Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1529/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
pepStat 1.40.0 (landing page) Gregory C Imholte
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 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 | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the pepStat package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pepStat.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: pepStat |
Version: 1.40.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pepStat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pepStat_1.40.0.tar.gz |
StartedAt: 2024-11-20 01:05:42 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 01:11:09 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 327.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pepStat.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pepStat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pepStat_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/pepStat.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pepStat/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pepStat’ version ‘1.40.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘pepStat’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 ... NOTE Warning: no function found corresponding to methods exports from ‘pepStat’ for: ‘end’, ‘start’, ‘values’ A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .findFDR : <anonymous>: no visible global function definition for ‘median’ .sanitize_mapping_file2: no visible global function definition for ‘read.csv’ create_db: no visible global function definition for ‘mcols<-’ create_db: no visible global function definition for ‘mcols’ getPlotCoords: no visible global function definition for ‘values’ getWeightedEstimator : <anonymous>: no visible global function definition for ‘lm.fit’ getWeightedEstimator : <anonymous>: no visible global function definition for ‘lm.wfit’ getWeightedEstimator : <anonymous> : <anonymous>: no visible global function definition for ‘sd’ getZpep: no visible global function definition for ‘values’ getZpep : <anonymous>: no visible global function definition for ‘values’ plotArrayImage: no visible global function definition for ‘dev.interactive’ plotArrayImage: no visible global function definition for ‘devAskNewPage’ plotArrayImage: no visible global function definition for ‘dev.hold’ plotArrayImage: no visible global function definition for ‘dev.flush’ plotArrayResiduals: no visible global function definition for ‘dev.interactive’ plotArrayResiduals: no visible global function definition for ‘devAskNewPage’ plotArrayResiduals: no visible global function definition for ‘dev.hold’ plotArrayResiduals: no visible global function definition for ‘dev.flush’ summarizePeptides: no visible global function definition for ‘values<-’ summarizePeptides: no visible global function definition for ‘values’ coerce,peptideSet-ExpressionSet: no visible global function definition for ‘annotation’ end,peptideSet: no visible global function definition for ‘end’ featureID,peptideSet: no visible global function definition for ‘values’ pepZscore,GRanges: no visible global function definition for ‘values’ peptide,peptideSet: no visible global function definition for ‘values’ peptide<-,peptideSet-character: no visible global function definition for ‘values’ peptide<-,peptideSet-character: no visible global function definition for ‘values<-’ position,peptideSet: no visible global function definition for ‘start’ position,peptideSet: no visible global function definition for ‘end’ start,peptideSet: no visible global function definition for ‘start’ values,peptideSet: no visible global function definition for ‘values’ values<-,peptideSet: no visible global function definition for ‘values<-’ write.pSet,peptideSet: no visible global function definition for ‘start’ write.pSet,peptideSet: no visible global function definition for ‘end’ write.pSet,peptideSet: no visible global function definition for ‘write.csv’ Undefined global functions or variables: annotation dev.flush dev.hold dev.interactive devAskNewPage end lm.fit lm.wfit mcols mcols<- median read.csv sd start values values<- write.csv Consider adding importFrom("grDevices", "dev.flush", "dev.hold", "dev.interactive", "devAskNewPage") importFrom("stats", "end", "lm.fit", "lm.wfit", "median", "sd", "start") importFrom("utils", "read.csv", "write.csv") 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/pepStat.Rcheck/00check.log’ for details.
pepStat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pepStat ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘pepStat’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘GenomicRanges’ for request: ‘mcols<-’ when loading ‘pepStat’ No methods found in package ‘GenomicRanges’ for request: ‘mcols’ when loading ‘pepStat’ No methods found in package ‘IRanges’ for request: ‘values<-’ when loading ‘pepStat’ No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘pepStat’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘GenomicRanges’ for request: ‘mcols<-’ when loading ‘pepStat’ No methods found in package ‘GenomicRanges’ for request: ‘mcols’ when loading ‘pepStat’ No methods found in package ‘IRanges’ for request: ‘values<-’ when loading ‘pepStat’ No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘pepStat’ ** testing if installed package can be loaded from final location No methods found in package ‘GenomicRanges’ for request: ‘mcols<-’ when loading ‘pepStat’ No methods found in package ‘GenomicRanges’ for request: ‘mcols’ when loading ‘pepStat’ No methods found in package ‘IRanges’ for request: ‘values<-’ when loading ‘pepStat’ No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘pepStat’ ** testing if installed package keeps a record of temporary installation path * DONE (pepStat)
pepStat.Rcheck/pepStat-Ex.timings
name | user | system | elapsed | |
create_db | 0.066 | 0.001 | 0.067 | |
makeCalls | 2.943 | 0.059 | 3.016 | |
makePeptideSet | 1.022 | 0.028 | 1.050 | |
normalizeArray | 2.793 | 0.045 | 2.841 | |
plotArray | 2.580 | 0.037 | 2.664 | |
restab | 2.608 | 0.045 | 2.664 | |
shinyPepStat | 0 | 0 | 0 | |
slidingMean | 2.667 | 0.041 | 2.715 | |
summarizePeptides | 2.604 | 0.038 | 2.647 | |