Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:03 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the diggit package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 504/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
diggit 1.24.0 (landing page) Mariano J Alvarez
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: diggit |
Version: 1.24.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diggit.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings diggit_1.24.0.tar.gz |
StartedAt: 2021-10-14 22:21:06 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:27:29 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 383.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: diggit.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:diggit.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings diggit_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/diggit.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'diggit/DESCRIPTION' ... OK * this is package 'diggit' version '1.24.0' * 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 documentation object 'aecdf': 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed marina-methods 78.44 14.67 93.13 aqtl-methods 13.25 1.72 15.73 conditional-methods 12.69 2.08 14.76 diggit-plot 12.36 1.53 13.89 diggit-methods 6.81 0.25 7.12 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed marina-methods 73.31 17.49 90.81 conditional-methods 12.50 0.23 12.73 aqtl-methods 12.20 0.38 12.58 diggit-plot 12.30 0.24 12.53 diggit-methods 5.50 0.09 5.60 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... 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 'C:/Users/biocbuild/bbs-3.13-bioc/meat/diggit.Rcheck/00check.log' for details.
diggit.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/diggit_1.24.0.tar.gz && rm -rf diggit.buildbin-libdir && mkdir diggit.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=diggit.buildbin-libdir diggit_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL diggit_1.24.0.zip && rm diggit_1.24.0.tar.gz diggit_1.24.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 25785 100 25785 0 0 214k 0 --:--:-- --:--:-- --:--:-- 217k install for i386 * installing *source* package 'diggit' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'diggit' finding HTML links ... done aecdf html aqtl-methods html conditional-methods html correlation html diggit-class html diggit-methods html diggit-plot html fcnv-methods html marina-methods html mutualInfo html ** 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 install for x64 * installing *source* package 'diggit' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'diggit' as diggit_1.24.0.zip * DONE (diggit) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'diggit' successfully unpacked and MD5 sums checked
diggit.Rcheck/examples_i386/diggit-Ex.timings
|
diggit.Rcheck/examples_x64/diggit-Ex.timings
|