method         4.66   0.42    5.68
getReference-IpdDb-method       4.72   0.31    5.42
getStructure-IpdDb-method       4.50   0.41    5.31
getLoci-IpdDb-method            4.42   0.31    5.31
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
IpdDb                           8.67   0.61   10.19
getAlleles-IpdDb-method         5.18   0.38    5.94
getClosestComplete-IpdDb-method 5.05   0.46    5.92
getLoci-IpdDb-method            4.97   0.33    5.90
loadKirData                     4.75   0.40    5.55
getStructure-IpdDb-method       4.69   0.32    5.42
loadHlaData                     4.53   0.45    5.40
getReference-IpdDb-method       4.48   0.39    5.29
* 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: OK


Installation output

ipdDb.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ipdDb_1.12.0.tar.gz && rm -rf ipdDb.buildbin-libdir && mkdir ipdDb.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ipdDb.buildbin-libdir ipdDb_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ipdDb_1.12.0.zip && rm ipdDb_1.12.0.tar.gz ipdDb_1.12.0.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
100 16203  100 16203    0     0   137k      0 --:--:-- --:--:-- --:--:--  138k

install for i386

* installing *source* package 'ipdDb' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ipdDb'
    finding HTML links ... done
    IpdDb                                   html  
    getAlleles-IpdDb-method                 html  
    getClosestComplete-IpdDb-method         html  
    getLoci-IpdDb-method                    html  
    getReference-IpdDb-method               html  
    getStructure-IpdDb-method               html  
    ipdDbPackage                            html  
    loadHlaData                             html  
    loadKirData                             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 'ipdDb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ipdDb' as ipdDb_1.12.0.zip
* DONE (ipdDb)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ipdDb' successfully unpacked and MD5 sums checked

Tests output

ipdDb.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)
> library(ipdDb)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

The following object is masked from 'package:Biobase':

    cache

> 
> test_check("ipdDb")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 41 ]
> 
> proc.time()
   user  system elapsed 
  24.26    2.34   31.78 

ipdDb.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)
> library(ipdDb)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

The following object is masked from 'package:Biobase':

    cache

> 
> test_check("ipdDb")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 41 ]
> 
> proc.time()
   user  system elapsed 
  24.45    1.79   28.09 

Example timings

ipdDb.Rcheck/examples_i386/ipdDb-Ex.timings

nameusersystemelapsed
IpdDb 7.58 0.9812.14
getAlleles-IpdDb-method4.660.425.68
getClosestComplete-IpdDb-method 4.74 0.4310.38
getLoci-IpdDb-method4.420.315.31
getReference-IpdDb-method4.720.315.42
getStructure-IpdDb-method4.500.415.31
loadHlaData5.540.506.47
loadKirData4.880.315.67

ipdDb.Rcheck/examples_x64/ipdDb-Ex.timings

nameusersystemelapsed
IpdDb 8.67 0.6110.19
getAlleles-IpdDb-method5.180.385.94
getClosestComplete-IpdDb-method5.050.465.92
getLoci-IpdDb-method4.970.335.90
getReference-IpdDb-method4.480.395.29
getStructure-IpdDb-method4.690.325.42
loadHlaData4.530.455.40
loadKirData4.750.405.55