| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-30 11:35:37 -0400 (Thu, 30 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
| 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 872/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ginmappeR 1.0.0 (landing page) Fernando Sola
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: ginmappeR |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ginmappeR_1.0.0.tar.gz |
| StartedAt: 2024-05-29 21:09:26 -0400 (Wed, 29 May 2024) |
| EndedAt: 2024-05-29 21:14:07 -0400 (Wed, 29 May 2024) |
| EllapsedTime: 281.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ginmappeR.Rcheck |
| Warnings: NA |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ginmappeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ginmappeR_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ginmappeR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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 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 3.196 0.140 14.312
getKEGG2NCBINucleotide 0.566 0.015 6.908
getCARD2UniProt 0.435 0.035 6.600
getNCBINucleotide2KEGG 0.251 0.028 7.702
getNCBIGene2KEGG 0.221 0.020 7.224
getNCBIProtein2KEGG 0.159 0.020 11.831
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
1 Test Suite :
ginmappeR RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in /private/tmp/RtmpDSq2zl/RLIBS_752133d116cd/ginmappeR/unitTests/test_UniProt.R: Error while sourcing /private/tmp/RtmpDSq2zl/RLIBS_752133d116cd/ginmappeR/unitTests/test_UniProt.R : Error in RUnit::checkTrue(length(getUniProtSimilarGenes("G0L217", clusterIdentity = "0.5", :
Test not TRUE
Test files with failing tests
test_UniProt.R
/private/tmp/RtmpDSq2zl/RLIBS_752133d116cd/ginmappeR/unitTests/test_UniProt.R
Error in BiocGenerics:::testPackage("ginmappeR") :
unit tests failed for package ginmappeR
Execution halted
* 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 ERROR, 1 NOTE
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/ginmappeR.Rcheck/00check.log’
for details.
ginmappeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ginmappeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)
ginmappeR.Rcheck/tests/runTests.Rout.fail
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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/RtmprLZyoA/card-data
Using a CARD database version downloaded on Wed 05/29/2024 21:13:27, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Wed 05/29/2024 21:13:27, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Wed 05/29/2024 21:13:27, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Wed 05/29/2024 21:13:27, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Wed 05/29/2024 21:13:27, please consider updating it with updateCARDDataBase() function.
Using a CARD database version downloaded on Wed 05/29/2024 21:13:27, please consider updating it with updateCARDDataBase() function.
Testing getUniProtSimilarGenes
Error in RUnit::checkTrue(length(getUniProtSimilarGenes("G0L217", clusterIdentity = "0.5", :
Test not TRUE
RUNIT TEST PROTOCOL -- Wed May 29 21:13:55 2024
***********************************************
Number of test functions: 1
Number of errors: 1
Number of failures: 0
1 Test Suite :
ginmappeR RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in /private/tmp/RtmpDSq2zl/RLIBS_752133d116cd/ginmappeR/unitTests/test_UniProt.R: Error while sourcing /private/tmp/RtmpDSq2zl/RLIBS_752133d116cd/ginmappeR/unitTests/test_UniProt.R : Error in RUnit::checkTrue(length(getUniProtSimilarGenes("G0L217", clusterIdentity = "0.5", :
Test not TRUE
Test files with failing tests
test_UniProt.R
/private/tmp/RtmpDSq2zl/RLIBS_752133d116cd/ginmappeR/unitTests/test_UniProt.R
Error in BiocGenerics:::testPackage("ginmappeR") :
unit tests failed for package ginmappeR
Execution halted
ginmappeR.Rcheck/ginmappeR-Ex.timings
| name | user | system | elapsed | |
| getCARD2KEGG | 3.196 | 0.140 | 14.312 | |
| getCARD2NCBIGene | 0.143 | 0.008 | 1.317 | |
| getCARD2NCBINucleotide | 0.438 | 0.017 | 1.368 | |
| getCARD2NCBIProtein | 0.005 | 0.002 | 0.831 | |
| getCARD2UniProt | 0.435 | 0.035 | 6.600 | |
| getKEGG2CARD | 0.171 | 0.007 | 1.797 | |
| getKEGG2NCBIGene | 0.087 | 0.003 | 2.821 | |
| getKEGG2NCBINucleotide | 0.566 | 0.015 | 6.908 | |
| getKEGG2NCBIProtein | 0.063 | 0.003 | 1.975 | |
| getKEGG2UniProt | 0.001 | 0.001 | 0.226 | |
| getNCBIGene2CARD | 0.108 | 0.006 | 4.082 | |
| getNCBIGene2KEGG | 0.221 | 0.020 | 7.224 | |
| getNCBIGene2NCBINucleotide | 0.034 | 0.003 | 2.867 | |
| getNCBIGene2NCBIProtein | 0.035 | 0.004 | 2.325 | |
| getNCBIGene2UniProt | 0.001 | 0.000 | 0.242 | |
| getNCBIIdenticalProteins | 0.020 | 0.003 | 2.059 | |
| getNCBINucleotide2CARD | 0.055 | 0.004 | 0.295 | |
| getNCBINucleotide2KEGG | 0.251 | 0.028 | 7.702 | |
| getNCBINucleotide2NCBIGene | 0.022 | 0.003 | 1.489 | |
| getNCBINucleotide2NCBIProtein | 0.069 | 0.005 | 0.768 | |
| getNCBINucleotide2UniProt | 0.002 | 0.001 | 0.103 | |
| getNCBIProtein2CARD | 0.056 | 0.004 | 0.291 | |
| getNCBIProtein2KEGG | 0.159 | 0.020 | 11.831 | |
| getNCBIProtein2NCBIGene | 0.020 | 0.004 | 1.106 | |
| getNCBIProtein2NCBINucleotide | 0.068 | 0.005 | 0.790 | |
| getNCBIProtein2UniProt | 0.215 | 0.013 | 4.857 | |
| getUniProt2CARD | 0.231 | 0.010 | 1.795 | |
| getUniProt2KEGG | 0.024 | 0.002 | 0.847 | |
| getUniProt2NCBIGene | 0 | 0 | 0 | |
| getUniProt2NCBINucleotide | 0.150 | 0.006 | 3.790 | |
| getUniProt2NCBIProtein | 0 | 0 | 0 | |
| getUniProtSimilarGenes | 0.039 | 0.004 | 1.429 | |