Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1278/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
miRNApath 1.66.0 (landing page) James M. Ward
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the miRNApath package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miRNApath.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: miRNApath |
Version: 1.66.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:miRNApath.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings miRNApath_1.66.0.tar.gz |
StartedAt: 2024-12-20 02:48:30 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 02:52:54 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 264.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: miRNApath.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:miRNApath.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings miRNApath_1.66.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/miRNApath.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘miRNApath/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘miRNApath’ version ‘1.66.0’ * 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 ‘miRNApath’ 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Initial release. Cannot process chunk/lines: Changed objects to S4 format Cannot process chunk/lines: Updated runEnrichment and mirnaTable to remove the "Enriched by miRNA" Cannot process chunk/lines: concatenated strings, which were way too long to be useful. Cannot process chunk/lines: Updated the miRNA-gene counts methodology; fixed Cannot process chunk/lines: the strategy for ignoring pathways with no hits. Cannot process chunk/lines: Updated permutation logic to handle empty when permutations Cannot process chunk/lines: show enrichment in only a subset of overall pathways. * 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 ‘miRNApath’ for: ‘show’ 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE loadmirnapath: no visible global function definition for ‘read.table’ loadmirnapath: no visible global function definition for ‘new’ loadmirnapathways: no visible global function definition for ‘read.table’ loadmirnatogene: no visible global function definition for ‘read.table’ mirnaTable: no visible global function definition for ‘reshape’ runEnrichment : <anonymous> : <anonymous>: no visible global function definition for ‘phyper’ runEnrichment: no visible global function definition for ‘slotNames’ Undefined global functions or variables: new phyper read.table reshape slotNames Consider adding importFrom("methods", "new", "slotNames") importFrom("stats", "phyper", "reshape") importFrom("utils", "read.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) runEnrichment.Rd:119: 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 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 mirnaTable 16.671 0.034 16.704 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/miRNApath.Rcheck/00check.log’ for details.
miRNApath.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL miRNApath ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘miRNApath’ ... ** using staged installation ** R ** data ** 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 (miRNApath)
miRNApath.Rcheck/miRNApath-Ex.timings
name | user | system | elapsed | |
checkColumns | 0 | 0 | 0 | |
convertFoldChange | 0 | 0 | 0 | |
filtermirnapath | 0.031 | 0.001 | 0.032 | |
loadmirnapath | 0.032 | 0.003 | 0.035 | |
loadmirnapathways | 0.042 | 0.001 | 0.043 | |
loadmirnatogene | 0.085 | 0.003 | 0.087 | |
miRNApath-package | 0 | 0 | 0 | |
mirnaTable | 16.671 | 0.034 | 16.704 | |
mirnaobj | 0.016 | 0.000 | 0.016 | |
mirnapath-class | 0.016 | 0.000 | 0.016 | |
runEnrichment | 0 | 0 | 0 | |