Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1961/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SIM 1.76.0 (landing page) Renee X. de Menezes
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the SIM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SIM.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: SIM |
Version: 1.76.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SIM.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SIM_1.76.0.tar.gz |
StartedAt: 2024-12-20 05:30:21 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:32:43 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 142.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: SIM.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SIM.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SIM_1.76.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SIM.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘SIM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SIM’ version ‘1.76.0’ * 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 ‘SIM’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 ... NOTE 'library' or 'require' call to ‘biomaRt’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Package in Depends field not imported from: ‘quantreg’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘SIM/R/zzz.R’: .onAttach calls: library.dynam("SIM", pkg, lib) See section ‘Good practice’ in '?.onAttach'. dependent.heatmap: warning in get(as.character(adjust[[2]]), env = attr(adjust, ".Environment")): partial argument match of 'env' to 'envir' sim.plot.zoom.in: warning in eval(call, env = attr(call, "env")): partial argument match of 'env' to 'envir' sim.update.chrom.table: warning in factor(table$name, level = c(1:22, "X", "Y")): partial argument match of 'level' to 'levels' assemble.data: no visible binding for global variable ‘chrom.table’ convertGenomicRegion: no visible binding for global variable ‘chrom.table’ dependent.heatmap: no visible global function definition for ‘strwidth’ getoverlappingregions: no visible global function definition for ‘useMart’ getoverlappingregions: no visible global function definition for ‘getBM’ independent.heatmap: no visible global function definition for ‘strwidth’ link.metadata: no visible binding for global variable ‘expr.data’ link.metadata: no visible binding for global variable ‘hgu133plus2CHR’ link.metadata: no visible binding for global variable ‘hgu133plus2CHRLOC’ link.metadata: no visible binding for global variable ‘hgu133plus2SYMBOL’ plotCytobands: no visible binding for global variable ‘chrom.table’ sim.plot.overlapping.indep.dep.features: no visible global function definition for ‘box’ sim.plot.pvals.on.genome: no visible binding for global variable ‘chrom.table’ sim.update.chrom.table: no visible global function definition for ‘dbConnect’ sim.update.chrom.table: no visible global function definition for ‘MySQL’ sim.update.chrom.table: no visible global function definition for ‘dbGetQuery’ Undefined global functions or variables: MySQL box chrom.table dbConnect dbGetQuery expr.data getBM hgu133plus2CHR hgu133plus2CHRLOC hgu133plus2SYMBOL strwidth useMart Consider adding importFrom("graphics", "box", "strwidth") to your NAMESPACE file. * checking Rd files ... WARNING checkRd: (5) integrated.analysis.Rd:116: \item in \value must have non-empty label * 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 data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed SIM-package 5.547 0.18 5.726 * 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: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/SIM.Rcheck/00check.log’ for details.
SIM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL SIM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘SIM’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c withinWindow.c -o withinWindow.o gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o SIM.so withinWindow.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-SIM/00new/SIM/libs ** R ** data ** 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 ** 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 (SIM)
SIM.Rcheck/SIM-Ex.timings
name | user | system | elapsed | |
RESOURCERER.annotation.to.ID | 0 | 0 | 0 | |
SIM-package | 5.547 | 0.180 | 5.726 | |
acgh.data | 0.001 | 0.000 | 0.001 | |
assemble.data | 0.021 | 0.001 | 0.022 | |
chrom.table | 0.001 | 0.000 | 0.001 | |
expr.data | 0.001 | 0.000 | 0.002 | |
getoverlappingregions | 0 | 0 | 0 | |
impute.nas.by.surrounding | 0 | 0 | 0 | |
integrated.analysis | 4.305 | 0.041 | 4.346 | |
link.metadata | 0 | 0 | 0 | |
samples | 0.001 | 0.000 | 0.001 | |
sim.plot.overlapping.indep.dep.features | 0.035 | 0.001 | 0.037 | |
sim.plot.pvals.on.genome | 0.104 | 0.005 | 0.109 | |
sim.plot.pvals.on.region | 0.011 | 0.002 | 0.013 | |
sim.plot.zoom.in | 0.461 | 0.001 | 0.463 | |
sim.plot.zscore.heatmap | 0.563 | 0.022 | 0.585 | |
sim.update.chrom.table | 0 | 0 | 0 | |
tabulate.pvals | 0.004 | 0.000 | 0.004 | |
tabulate.top.dep.features | 0.012 | 0.000 | 0.012 | |
tabulate.top.indep.features | 0.008 | 0.002 | 0.009 | |