Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:39 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 981/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
iBBiG 1.49.0 (landing page) Aedin Culhane
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the iBBiG package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iBBiG.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: iBBiG |
Version: 1.49.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:iBBiG.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings iBBiG_1.49.0.tar.gz |
StartedAt: 2024-08-21 00:00:33 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 00:02:41 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 128.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: iBBiG.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:iBBiG.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings iBBiG_1.49.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/iBBiG.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘iBBiG/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘iBBiG’ version ‘1.49.0’ * checking package namespace information ... NOTE Found export directives that require package ‘methods’: ‘exportClasses’ ‘exportMethods’ Remove all such namespace directives (if obsolete) or ensure that the DESCRIPTION Depends or Imports field contains ‘methods’. * 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 ‘iBBiG’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 dependencies in R code ... NOTE 'library' or 'require' call to ‘biclust’ which was already attached by Depends. Please remove these calls from your code. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE addSignal: no visible global function definition for ‘runif’ iBBiG: no visible global function definition for ‘new’ makeArtificial: no visible global function definition for ‘runif’ makeArtificial: no visible global function definition for ‘new’ Clusterscores,iBBiG: no visible global function definition for ‘slot’ Clusterscores<-,iBBiG: no visible global function definition for ‘slot<-’ Clusterscores<-,iBBiG: no visible global function definition for ‘validObject’ Number,iBBiG: no visible global function definition for ‘slot’ Number<-,iBBiG: no visible global function definition for ‘slot<-’ Number<-,iBBiG: no visible global function definition for ‘validObject’ NumberxCol,iBBiG: no visible global function definition for ‘slot’ NumberxCol<-,iBBiG: no visible global function definition for ‘slot<-’ NumberxCol<-,iBBiG: no visible global function definition for ‘validObject’ Parameters,iBBiG: no visible global function definition for ‘slot’ Parameters<-,iBBiG: no visible global function definition for ‘slot<-’ Parameters<-,iBBiG: no visible global function definition for ‘validObject’ RowScorexNumber,iBBiG: no visible global function definition for ‘slot’ RowScorexNumber<-,iBBiG: no visible global function definition for ‘slot<-’ RowScorexNumber<-,iBBiG: no visible global function definition for ‘validObject’ RowxNumber,iBBiG: no visible global function definition for ‘slot’ RowxNumber<-,iBBiG: no visible global function definition for ‘slot<-’ RowxNumber<-,iBBiG: no visible global function definition for ‘validObject’ Seeddata,iBBiG: no visible global function definition for ‘slot’ Seeddata<-,iBBiG: no visible global function definition for ‘slot<-’ Seeddata<-,iBBiG: no visible global function definition for ‘validObject’ analyzeClust,Biclust-iBBiG: no visible global function definition for ‘as’ analyzeClust,list-iBBiG: no visible global function definition for ‘new’ coerce,Biclust-iBBiG: no visible global function definition for ‘new’ info,iBBiG: no visible global function definition for ‘slot’ info<-,iBBiG: no visible global function definition for ‘slot<-’ info<-,iBBiG: no visible global function definition for ‘validObject’ plot,iBBiG-ANY: no visible global function definition for ‘layout’ plot,iBBiG-ANY: no visible global function definition for ‘colors’ plot,iBBiG-ANY: no visible global function definition for ‘image’ plot,iBBiG-ANY: no visible global function definition for ‘legend’ plot,iBBiG-ANY: no visible binding for global variable ‘title’ plot,iBBiG-ANY: no visible global function definition for ‘title’ plot,iBBiG-ANY: no visible global function definition for ‘barplot’ Undefined global functions or variables: as barplot colors image layout legend new runif slot slot<- title validObject Consider adding importFrom("grDevices", "colors") importFrom("graphics", "barplot", "image", "layout", "legend", "title") importFrom("methods", "as", "new", "slot", "slot<-", "validObject") importFrom("stats", "runif") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/iBBiG/libs/iBBiG.so’: Found ‘rand’, possibly from ‘rand’ (C) Found ‘srand’, possibly from ‘srand’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed iBBiG 23.737 0.059 23.797 iBBiG-package 21.784 0.092 21.876 iBBiG-class 19.625 0.180 19.805 * 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: 5 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/iBBiG.Rcheck/00check.log’ for details.
iBBiG.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL iBBiG ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘iBBiG’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_init_iBBiG.c -o R_init_iBBiG.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c iBBiG.c -o iBBiG.o gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o iBBiG.so R_init_iBBiG.o iBBiG.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-iBBiG/00new/iBBiG/libs ** R ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (iBBiG)
iBBiG.Rcheck/iBBiG-Ex.timings
name | user | system | elapsed | |
iBBiG-class | 19.625 | 0.180 | 19.805 | |
iBBiG-package | 21.784 | 0.092 | 21.876 | |
iBBiG | 23.737 | 0.059 | 23.797 | |
makeArtificial | 0.458 | 0.013 | 0.470 | |