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This page was generated on 2024-05-04 11:36:37 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 872/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ginmappeR 1.0.0  (landing page)
Fernando Sola
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/ginmappeR
git_branch: RELEASE_3_19
git_last_commit: f482726
git_last_commit_date: 2024-04-30 11:54:59 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for ginmappeR on nebbiolo1


To the developers/maintainers of the ginmappeR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ginmappeR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ginmappeR
Version: 1.0.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ginmappeR_1.0.0.tar.gz
StartedAt: 2024-05-03 23:43:59 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 23:52:28 -0400 (Fri, 03 May 2024)
EllapsedTime: 509.1 seconds
RetCode: 0
Status:   OK  
CheckDir: ginmappeR.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ginmappeR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ginmappeR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ginmappeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ginmappeR’ version ‘1.0.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ginmappeR’ 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
getCARD2KEGG           1.847  0.121  12.374
getCARD2UniProt        0.624  0.056   9.436
getNCBIProtein2KEGG    0.426  0.008  11.425
getNCBIGene2KEGG       0.408  0.025   7.116
getNCBIProtein2UniProt 0.382  0.016   5.409
getKEGG2NCBINucleotide 0.348  0.043   6.220
getNCBINucleotide2KEGG 0.355  0.016   7.571
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ginmappeR.Rcheck/00check.log’
for details.


Installation output

ginmappeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ginmappeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘ginmappeR’ ...
** using staged installation
** R
** 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 (ginmappeR)

Tests output

ginmappeR.Rcheck/tests/runTests.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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("ginmappeR")
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, aperm, 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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: RSQLite
Testing getKEGG2UniProt
Testing getKEGG2NCBIProtein, getKEGG2NCBINucleotide, getKEGG2NCBIGene
Testing getKEGG2CARD
Updating CARD database data...
CARD database downloaded successfully!
Located at /tmp/RtmpVPXo4A/card-data
Using a CARD database version downloaded on Fri 05/03/2024 23:47:34, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Fri 05/03/2024 23:47:34, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Fri 05/03/2024 23:47:34, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Fri 05/03/2024 23:47:34, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Fri 05/03/2024 23:47:34, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Fri 05/03/2024 23:47:34, please consider updating it with updateCARDDataBase() function.
Testing getUniProtSimilarGenes
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
Testing getUniProt2KEGG
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
The given ID "test" is not registered in UniProt database
Testing getUniProt2NCBIProtein, getUniProt2NCBINucleotide, getUniProt2NCBIGene
Testing getUniProt2CARD
Using a CARD database version downloaded on Fri 05/03/2024 23:47:34, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Fri 05/03/2024 23:47:34, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Fri 05/03/2024 23:47:34, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Fri 05/03/2024 23:47:34, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Fri 05/03/2024 23:47:34, please consider updating it with updateCARDDataBase() function.


RUNIT TEST PROTOCOL -- Fri May  3 23:52:23 2024 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ginmappeR 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 
 24.262   1.490 308.487 

Example timings

ginmappeR.Rcheck/ginmappeR-Ex.timings

nameusersystemelapsed
getCARD2KEGG 1.847 0.12112.374
getCARD2NCBIGene0.1710.0121.215
getCARD2NCBINucleotide0.5820.0321.015
getCARD2NCBIProtein0.0050.0000.405
getCARD2UniProt0.6240.0569.436
getKEGG2CARD0.1800.0041.647
getKEGG2NCBIGene0.1850.0002.745
getKEGG2NCBINucleotide0.3480.0436.220
getKEGG2NCBIProtein0.0770.0001.989
getKEGG2UniProt0.0010.0000.101
getNCBIGene2CARD0.1000.0113.715
getNCBIGene2KEGG0.4080.0257.116
getNCBIGene2NCBINucleotide0.0570.0003.280
getNCBIGene2NCBIProtein0.0580.0002.186
getNCBIGene2UniProt0.0020.0000.102
getNCBIIdenticalProteins0.0390.0001.710
getNCBINucleotide2CARD0.0730.0040.177
getNCBINucleotide2KEGG0.3550.0167.571
getNCBINucleotide2NCBIGene0.0460.0000.971
getNCBINucleotide2NCBIProtein0.1010.0040.660
getNCBINucleotide2UniProt0.0010.0010.101
getNCBIProtein2CARD0.0460.0020.150
getNCBIProtein2KEGG 0.426 0.00811.425
getNCBIProtein2NCBIGene0.0320.0001.023
getNCBIProtein2NCBINucleotide0.1120.0000.657
getNCBIProtein2UniProt0.3820.0165.409
getUniProt2CARD0.3890.0072.220
getUniProt2KEGG0.0370.0040.726
getUniProt2NCBIGene000
getUniProt2NCBINucleotide0.3110.0123.902
getUniProt2NCBIProtein000
getUniProtSimilarGenes0.1010.0001.155