Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-31 19:29:48 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 355/2233 | 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 | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 2024-05-31 05:05:43 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 05:09:40 -0400 (Fri, 31 May 2024) |
EllapsedTime: 236.5 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 4.4.0 RC (2024-04-16 r86468 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 80.80 4.00 84.79 sampleSize 50.16 2.55 52.83 sampleSizeParameters 25.16 1.33 26.58 sample_technicalVariance 7.43 0.26 7.70 * 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 | 0.05 | 0.01 | 0.07 | |
ZvaluesfrommultinomPlots | 1.17 | 0.05 | 1.22 | |
aclinicalProteomicsData-class | 0.05 | 0.01 | 0.07 | |
aclinicalProteomicsData-methods | 0.34 | 0.27 | 0.61 | |
betweensampleVariance | 1.26 | 0.23 | 1.50 | |
checkNo.replicates | 0.13 | 0.00 | 0.13 | |
clippda-package | 80.80 | 4.00 | 84.79 | |
f | 0 | 0 | 0 | |
fisherInformation | 0.06 | 0.00 | 0.07 | |
liverRawData | 0.01 | 0.00 | 0.01 | |
liver_pheno | 0 | 0 | 0 | |
liverdata | 1.57 | 0.20 | 1.77 | |
mostSimilarTwo | 0 | 0 | 0 | |
negativeIntensitiesCorrection | 0.23 | 0.03 | 0.26 | |
phenoDataFrame | 0.08 | 0.00 | 0.08 | |
pheno_urine | 0.00 | 0.02 | 0.02 | |
preProcRepeatedPeakData | 1.23 | 0.12 | 1.36 | |
proteomicsExprsData | 0.14 | 0.02 | 0.15 | |
proteomicspData | 0.1 | 0.0 | 0.1 | |
replicateCorrelations | 3.48 | 0.37 | 3.86 | |
sampleClusteredData | 0.19 | 0.08 | 0.26 | |
sampleSize | 50.16 | 2.55 | 52.83 | |
sampleSize3DscatterPlots | 0.03 | 0.00 | 0.03 | |
sampleSizeContourPlots | 0.03 | 0.00 | 0.03 | |
sampleSizeParameters | 25.16 | 1.33 | 26.58 | |
sample_technicalVariance | 7.43 | 0.26 | 7.70 | |
spectrumFilter | 1.07 | 0.11 | 1.17 | |
ztwo | 0 | 0 | 0 | |