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 11:05:00 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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 Cepo package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Cepo.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 290/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Cepo 1.4.0 (landing page) Hani Jieun Kim
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
Package: Cepo |
Version: 1.4.0 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:Cepo.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings Cepo_1.4.0.tar.gz |
StartedAt: 2023-04-10 19:36:48 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 19:41:45 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 296.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: Cepo.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:Cepo.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings Cepo_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/Cepo.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘Cepo/DESCRIPTION’ ... OK * this is package ‘Cepo’ version ‘1.4.0’ * package encoding: UTF-8 * 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 ‘Cepo’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... WARNING Invalid license file pointers: LICENSE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘patchwork’ A package should be listed in only one of these fields. * 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 loading without being on the library search path ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘purrr’ Package in Depends field not imported from: ‘GSEABase’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘rowMeans_withnames’ ‘rowSds_withnames’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE bootFastCepo : <anonymous>: no visible binding for global variable ‘.’ bootFastCepo: no visible binding for global variable ‘.’ Undefined global functions or variables: . * 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 ... WARNING Undocumented arguments in documentation object 'Cepo' ‘prefilter_pzero’ Documented arguments not in \usage in documentation object 'Cepo': ‘prefilter_pzeros’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotDensities 6.152 0.192 6.344 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘cepo.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.16-bioc/meat/Cepo.Rcheck/00check.log’ for details.
Cepo.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL Cepo ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘Cepo’ ... ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (Cepo)
Cepo.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(Cepo) Loading required package: GSEABase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: annotate Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: XML Loading required package: graph Attaching package: 'graph' The following object is masked from 'package:XML': addNode > > test_check("Cepo") Computed statistics: DataFrame with 50 rows and 3 columns a b c <numeric> <numeric> <numeric> gene38 0.551471 -0.441176 -0.11029412 gene41 0.404412 -0.411765 0.00735294 gene29 0.330882 0.117647 -0.44852941 gene21 0.325980 -0.181373 -0.14460784 gene32 0.321078 -0.289216 -0.03186275 ... ... ... ... gene1 -0.370098 0.05637255 0.3137255 gene24 -0.375000 0.12500000 0.2500000 gene45 -0.379902 0.00245098 0.3774510 gene2 -0.448529 0.33088235 0.1176471 gene4 -0.531863 0.57107843 -0.0392157 Computed p-values: DataFrame with 50 rows and 3 columns a b c <numeric> <numeric> <numeric> gene38 NA NA NA gene41 NA NA NA gene29 NA NA NA gene21 NA NA NA gene32 NA NA NA ... ... ... ... gene1 NA NA NA gene24 NA NA NA gene45 NA NA NA gene2 NA NA NA gene4 NA NA NA [ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ] > > proc.time() user system elapsed 13.876 1.783 15.370
Cepo.Rcheck/Cepo-Ex.timings
name | user | system | elapsed | |
Cepo | 0.469 | 0.060 | 0.529 | |
plotDensities | 6.152 | 0.192 | 6.344 | |
setCepoBPPARAM | 0 | 0 | 0 | |
topGenes | 0.028 | 0.000 | 0.028 | |