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 11:40 -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 361/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
clippda 1.55.0 (landing page) Stephen Nyangoma
| 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 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: 1.55.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:clippda.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings clippda_1.55.0.tar.gz |
StartedAt: 2024-08-20 23:26:03 -0400 (Tue, 20 Aug 2024) |
EndedAt: 2024-08-20 23:30:16 -0400 (Tue, 20 Aug 2024) |
EllapsedTime: 252.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: clippda.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:clippda.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings clippda_1.55.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/clippda.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'clippda/DESCRIPTION' ... OK * this is package 'clippda' version '1.55.0' * checking package namespace information ... NOTE Namespaces with empty importFrom: 'Biobase' 'tools' * checking package dependencies ... NOTE 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 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 86.77 4.66 91.42 sampleSize 51.51 2.58 54.09 sampleSizeParameters 27.21 1.33 28.55 sample_technicalVariance 7.03 0.38 7.41 * 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: 5 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/clippda.Rcheck/00check.log' for details.
clippda.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL clippda ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'clippda' ... ** 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 | 0.06 | 0.00 | 0.07 | |
ZvaluesfrommultinomPlots | 1.42 | 0.02 | 1.45 | |
aclinicalProteomicsData-class | 0.05 | 0.02 | 0.07 | |
aclinicalProteomicsData-methods | 0.53 | 0.34 | 0.87 | |
betweensampleVariance | 1.89 | 0.14 | 2.03 | |
checkNo.replicates | 0.12 | 0.00 | 0.12 | |
clippda-package | 86.77 | 4.66 | 91.42 | |
f | 0 | 0 | 0 | |
fisherInformation | 0.09 | 0.00 | 0.10 | |
liverRawData | 0.02 | 0.00 | 0.01 | |
liver_pheno | 0 | 0 | 0 | |
liverdata | 1.38 | 0.19 | 1.56 | |
mostSimilarTwo | 0 | 0 | 0 | |
negativeIntensitiesCorrection | 0.34 | 0.00 | 0.35 | |
phenoDataFrame | 0.05 | 0.00 | 0.06 | |
pheno_urine | 0.00 | 0.01 | 0.01 | |
preProcRepeatedPeakData | 0.97 | 0.11 | 1.08 | |
proteomicsExprsData | 0.19 | 0.00 | 0.18 | |
proteomicspData | 0.06 | 0.02 | 0.08 | |
replicateCorrelations | 4.22 | 0.22 | 4.44 | |
sampleClusteredData | 0.27 | 0.03 | 0.30 | |
sampleSize | 51.51 | 2.58 | 54.09 | |
sampleSize3DscatterPlots | 0.00 | 0.03 | 0.03 | |
sampleSizeContourPlots | 0.04 | 0.01 | 0.05 | |
sampleSizeParameters | 27.21 | 1.33 | 28.55 | |
sample_technicalVariance | 7.03 | 0.38 | 7.41 | |
spectrumFilter | 1.16 | 0.20 | 1.36 | |
ztwo | 0 | 0 | 0 | |