Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:09 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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 |
To the developers/maintainers of the IMMAN package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IMMAN.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 953/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
IMMAN 1.19.0 (landing page) Minoo Ashtiani
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: IMMAN |
Version: 1.19.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:IMMAN.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings IMMAN_1.19.0.tar.gz |
StartedAt: 2023-02-07 05:02:11 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 05:14:34 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 743.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: IMMAN.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:IMMAN.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings IMMAN_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/IMMAN.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘IMMAN/DESCRIPTION’ ... OK * this is package ‘IMMAN’ version ‘1.19.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘IMMAN’ 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 R 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 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 ... NOTE IMMAN: no visible binding for global variable ‘tem’ IMMAN : <anonymous>: no visible binding for global variable ‘tem’ Undefined global functions or variables: tem * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘IMMAN-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: IMMAN > ### Title: Interlog protein network reconstruction by Mapping and Mining > ### ANalysis > ### Aliases: IMMAN > > ### ** Examples > > > data(FruitFly) > data(Celegance) > > subFruitFly <- as.character(FruitFly$V1)[1:10] > subCelegance <- as.character(Celegance$V1)[1:10] > > ProteinLists = list(subFruitFly, subCelegance) > > List1_Species_ID = 7227 # taxonomy ID FruitFly > List2_Species_ID = 6239 # taxonomy ID Celegance > > Species_IDs = c(List1_Species_ID, List2_Species_ID) > > identityU = 30 > substitutionMatrix = "BLOSUM62" > gapOpening = -8 > gapExtension = -8 > NetworkShrinkage = FALSE > coverage = 1 > BestHit = TRUE > score_threshold = 400 > STRINGversion="11" > > # Run the IMMAN function for the parameters > output = IMMAN(ProteinLists, fileNames=NULL, Species_IDs, + identityU, substitutionMatrix, + gapOpening, gapExtension, BestHit, + coverage, NetworkShrinkage, + score_threshold, STRINGversion, + InputDirectory = getwd()) Step 1/4:Downloading amino acid sequences... Downloading amino acid sequences of List1 Downloading amino acid sequences of List2 Step 2/4: Alignment... Align List1 with List2 Step 3/4: Detection in STRING... Detecting List1 in STRING trying URL 'https://stringdb-static.org/download/protein.aliases.v11.0/7227.protein.aliases.v11.0.txt.gz' Content type 'application/octet-stream' length 4188915 bytes (4.0 MB) ================================================== downloaded 4.0 MB trying URL 'https://stringdb-static.org/download/protein.info.v11.0/7227.protein.info.v11.0.txt.gz' Content type 'application/octet-stream' length 687988 bytes (671 KB) ================================================== downloaded 671 KB Detecting List2 in STRING trying URL 'https://stringdb-static.org/download/protein.aliases.v11.0/6239.protein.aliases.v11.0.txt.gz' Content type 'application/octet-stream' length 2902021 bytes (2.8 MB) ================================================== downloaded 2.8 MB trying URL 'https://stringdb-static.org/download/protein.info.v11.0/6239.protein.info.v11.0.txt.gz' Content type 'application/octet-stream' length 675823 bytes (659 KB) ================================================== downloaded 659 KB Step 4/4: Retrieving String Network... Retrieving List1 trying URL 'https://stringdb-static.org/download/protein.links.v11.0/7227.protein.links.v11.0.txt.gz' Content type 'application/octet-stream' length 22010066 bytes (21.0 MB) ================================================== downloaded 21.0 MB Retrieving List2 trying URL 'https://stringdb-static.org/download/protein.links.v11.0/6239.protein.links.v11.0.txt.gz' Content type 'application/octet-stream' length 48132415 bytes (45.9 MB) ===================Killed * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘IMMAN.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/IMMAN.Rcheck/00check.log’ for details.
IMMAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL IMMAN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘IMMAN’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (IMMAN)
IMMAN.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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. > library(testthat) > library(IMMAN) > > test_check("IMMAN") trying URL 'https://stringdb-static.org/download/protein.aliases.v11.0/6239.protein.aliases.v11.0.txt.gz' Content type 'application/octet-stream' length 2902021 bytes (2.8 MB) ================================================== downloaded 2.8 MB trying URL 'https://stringdb-static.org/download/protein.info.v11.0/6239.protein.info.v11.0.txt.gz' Content type 'application/octet-stream' length 675823 bytes (659 KB) ================================================== downloaded 659 KB trying URL 'https://stringdb-static.org/download/protein.aliases.v11.0/7227.protein.aliases.v11.0.txt.gz' Content type 'application/octet-stream' length 4188915 bytes (4.0 MB) ================================================== downloaded 4.0 MB trying URL 'https://stringdb-static.org/download/protein.info.v11.0/7227.protein.info.v11.0.txt.gz' Content type 'application/octet-stream' length 687988 bytes (671 KB) ================================================== downloaded 671 KB trying URL 'https://stringdb-static.org/download/protein.links.v11.0/6239.protein.links.v11.0.txt.gz' Content type 'application/octet-stream' length 48132415 bytes (45.9 MB) ================================================== downloaded 45.9 MB trying URL 'https://stringdb-static.org/download/protein.links.v11.0/7227.protein.links.v11.0.txt.gz' Content type 'application/octet-stream' length 22010066 bytes (21.0 MB) ================================================== downloaded 21.0 MB [ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ] > > proc.time() user system elapsed 81.809 2.844 296.196
IMMAN.Rcheck/IMMAN-Ex.timings
name | user | system | elapsed | |
Celegance | 0.006 | 0.000 | 0.006 | |
FruitFly | 0.002 | 0.000 | 0.002 | |
H.sapiens | 0.002 | 0.000 | 0.002 | |