Fernando Sola
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/ginmappeR |
| git_branch: RELEASE_3_19 |
| git_last_commit: f195f37 |
| git_last_commit_date: 2024-10-07 03:56:36 -0400 (Mon, 07 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:40 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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 1.0.5 (landing page) Fernando Sola
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 1.0.5 |
| 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_1.0.5.tar.gz |
| StartedAt: 2024-10-17 06:08:41 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 06:22:48 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 847.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: ginmappeR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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_1.0.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ginmappeR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ginmappeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ginmappeR’ version ‘1.0.5’
* 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 8.977 0.427 20.913
getCARD2UniProt 3.887 0.217 22.950
getKEGG2NCBINucleotide 3.622 0.289 34.252
getUniProt2CARD 3.568 0.166 12.442
getNCBIProtein2KEGG 1.690 0.150 197.788
getNCBINucleotide2KEGG 1.603 0.124 52.363
getNCBIGene2KEGG 1.588 0.119 58.401
getNCBIProtein2UniProt 0.945 0.063 33.370
getNCBINucleotide2UniProt 0.936 0.063 19.427
getNCBIGene2UniProt 0.934 0.063 27.908
getUniProt2NCBINucleotide 0.702 0.052 9.418
getNCBIGene2NCBINucleotide 0.055 0.004 5.010
* 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:
Test not TRUE
Test files with failing tests
test_KEGG.R
/private/tmp/RtmpiBBXN0/RLIBS_110e120405c6a/ginmappeR/unitTests/test_KEGG.R
test_UniProt.R
/private/tmp/RtmpiBBXN0/RLIBS_110e120405c6a/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 4.4.1 (2024-06-14) -- "Race for Your Life"
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
|=.............................| Step 1: Translating from KEGG to UniProt
|==............................| Step 2: Connecting to KEGG web services
|===...........................| Step 3: Connecting to KEGG API and translating id aag:5579347 to Uniprot
|=.............................| Step 1: Translating from KEGG to UniProt
|==............................| Step 2: Connecting to KEGG web services
|===...........................| Step 3: Connecting to KEGG API and translating id aag:5579347 to Uniprot
|=.............................| Step 1: Translating from KEGG to UniProt
|=.............................| Step 1: Translating from KEGG to UniProt
|==............................| Step 2: Connecting to KEGG web services
|===...........................| Step 3: Connecting to KEGG API and translating id eco:b0204 to Uniprot
Testing getKEGG2NCBIProtein, getKEGG2NCBINucleotide, getKEGG2NCBIGene
|=.............................| Step 1: Translating from KEGG to NCBI Nucleotide
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|===...........................| Step 3: Connecting to KEGG web services
|====..........................| Step 4: Connecting to KEGG API and translating id llo:LLO_2673 to Uniprot
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
|=.............................| Step 1: Trying to get a direct translation for KEGG id llo:LLO_2673 to NCBI
|==............................| Step 2: Translating KEGG id llo:LLO_2673 to NCBI through similar genes strategy
API(s) connection failed:
Error in RUnit::checkEquals(testFunction, result) :
Modes: logical, character
target is logical, current is character
Testing getUniProtSimilarGenes
|=.............................| Step 1: Accessing UniProt similar genes database
|==............................| Step 2: Connecting to UniProt API and retrieving cluster of id G0L217
|===...........................| Step 3: Retrieving and parsing genes of cluster UniRef50_A0A6L9EH79
Error in RUnit::checkTrue(length(getUniProtSimilarGenes("G0L217", clusterIdentity = "0.5", :
Test not TRUE
RUNIT TEST PROTOCOL -- Thu Oct 17 06:22:33 2024
***********************************************
Number of test functions: 2
Number of errors: 2
Number of failures: 0
1 Test Suite :
ginmappeR RUnit Tests - 2 test functions, 2 errors, 0 failures
ERROR in /private/tmp/RtmpiBBXN0/RLIBS_110e120405c6a/ginmappeR/unitTests/test_KEGG.R: Error while sourcing /private/tmp/RtmpiBBXN0/RLIBS_110e120405c6a/ginmappeR/unitTests/test_KEGG.R : Error in RUnit::checkEquals(testFunction, result) :
Modes: logical, character
target is logical, current is character
ERROR in /private/tmp/RtmpiBBXN0/RLIBS_110e120405c6a/ginmappeR/unitTests/test_UniProt.R: Error while sourcing /private/tmp/RtmpiBBXN0/RLIBS_110e120405c6a/ginmappeR/unitTests/test_UniProt.R : Error in RUnit::checkTrue(length(getUniProtSimilarGenes("G0L217", clusterIdentity = "0.5", :
Test not TRUE
Test files with failing tests
test_KEGG.R
/private/tmp/RtmpiBBXN0/RLIBS_110e120405c6a/ginmappeR/unitTests/test_KEGG.R
test_UniProt.R
/private/tmp/RtmpiBBXN0/RLIBS_110e120405c6a/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 | 8.977 | 0.427 | 20.913 | |
| getCARD2NCBIGene | 0.334 | 0.020 | 1.481 | |
| getCARD2NCBINucleotide | 0.449 | 0.024 | 0.947 | |
| getCARD2NCBIProtein | 0.011 | 0.003 | 0.507 | |
| getCARD2UniProt | 3.887 | 0.217 | 22.950 | |
| getKEGG2CARD | 0.292 | 0.010 | 1.106 | |
| getKEGG2NCBIGene | 0.132 | 0.003 | 1.792 | |
| getKEGG2NCBINucleotide | 3.622 | 0.289 | 34.252 | |
| getKEGG2NCBIProtein | 0.135 | 0.011 | 1.394 | |
| getKEGG2UniProt | 0.003 | 0.001 | 0.105 | |
| getNCBIGene2CARD | 0.209 | 0.011 | 3.932 | |
| getNCBIGene2KEGG | 1.588 | 0.119 | 58.401 | |
| getNCBIGene2NCBINucleotide | 0.055 | 0.004 | 5.010 | |
| getNCBIGene2NCBIProtein | 0.061 | 0.005 | 1.999 | |
| getNCBIGene2UniProt | 0.934 | 0.063 | 27.908 | |
| getNCBIIdenticalProteins | 0.039 | 0.003 | 1.706 | |
| getNCBINucleotide2CARD | 0.107 | 0.006 | 0.657 | |
| getNCBINucleotide2KEGG | 1.603 | 0.124 | 52.363 | |
| getNCBINucleotide2NCBIGene | 0.040 | 0.003 | 1.167 | |
| getNCBINucleotide2NCBIProtein | 0.102 | 0.005 | 0.637 | |
| getNCBINucleotide2UniProt | 0.936 | 0.063 | 19.427 | |
| getNCBIProtein2CARD | 0.104 | 0.006 | 0.831 | |
| getNCBIProtein2KEGG | 1.690 | 0.150 | 197.788 | |
| getNCBIProtein2NCBIGene | 0.039 | 0.003 | 2.480 | |
| getNCBIProtein2NCBINucleotide | 0.103 | 0.005 | 2.526 | |
| getNCBIProtein2UniProt | 0.945 | 0.063 | 33.370 | |
| getUniProt2CARD | 3.568 | 0.166 | 12.442 | |
| getUniProt2KEGG | 0.033 | 0.002 | 0.809 | |
| getUniProt2NCBIGene | 0.000 | 0.001 | 0.000 | |
| getUniProt2NCBINucleotide | 0.702 | 0.052 | 9.418 | |
| getUniProt2NCBIProtein | 0.000 | 0.001 | 0.000 | |
| getUniProtSimilarGenes | 0.074 | 0.010 | 1.204 | |