Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:21 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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To the developers/maintainers of the prebs package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/prebs.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 1503/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
prebs 1.39.0 (landing page) Karolis Uziela
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: prebs |
Version: 1.39.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:prebs.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings prebs_1.39.0.tar.gz |
StartedAt: 2023-02-07 11:44:56 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 11:58:55 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 839.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: prebs.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:prebs.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings prebs_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/prebs.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘prebs/DESCRIPTION’ ... OK * this is package ‘prebs’ version ‘1.39.0’ * 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 ‘prebs’ 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 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function call to a different package: .Call("rma_c_complete_copy", ..., PACKAGE = "affy") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE granges_from_cdf: no visible global function definition for ‘read.table’ is.installed: no visible global function definition for ‘installed.packages’ Undefined global functions or variables: installed.packages read.table Consider adding importFrom("utils", "installed.packages", "read.table") 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘prebs-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: calc_prebs > ### Title: Calculate PREBS values > ### Aliases: calc_prebs > > ### ** Examples > > if (require(prebsdata)) { + # Get full paths to data files in \code{prebsdata} package + bam_file1 <- system.file(file.path("sample_bam_files", "input1.bam"), package="prebsdata") + bam_file2 <- system.file(file.path("sample_bam_files", "input2.bam"), package="prebsdata") + bam_files <- c(bam_file1, bam_file2) + custom_cdf_mapping1 <- system.file(file.path("custom-cdf", "HGU133Plus2_Hs_ENSG_mapping.txt"), + package="prebsdata") + custom_cdf_mapping2 <- system.file(file.path("custom-cdf", "HGU133A2_Hs_ENSG_mapping.txt"), + package="prebsdata") + manufacturer_cdf_mapping <- system.file(file.path("manufacturer-cdf", "HGU133Plus2_mapping.txt"), + package="prebsdata") + if (interactive()) { + # Run PREBS using custom CDF without parallelization ("rpa" mode) + prebs_values <- calc_prebs(bam_files, custom_cdf_mapping1) + head(exprs(prebs_values)) + + # Run PREBS using custom CDF without parallelization ("rma" mode) + prebs_values <- calc_prebs(bam_files, custom_cdf_mapping1, sum.method="rma") + head(exprs(prebs_values)) + + # Run PREBS using custom CDF with parallelization + library(parallel) + N_CORES = 2 + CLUSTER <- makeCluster(N_CORES) + prebs_values <- calc_prebs(bam_files, custom_cdf_mapping1, cluster=CLUSTER) + stopCluster(CLUSTER) + + # Run PREBS using another custom CDF + prebs_values <- calc_prebs(bam_files, custom_cdf_mapping2) + + # Run PREBS and return data frame instead of ExpressionSet object + prebs_values <- calc_prebs(bam_files, custom_cdf_mapping1, output_eset=FALSE) + head(prebs_values) + } + + # Run PREBS using Manufacturer's CDF (outputs probe set expressions) + prebs_values <- calc_prebs(bam_files, manufacturer_cdf_mapping) + head(exprs(prebs_values)) + + # Same as above, but state CDF package name explicitly + prebs_values <- calc_prebs(bam_files, manufacturer_cdf_mapping, cdf_name="hgu133plus2cdf") + } Loading required package: prebsdata Inferred name for CDF package: HGU133Plus2_mapping.txt -> hgu133plus2cdf Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘hgu133plus2cdf’ Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘hgu133plus2cdf’ [1] "Finished: input1.bam" [1] "Finished: input2.bam" Note: Some probe IDs contain duplicates. If you are using manufacturer's CDF then you can ignore this message. Killed * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘prebs.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/prebs.Rcheck/00check.log’ for details.
prebs.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL prebs ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘prebs’ ... ** 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 (prebs)
prebs.Rcheck/prebs-Ex.timings
name | user | system | elapsed |