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This page was generated on 2024-05-04 11:40:35 -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 kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ginmappeR
Version: 1.0.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings ginmappeR_1.0.0.tar.gz
StartedAt: 2024-05-04 08:01:49 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 08:16:41 -0000 (Sat, 04 May 2024)
EllapsedTime: 892.7 seconds
RetCode: 0
Status:   OK  
CheckDir: ginmappeR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --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: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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              2.180  0.249  32.036
getCARD2UniProt           0.511  0.044  43.400
getNCBIGene2KEGG          0.326  0.068  13.421
getNCBINucleotide2KEGG    0.360  0.013  15.783
getKEGG2NCBINucleotide    0.322  0.027  21.466
getNCBIProtein2UniProt    0.299  0.012  12.100
getUniProt2CARD           0.277  0.004   6.216
getNCBIProtein2KEGG       0.217  0.024  14.931
getUniProt2NCBINucleotide 0.221  0.006   7.771
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* 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

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL ginmappeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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: aarch64-unknown-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 /home/biocbuild/tmp/Rtmphc6Y6M/card-data
Using a CARD database version downloaded on Sat 05/04/2024 08:08:39, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Sat 05/04/2024 08:08:39, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Sat 05/04/2024 08:08:39, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Sat 05/04/2024 08:08:39, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Sat 05/04/2024 08:08:39, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Sat 05/04/2024 08:08:39, 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 Sat 05/04/2024 08:08:39, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Sat 05/04/2024 08:08:39, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Sat 05/04/2024 08:08:39, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Sat 05/04/2024 08:08:39, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Sat 05/04/2024 08:08:39, please consider updating it with updateCARDDataBase() function.


RUNIT TEST PROTOCOL -- Sat May  4 08:16:35 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 
 23.223   1.774 503.969 

Example timings

ginmappeR.Rcheck/ginmappeR-Ex.timings

nameusersystemelapsed
getCARD2KEGG 2.180 0.24932.036
getCARD2NCBIGene0.1030.0472.238
getCARD2NCBINucleotide0.6580.3941.456
getCARD2NCBIProtein0.0020.0040.406
getCARD2UniProt 0.511 0.04443.400
getKEGG2CARD0.1690.0031.227
getKEGG2NCBIGene0.1130.0004.642
getKEGG2NCBINucleotide 0.322 0.02721.466
getKEGG2NCBIProtein0.0890.0111.805
getKEGG2UniProt0.0020.0000.101
getNCBIGene2CARD0.1140.0134.861
getNCBIGene2KEGG 0.326 0.06813.421
getNCBIGene2NCBINucleotide0.0570.0034.700
getNCBIGene2NCBIProtein0.0410.0042.388
getNCBIGene2UniProt0.0010.0000.102
getNCBIIdenticalProteins0.0310.0012.198
getNCBINucleotide2CARD0.0490.0000.149
getNCBINucleotide2KEGG 0.360 0.01315.783
getNCBINucleotide2NCBIGene0.0440.0032.405
getNCBINucleotide2NCBIProtein0.0600.0040.814
getNCBINucleotide2UniProt0.0010.0000.101
getNCBIProtein2CARD0.0480.0000.148
getNCBIProtein2KEGG 0.217 0.02414.931
getNCBIProtein2NCBIGene0.0340.0092.120
getNCBIProtein2NCBINucleotide0.0780.0000.873
getNCBIProtein2UniProt 0.299 0.01212.100
getUniProt2CARD0.2770.0046.216
getUniProt2KEGG0.0320.0000.840
getUniProt2NCBIGene000
getUniProt2NCBINucleotide0.2210.0067.771
getUniProt2NCBIProtein0.0000.0010.000
getUniProtSimilarGenes0.0450.0032.756