Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:41 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 567/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
diggit 1.39.0 (landing page) Mariano J Alvarez
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | TIMEOUT | skipped | ||||||||||
To the developers/maintainers of the diggit package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/diggit.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: diggit |
Version: 1.39.0 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:diggit.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings diggit_1.39.0.tar.gz |
StartedAt: 2024-12-24 00:09:30 -0500 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 00:14:06 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 276.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: diggit.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:diggit.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings diggit_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/diggit.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 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 'diggit/DESCRIPTION' ... OK * this is package 'diggit' 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 whether package 'diggit' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... WARNING Invalid citation information in 'inst/CITATION': Error in citeEntry(entry = "article", author = c(person(c("Mariano", "J"), "Alvarez"), person(c("James", "C"), "Chen"), person("Andrea", "Califano")), title = "{DIGGIT}: a Bioconductor package to infer genetic variants driving cellular phenotypes", journal = "Bioinformatics", year = 2015, volume = 31, number = 24, pages = "4032--4", textVersion = "Alvarez, M.J., Chen, J.C., and Califano, A. (2015) DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes. Bioinformatics 31(24):4032--4."): could not find function "citeEntry" * 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 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 aecdf: no visible global function definition for 'quantile' aecdf: no visible global function definition for 'ecdf' aecdf: no visible global function definition for 'knots' aecdf: no visible global function definition for 'lm' aecdf: no visible global function definition for 'approxfun' aecdf : dnull: no visible global function definition for 'predict' aecdf : dnull: no visible global function definition for 'qnorm' conditionalInternal: no visible global function definition for 'p.adjust' conditionalInternal : <anonymous>: no visible global function definition for 'fisher.test' conditionalInternal: no visible global function definition for 'hclust' conditionalInternal: no visible global function definition for 'as.dist' conditionalInternal: no visible global function definition for 'cutree' conditionalInternal : <anonymous> : <anonymous> : <anonymous>: no visible global function definition for 'fisher.test' conditionalInternal : <anonymous> : <anonymous>: no visible global function definition for 'fisher.test' correlation : <anonymous>: no visible global function definition for 'cor' correlation: no visible global function definition for 'cor' cortest: no visible global function definition for 'pnorm' distMode: no visible global function definition for 'density' fet: no visible global function definition for 'fisher.test' internalMIfb: no visible global function definition for 'dnorm' mutualInfo: no visible global function definition for 'qnorm' mutualInfo: no visible global function definition for 'combn' mutualInfo: no visible global function definition for 'txtProgressBar' mutualInfo : <anonymous>: no visible global function definition for 'setTxtProgressBar' plothm: no visible global function definition for 'rgb2hsv' plothm: no visible global function definition for 'col2rgb' plothm: no visible global function definition for 'hsv' plothm: no visible global function definition for 'image' plothm: no visible global function definition for 'box' aqtl,diggit: no visible global function definition for 'p.adjust' aqtl,diggit: no visible global function definition for 'pnorm' conditional,diggit: no visible global function definition for 'p.adjust' conditional,diggit: no visible global function definition for 'pnorm' conditional,diggit: no visible global function definition for 'txtProgressBar' conditional,diggit : <anonymous>: no visible global function definition for 'setTxtProgressBar' marina,matrix: no visible global function definition for 'qnorm' mindyFiltering,diggit: no visible global function definition for 'p.adjust' plot,diggit-ANY: no visible global function definition for 'abline' plot,diggit-ANY: no visible global function definition for 'text' plot,diggit-ANY: no visible global function definition for 'axis' Undefined global functions or variables: abline approxfun as.dist axis box col2rgb combn cor cutree density dnorm ecdf fisher.test hclust hsv image knots lm p.adjust pnorm predict qnorm quantile rgb2hsv setTxtProgressBar text txtProgressBar Consider adding importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv") importFrom("graphics", "abline", "axis", "box", "image", "text") importFrom("stats", "approxfun", "as.dist", "cor", "cutree", "density", "dnorm", "ecdf", "fisher.test", "hclust", "knots", "lm", "p.adjust", "pnorm", "predict", "qnorm", "quantile") importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'plot' and siglist 'diggit,ANY' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'aecdf.Rd': aecdf Code: function(dnull, symmetric = FALSE, n = 100) Docs: function(dnull, symmetric = FALSE) Argument names in code not in docs: n * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed marina-methods 90.95 26.73 117.73 conditional-methods 16.53 2.11 18.64 diggit-plot 16.18 2.29 18.47 aqtl-methods 15.79 2.01 18.16 diggit-methods 5.03 0.36 5.40 * 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: 3 WARNINGs, 2 NOTEs See 'E:/biocbuild/bbs-3.21-bioc/meat/diggit.Rcheck/00check.log' for details.
diggit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL diggit ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'diggit' ... ** 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 (diggit)
diggit.Rcheck/diggit-Ex.timings
name | user | system | elapsed | |
aqtl-methods | 15.79 | 2.01 | 18.16 | |
conditional-methods | 16.53 | 2.11 | 18.64 | |
correlation | 0 | 0 | 0 | |
diggit-class | 1.43 | 0.03 | 1.47 | |
diggit-methods | 5.03 | 0.36 | 5.40 | |
diggit-plot | 16.18 | 2.29 | 18.47 | |
fcnv-methods | 2.00 | 0.03 | 2.03 | |
marina-methods | 90.95 | 26.73 | 117.73 | |
mutualInfo | 2.95 | 0.18 | 3.13 | |