Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-03 11:41 -0400 (Thu, 03 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4716 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
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 751/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
frma 1.57.0 (landing page) Matthew N. McCall
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
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 frma package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/frma.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: frma |
Version: 1.57.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:frma.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings frma_1.57.0.tar.gz |
StartedAt: 2024-10-02 21:51:28 -0400 (Wed, 02 Oct 2024) |
EndedAt: 2024-10-02 21:54:33 -0400 (Wed, 02 Oct 2024) |
EllapsedTime: 184.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: frma.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:frma.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings frma_1.57.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/frma.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘frma/DESCRIPTION’ ... OK * this is package ‘frma’ version ‘1.57.0’ * 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 ‘frma’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘Biobase’ 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 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 loading without being on the library search path ... 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 GNUSE: no visible binding for global variable ‘median’ GNUSE: no visible binding for global variable ‘quantile’ GNUSE: no visible global function definition for ‘boxplot’ barcode: no visible global function definition for ‘pnorm’ batchFit: no visible global function definition for ‘median’ randomeffects<-,frmaExpressionSet: no visible global function definition for ‘validObject’ residuals<-,frmaExpressionSet: no visible global function definition for ‘validObject’ se.exprs<-,ExpressionSet: no visible global function definition for ‘validObject’ se.exprs<-,frmaExpressionSet: no visible global function definition for ‘validObject’ weights<-,frmaExpressionSet: no visible global function definition for ‘validObject’ Undefined global functions or variables: boxplot median pnorm quantile validObject Consider adding importFrom("graphics", "boxplot") importFrom("methods", "validObject") importFrom("stats", "median", "pnorm", "quantile") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) frma.Rd:19: Escaped LaTeX specials: \_ \_ checkRd: (-1) frma.Rd:20: Escaped LaTeX specials: \_ \_ \_ * 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘frma-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: GNUSE > ### Title: GNUSE > ### Aliases: GNUSE > ### Keywords: manip > > ### ** Examples > > library(frma) > library(frmaExampleData) > data(AffyBatchExample) > object <- frma(AffyBatchExample) Warning in gzfile(file, "rb") : cannot open compressed file '/tmp/Rtmp1pSNPo/repos_https%3A%2F%2Fcloud.r-project.org%2Fsrc%2Fcontrib.rds', probable reason 'No such file or directory' Warning in read.dcf(file = tmpf) : cannot open compressed file '/tmp/Rtmp1pSNPo/filed05e4e9b580', probable reason 'No such file or directory' Warning: unable to access index for repository https://cloud.r-project.org/src/contrib: cannot open the connection also installing the dependencies ‘png’, ‘KEGGREST’, ‘AnnotationDbi’ trying URL 'https://cloud.r-project.org/src/contrib/png_0.1-8.tar.gz' Content type 'application/x-gzip' length 24880 bytes (24 KB) ================================================== downloaded 24 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/KEGGREST_1.44.1.tar.gz' Content type 'application/x-gzip' length 22979 bytes (22 KB) ================================================== downloaded 22 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/AnnotationDbi_1.66.0.tar.gz' Content type 'application/x-gzip' length 4359386 bytes (4.2 MB) ======= downloaded 607 KB Warning in download.file(url, destfile, method, mode = "wb", ...) : downloaded length 622021 != reported length 4359386 Warning in download.file(url, destfile, method, mode = "wb", ...) : URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/AnnotationDbi_1.66.0.tar.gz': status was 'Failed writing received data to disk/application' Error in download.file(url, destfile, method, mode = "wb", ...) : download from 'https://bioconductor.org/packages/3.19/bioc/src/contrib/AnnotationDbi_1.66.0.tar.gz' failed Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package ‘AnnotationDbi’ failed Warning in download.file(url, destfile, method, mode = "wb", ...) : URL https://bioconductor.org/packages/3.19/data/annotation/src/contrib/hgu133acdf_2.18.0.tar.gz: cannot open destfile '/tmp/Rtmp1pSNPo/downloaded_packages/hgu133acdf_2.18.0.tar.gz', reason 'No space left on device' Warning in download.file(url, destfile, method, mode = "wb", ...) : download had nonzero exit status Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package ‘hgu133acdf’ failed Warning in dir.create(tmpd2) : cannot create dir '/tmp/Rtmp1pSNPo/filed05e2b40561d', reason 'No space left on device' Error in install.packages(cdfname, lib = lib, repos = repositories(), : unable to create temporary directory ‘/tmp/Rtmp1pSNPo/filed05e2b40561d’ Calls: frma ... .local -> getCdfInfo -> cdfFromBioC -> install.packages Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘frma.Rnw’ using Sweave Loading required package: Biobase 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, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. also installing the dependencies ‘png’, ‘KEGGREST’, ‘AnnotationDbi’ trying URL 'https://cloud.r-project.org/src/contrib/png_0.1-8.tar.gz' Content type 'application/x-gzip' length 24880 bytes (24 KB) ================================================== downloaded 24 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/KEGGREST_1.44.1.tar.gz' Content type 'application/x-gzip' length 22979 bytes (22 KB) ================================================== downloaded 22 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/AnnotationDbi_1.66.0.tar.gz' Content type 'application/x-gzip' length 4359386 bytes (4.2 MB) ======== downloaded 759 KB Warning in download.file(url, destfile, method, mode = "wb", ...) : downloaded length 777443 != reported length 4359386 Warning in download.file(url, destfile, method, mode = "wb", ...) : URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/AnnotationDbi_1.66.0.tar.gz': status was 'Failed writing received data to disk/application' Error in download.file(url, destfile, method, mode = "wb", ...) : download from 'https://bioconductor.org/packages/3.19/bioc/src/contrib/AnnotationDbi_1.66.0.tar.gz' failed Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package ‘AnnotationDbi’ failed Warning in download.file(url, destfile, method, mode = "wb", ...) : URL https://bioconductor.org/packages/3.19/data/annotation/src/contrib/hgu133acdf_2.18.0.tar.gz: cannot open destfile '/tmp/RtmpmggLtE/downloaded_packages/hgu133acdf_2.18.0.tar.gz', reason 'No space left on device' Warning in download.file(url, destfile, method, mode = "wb", ...) : download had nonzero exit status Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package ‘hgu133acdf’ failed Warning in dir.create(tmpd2) : cannot create dir '/tmp/RtmpmggLtE/filed7c51f4dd458', reason 'No space left on device' Error: processing vignette 'frma.Rnw' failed with diagnostics: chunk 3 Error in install.packages(cdfname, lib = lib, repos = repositories(), : unable to create temporary directory ‘/tmp/RtmpmggLtE/filed7c51f4dd458’ --- failed re-building ‘frma.Rnw’ SUMMARY: processing the following file failed: ‘frma.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/frma.Rcheck/00check.log’ for details.
frma.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL frma ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘frma’ ... ** using staged installation ** R ** 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 (frma)
frma.Rcheck/frma-Ex.timings
name | user | system | elapsed |