Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:06 -0400 (Fri, 15 Oct 2021).

CHECK results for GenomeInfoDb on tokay2

To the developers/maintainers of the GenomeInfoDb package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomeInfoDb.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 736/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomeInfoDb 1.28.4  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/GenomeInfoDb
git_branch: RELEASE_3_13
git_last_commit: 3de2a41
git_last_commit_date: 2021-09-03 15:49:43 -0400 (Fri, 03 Sep 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: GenomeInfoDb
Version: 1.28.4
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomeInfoDb.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GenomeInfoDb_1.28.4.tar.gz
StartedAt: 2021-10-14 23:35:20 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 23:56:55 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 1294.4 seconds
RetCode: 0
Status:   OK  
CheckDir: GenomeInfoDb.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomeInfoDb.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings GenomeInfoDb_1.28.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/GenomeInfoDb.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomeInfoDb/DESCRIPTION' ... OK
* this is package 'GenomeInfoDb' version '1.28.4'
* 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 'GenomeInfoDb' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
* 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 ... NOTE
Unexported object imported by a ':::' call: 'utils:::.roman2numeric'
  See the note in ?`:::` about the use of this operator.
* 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
loadTaxonomyDb          8.19   0.52    8.70
GenomeDescription-class 6.26   0.64    6.91
seqlevels-wrappers      4.42   0.93    5.35
seqinfo                 4.75   0.36    5.11
seqlevelsStyle          4.48   0.49   11.80
getChromInfoFromUCSC    2.66   1.04    6.45
getChromInfoFromEnsembl 0.82   0.11   45.31
getChromInfoFromNCBI    0.30   0.03    7.60
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
GenomeDescription-class 9.72   0.36   10.07
loadTaxonomyDb          9.11   0.09    9.21
seqinfo                 6.12   0.22    6.35
seqlevelsStyle          4.77   0.26   11.94
getChromInfoFromUCSC    2.18   1.10    6.08
getChromInfoFromEnsembl 1.54   0.17   43.86
getChromInfoFromNCBI    0.25   0.01    7.22
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'run_unitTests.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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/GenomeInfoDb.Rcheck/00check.log'
for details.



Installation output

GenomeInfoDb.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GenomeInfoDb_1.28.4.tar.gz && rm -rf GenomeInfoDb.buildbin-libdir && mkdir GenomeInfoDb.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomeInfoDb.buildbin-libdir GenomeInfoDb_1.28.4.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GenomeInfoDb_1.28.4.zip && rm GenomeInfoDb_1.28.4.tar.gz GenomeInfoDb_1.28.4.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 3090k  100 3090k    0     0  4836k      0 --:--:-- --:--:-- --:--:-- 4844k

install for i386

* installing *source* package 'GenomeInfoDb' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomeInfoDb'
    finding HTML links ... done
    GenomeDescription-class                 html  
    GenomeInfoDb-internals                  html  
    Seqinfo-class                           html  
    fetchExtendedChromInfoFromUCSC          html  
    getChromInfoFromEnsembl                 html  
    getChromInfoFromNCBI                    html  
    getChromInfoFromUCSC                    html  
    loadTaxonomyDb                          html  
    mapGenomeBuilds                         html  
    rankSeqlevels                           html  
    seqinfo                                 html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/GenomeInfoDb.buildbin-libdir/00LOCK-GenomeInfoDb/00new/GenomeInfoDb/help/seqinfo.html
    seqlevels-wrappers                      html  
    seqlevelsStyle                          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 'GenomeInfoDb' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomeInfoDb' as GenomeInfoDb_1.28.4.zip
* DONE (GenomeInfoDb)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'GenomeInfoDb' successfully unpacked and MD5 sums checked

Tests output

GenomeInfoDb.Rcheck/tests_i386/run_unitTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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.

> require("GenomeInfoDb") || stop("unable to load GenomeInfoDb package")
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

[1] TRUE
> GenomeInfoDb:::.test()


RUNIT TEST PROTOCOL -- Thu Oct 14 23:48:21 2021 
*********************************************** 
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomeInfoDb RUnit Tests - 21 test functions, 0 errors, 0 failures
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
 355.75   16.78  495.60 

GenomeInfoDb.Rcheck/tests_x64/run_unitTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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.

> require("GenomeInfoDb") || stop("unable to load GenomeInfoDb package")
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

[1] TRUE
> GenomeInfoDb:::.test()


RUNIT TEST PROTOCOL -- Thu Oct 14 23:56:45 2021 
*********************************************** 
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomeInfoDb RUnit Tests - 21 test functions, 0 errors, 0 failures
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
 365.10   16.06  503.87 

Example timings

GenomeInfoDb.Rcheck/examples_i386/GenomeInfoDb-Ex.timings

nameusersystemelapsed
GenomeDescription-class6.260.646.91
Seqinfo-class0.300.060.36
fetchExtendedChromInfoFromUCSC000
getChromInfoFromEnsembl 0.82 0.1145.31
getChromInfoFromNCBI0.300.037.60
getChromInfoFromUCSC2.661.046.45
loadTaxonomyDb8.190.528.70
mapGenomeBuilds0.090.000.11
rankSeqlevels0.280.010.30
seqinfo4.750.365.11
seqlevels-wrappers4.420.935.35
seqlevelsStyle 4.48 0.4911.80

GenomeInfoDb.Rcheck/examples_x64/GenomeInfoDb-Ex.timings

nameusersystemelapsed
GenomeDescription-class 9.72 0.3610.07
Seqinfo-class0.50.00.5
fetchExtendedChromInfoFromUCSC000
getChromInfoFromEnsembl 1.54 0.1743.86
getChromInfoFromNCBI0.250.017.22
getChromInfoFromUCSC2.181.106.08
loadTaxonomyDb9.110.099.21
mapGenomeBuilds0.040.000.04
rankSeqlevels0.100.020.11
seqinfo6.120.226.35
seqlevels-wrappers4.270.174.43
seqlevelsStyle 4.77 0.2611.94