Back to Build/check report for BioC 3.21 experimental data |
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This page was generated on 2024-10-28 02:38 -0400 (Mon, 28 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4649 |
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 90/429 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
davidTiling 1.45.0 (landing page) Wolfgang Huber
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||
To the developers/maintainers of the davidTiling package: - 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: davidTiling |
Version: 1.45.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:davidTiling.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings davidTiling_1.45.0.tar.gz |
StartedAt: 2024-10-27 23:00:28 -0400 (Sun, 27 Oct 2024) |
EndedAt: 2024-10-27 23:08:02 -0400 (Sun, 27 Oct 2024) |
EllapsedTime: 453.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: davidTiling.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:davidTiling.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings davidTiling_1.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/davidTiling.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘davidTiling/DESCRIPTION’ ... OK * this is package ‘davidTiling’ version ‘1.45.0’ * 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 ‘davidTiling’ can be installed ... OK * checking installed package size ... INFO installed size is 538.5Mb sub-directories of 1Mb or more: celfiles 306.2Mb data 229.6Mb website 2.3Mb * checking package 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘Biobase’ ‘GO.db’ ‘tilingArray’ 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 GOHyperG: no visible global function definition for ‘phyper’ GOHyperG: no visible binding for global variable ‘GOTERM’ GOHyperG: no visible global function definition for ‘replaceSystematicByCommonName’ GOHyperG: no visible global function definition for ‘Term’ GOHyperG: no visible global function definition for ‘abline’ colMedians: no visible binding for global variable ‘median’ getAllGO: no visible binding for global variable ‘GOMFANCESTOR’ getAllGO: no visible binding for global variable ‘GOBPANCESTOR’ getAllGO: no visible binding for global variable ‘GOCCANCESTOR’ movingWindow: no visible global function definition for ‘median’ movingWindow : <anonymous>: no visible global function definition for ‘median’ scatterWithHist: no visible global function definition for ‘hist’ scatterWithHist: no visible global function definition for ‘layout’ scatterWithHist: no visible global function definition for ‘par’ scatterWithHist: no visible global function definition for ‘barplot’ scatterWithHist: no visible global function definition for ‘text’ scoreSegments: no visible global function definition for ‘data’ scoreSegments: no visible binding for global variable ‘yeastFeatures’ scoreSegments: no visible binding for global variable ‘chrs’ scoreSegments: no visible global function definition for ‘otherStrand’ scoreSegments: no visible global function definition for ‘median’ scoreSegments: no visible global function definition for ‘posMin’ showDens: no visible global function definition for ‘hist’ showDens: no visible global function definition for ‘axis’ showDens: no visible global function definition for ‘polygon’ zscore: no visible global function definition for ‘sd’ Undefined global functions or variables: GOBPANCESTOR GOCCANCESTOR GOMFANCESTOR GOTERM Term abline axis barplot chrs data hist layout median otherStrand par phyper polygon posMin replaceSystematicByCommonName sd text yeastFeatures Consider adding importFrom("graphics", "abline", "axis", "barplot", "hist", "layout", "par", "polygon", "text") importFrom("stats", "median", "phyper", "sd") importFrom("utils", "data") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: GOHyperG.Rd:34-35: Dropping empty section \examples prepare_Rd: getGO.Rd:32-33: Dropping empty section \examples prepare_Rd: scatterWithHist.Rd:19-20: Dropping empty section \details prepare_Rd: scoreSegments.Rd:103-104: Dropping empty section \examples * 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’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘Archi_RT_positions.txt’ ‘strongConservedNovelIsolated.txt’ ‘utrmap-GOcategories.txt’ Package has no Sweave vignette sources and no VignetteBuilder field. * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed davidTiling 23.975 0.894 24.87 * checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file? * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.21-data-experiment/meat/davidTiling.Rcheck/00check.log’ for details.
davidTiling.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL davidTiling ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘davidTiling’ ... ** 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 (davidTiling)
davidTiling.Rcheck/davidTiling-Ex.timings
name | user | system | elapsed | |
davidTiling | 23.975 | 0.894 | 24.870 | |
getAttributeField | 0.001 | 0.000 | 0.001 | |
gff | 0.331 | 0.017 | 0.350 | |
probeAnno | 4.568 | 0.181 | 4.749 | |
scatterWithHist | 0.018 | 0.000 | 0.018 | |
showDens | 0.003 | 0.001 | 0.005 | |
yeastFeatures | 0.002 | 0.000 | 0.003 | |