Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:26 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 SIM package: - Please 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 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 1875/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SIM 1.68.0 (landing page) Renee X. de Menezes
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: SIM |
Version: 1.68.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SIM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SIM_1.68.0.tar.gz |
StartedAt: 2023-04-10 22:42:51 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 22:45:05 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 133.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SIM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SIM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SIM_1.68.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/SIM.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SIM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SIM’ version ‘1.68.0’ * 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 * 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 ... 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 ... 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 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed SIM-package 5.13 0.262 5.583 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.16-bioc/meat/SIM.Rcheck/00check.log’ for details.
SIM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SIM ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘SIM’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c withinWindow.c -o withinWindow.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o SIM.so withinWindow.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/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 | 5.130 | 0.262 | 5.583 | |
acgh.data | 0.001 | 0.001 | 0.003 | |
assemble.data | 0.024 | 0.006 | 0.031 | |
chrom.table | 0.001 | 0.001 | 0.003 | |
expr.data | 0.001 | 0.001 | 0.003 | |
getoverlappingregions | 0.000 | 0.001 | 0.000 | |
impute.nas.by.surrounding | 0.000 | 0.000 | 0.001 | |
integrated.analysis | 3.644 | 0.048 | 3.701 | |
link.metadata | 0 | 0 | 0 | |
samples | 0.001 | 0.001 | 0.002 | |
sim.plot.overlapping.indep.dep.features | 0.032 | 0.006 | 0.039 | |
sim.plot.pvals.on.genome | 0.095 | 0.021 | 0.117 | |
sim.plot.pvals.on.region | 0.010 | 0.002 | 0.012 | |
sim.plot.zoom.in | 0.183 | 0.018 | 0.202 | |
sim.plot.zscore.heatmap | 0.274 | 0.031 | 0.309 | |
sim.update.chrom.table | 0 | 0 | 0 | |
tabulate.pvals | 0.003 | 0.001 | 0.004 | |
tabulate.top.dep.features | 0.010 | 0.003 | 0.013 | |
tabulate.top.indep.features | 0.009 | 0.002 | 0.011 | |