Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-22 11:35:42 -0400 (Wed, 22 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 3444 |
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 833/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicFiles 1.40.0 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the GenomicFiles package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicFiles.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: GenomicFiles |
Version: 1.40.0 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicFiles.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GenomicFiles_1.40.0.tar.gz |
StartedAt: 2024-05-22 02:14:49 -0400 (Wed, 22 May 2024) |
EndedAt: 2024-05-22 02:23:35 -0400 (Wed, 22 May 2024) |
EllapsedTime: 525.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GenomicFiles.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicFiles.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GenomicFiles_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/GenomicFiles.Rcheck' * using R version 4.4.0 (2024-04-24 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 'GenomicFiles/DESCRIPTION' ... OK * this is package 'GenomicFiles' version '1.40.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'MatrixGenerics', 'GenomicRanges', 'SummarizedExperiment', 'BiocParallel', 'Rsamtools', 'rtracklayer' 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 'GenomicFiles' 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: 'S4Vectors:::selectSome' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... WARNING checkRd: (5) GenomicFiles-class.Rd:40-43: \item in \describe must have non-empty label checkRd: (5) VcfStack-class.Rd:61-89: \item in \describe must have non-empty label checkRd: (5) VcfStack-class.Rd:90-105: \item in \describe must have non-empty label checkRd: (5) pack-methods.Rd:57-61: \item in \describe must have non-empty label checkRd: (-1) reduceByFile-methods.Rd:132-139: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) reduceByFile-methods.Rd:140-143: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) reduceByRange-methods.Rd:143-150: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) reduceByRange-methods.Rd:151-154: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) registry-utils.Rd:45-59: Lost braces in \itemize; meant \describe ? checkRd: (-1) registry-utils.Rd:60-63: Lost braces in \itemize; meant \describe ? checkRd: (-1) registry-utils.Rd:64-68: Lost braces in \itemize; meant \describe ? * 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 'GenomicFiles-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: GenomicFiles > ### Title: GenomicFiles objects > ### Aliases: GenomicFiles class:GenomicFiles GenomicFiles-class > ### GenomicFiles,GenomicRanges_OR_GRangesList,character-method > ### GenomicFiles,GenomicRanges_OR_GRangesList,List-method > ### GenomicFiles,GenomicRanges_OR_GRangesList,list-method > ### GenomicFiles,missing,ANY-method GenomicFiles,missing,missing-method > ### files<- files files,GenomicFiles-method > ### files<-,GenomicFiles,character-method > ### files<-,GenomicFiles,List-method dimnames<-,GenomicFiles,list-method > ### colData<-,GenomicFiles,DataFrame-method [,GenomicFiles,ANY,ANY-method > ### [,GenomicFiles,ANY,ANY,ANY-method show,GenomicFiles-method > ### Keywords: classes methods > > ### ** Examples > > ## ----------------------------------------------------------------------- > ## Basic Use > ## ----------------------------------------------------------------------- > > if (require(RNAseqData.HNRNPC.bam.chr14)) { + fl <- RNAseqData.HNRNPC.bam.chr14_BAMFILES + rd <- GRanges("chr14", + IRanges(c(62262735, 63121531, 63980327), width=214700)) + cd <- DataFrame(method=rep("RNASeq", length(fl)), + format=rep("bam", length(fl))) + + ## Construct an instance of the class: + gf <- GenomicFiles(files = fl, rowRanges = rd, colData = cd) + gf + + ## Subset on ranges or files for different experimental runs. + dim(gf) + gf_sub <- gf[2, 3:4] + dim(gf_sub) + + ## When summarize = TRUE and no REDUCE is provided the reduceBy* + ## functions output a SummarizedExperiment object. + MAP <- function(range, file, ...) { + requireNamespace("GenomicFiles", quietly=TRUE) ## for coverage() + requireNamespace("Rsamtools", quietly=TRUE) ## for ScanBamParam() + param = Rsamtools::ScanBamParam(which=range) + GenomicFiles::coverage(file, param=param)[range] + } + se <- reduceByRange(gf, MAP=MAP, summarize=TRUE) + se + + ## Data from the rowRanges, colData and metadata slots in the + ## GenomicFiles are transferred to the SummarizedExperiment. + colData(se) + + ## Results are in the assays slot. + assays(se) + } Loading required package: RNAseqData.HNRNPC.bam.chr14 Warning in socketConnection(port = port, server = TRUE, blocking = TRUE, : port 11496 cannot be opened Error in socketConnection(port = port, server = TRUE, blocking = TRUE, : cannot open the connection Calls: reduceByRange ... <Anonymous> -> <Anonymous> -> newSOCKnode -> socketConnection Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'GenomicFiles_unit_tests.R' 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: 1 ERROR, 1 WARNING, 2 NOTEs See 'F:/biocbuild/bbs-3.19-bioc/meat/GenomicFiles.Rcheck/00check.log' for details.
GenomicFiles.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL GenomicFiles ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'GenomicFiles' ... ** 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 (GenomicFiles)
GenomicFiles.Rcheck/tests/GenomicFiles_unit_tests.Rout
R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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. > BiocGenerics:::testPackage("GenomicFiles") 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, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit RUNIT TEST PROTOCOL -- Wed May 22 02:23:25 2024 *********************************************** Number of test functions: 20 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomicFiles RUnit Tests - 20 test functions, 0 errors, 0 failures Number of test functions: 20 Number of errors: 0 Number of failures: 0 Warning message: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence 19. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. > > proc.time() user system elapsed 61.78 1.64 244.62
GenomicFiles.Rcheck/GenomicFiles-Ex.timings
name | user | system | elapsed |