Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 370/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
clippda 1.58.0 (landing page) Stephen Nyangoma
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the clippda package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/clippda.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: clippda |
Version: 1.58.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:clippda.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings clippda_1.58.0.tar.gz |
StartedAt: 2025-10-14 16:19:46 -0400 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 16:24:28 -0400 (Tue, 14 Oct 2025) |
EllapsedTime: 281.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: clippda.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:clippda.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings clippda_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/clippda.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘clippda/DESCRIPTION’ ... OK * this is package ‘clippda’ version ‘1.58.0’ * checking package namespace information ... NOTE Namespaces with empty importFrom: ‘Biobase’ ‘tools’ * checking package dependencies ... INFO Depends: includes the non-default packages: 'limma', 'statmod', 'rgl', 'lattice', 'scatterplot3d', 'Biobase', 'tools' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘clippda’ 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 dependencies in R code ... NOTE 'library' or 'require' calls to packages already attached by Depends: ‘lattice’ ‘limma’ ‘rgl’ ‘scatterplot3d’ ‘statmod’ Please remove these calls from your code. Packages in Depends field not imported from: ‘lattice’ ‘rgl’ 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 ZvaluescasesVcontrolsPlots: no visible global function definition for ‘lines’ ZvaluescasesVcontrolsPlots: no visible global function definition for ‘legend’ ZvaluesfrommultinomPlots: no visible global function definition for ‘rmultinom’ ZvaluesfrommultinomPlots: no visible global function definition for ‘density’ ZvaluesfrommultinomPlots: no visible global function definition for ‘lines’ ZvaluesfrommultinomPlots: no visible global function definition for ‘legend’ ZvaluesfrommultinomPlots: no visible global function definition for ‘cloud’ ZvaluesfrommultinomPlots: no visible global function definition for ‘var’ Undefined global functions or variables: cloud density legend lines rmultinom var Consider adding importFrom("graphics", "legend", "lines") importFrom("stats", "density", "rmultinom", "var") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) show-methods.Rd:11-18: Lost braces 11 | {object = "aclinicalProteomicsData"}{ | ^ * 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 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 clippda-package 103.691 4.092 109.090 sampleSize 62.945 2.358 65.966 sampleSizeParameters 30.474 1.369 32.235 sample_technicalVariance 8.514 0.348 8.941 replicateCorrelations 5.630 0.169 5.838 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/clippda.Rcheck/00check.log’ for details.
clippda.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL clippda ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘clippda’ ... ** this is package ‘clippda’ version ‘1.58.0’ ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (clippda)
clippda.Rcheck/clippda-Ex.timings
name | user | system | elapsed | |
ZvaluescasesVcontrolsPlots | 0.011 | 0.002 | 0.013 | |
ZvaluesfrommultinomPlots | 1.234 | 0.068 | 1.318 | |
aclinicalProteomicsData-class | 0.050 | 0.007 | 0.079 | |
aclinicalProteomicsData-methods | 0.256 | 0.399 | 0.670 | |
betweensampleVariance | 1.206 | 0.093 | 1.310 | |
checkNo.replicates | 0.094 | 0.009 | 0.108 | |
clippda-package | 103.691 | 4.092 | 109.090 | |
f | 0.000 | 0.001 | 0.001 | |
fisherInformation | 0.064 | 0.009 | 0.074 | |
liverRawData | 0.005 | 0.003 | 0.008 | |
liver_pheno | 0.001 | 0.002 | 0.004 | |
liverdata | 1.370 | 0.211 | 1.601 | |
mostSimilarTwo | 0.002 | 0.000 | 0.002 | |
negativeIntensitiesCorrection | 0.307 | 0.067 | 0.376 | |
phenoDataFrame | 0.046 | 0.007 | 0.054 | |
pheno_urine | 0.001 | 0.002 | 0.003 | |
preProcRepeatedPeakData | 1.295 | 0.180 | 1.492 | |
proteomicsExprsData | 0.118 | 0.009 | 0.127 | |
proteomicspData | 0.055 | 0.010 | 0.065 | |
replicateCorrelations | 5.630 | 0.169 | 5.838 | |
sampleClusteredData | 0.304 | 0.032 | 0.344 | |
sampleSize | 62.945 | 2.358 | 65.966 | |
sampleSize3DscatterPlots | 0.020 | 0.003 | 0.023 | |
sampleSizeContourPlots | 0.028 | 0.004 | 0.031 | |
sampleSizeParameters | 30.474 | 1.369 | 32.235 | |
sample_technicalVariance | 8.514 | 0.348 | 8.941 | |
spectrumFilter | 1.197 | 0.132 | 1.337 | |
ztwo | 0.000 | 0.000 | 0.001 | |