Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:19:06 -0400 (Wed, 16 Oct 2019).
Package 1212/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
pickgene 1.56.0 Brian S. Yandell
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: pickgene |
Version: 1.56.0 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pickgene.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings pickgene_1.56.0.tar.gz |
StartedAt: 2019-10-16 05:59:12 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 05:59:43 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 30.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: pickgene.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pickgene.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings pickgene_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/pickgene.Rcheck' * using R version 3.6.1 (2019-07-05) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'pickgene/DESCRIPTION' ... OK * this is package 'pickgene' version '1.56.0' * 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 'pickgene' can be installed ... WARNING Found the following significant warnings: Note: possible error in 'oddsplot(exp(data[[x]]), ': unused argument (chip = "") See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/pickgene.Rcheck/00install.out' for details. Information on the location(s) of code generating the 'Note's can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to 'yes'. * 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 * 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 do.oddsplot: warning in em.ggb(data[[conditions[1]]], data[[conditions[2]]], theta, theta[1:3], print = TRUE): partial argument match of 'print' to 'printit' pickgene.poly: warning in pickgene.two(y[, i], intensity, geneid = geneID, singlelevel = singlelevel, npick = npickgene, ylab = ylabs[i], ...): partial argument match of 'npick' to 'npickgene' lod.plot: possible error in oddsplot(exp(data[[x]]), exp(data[[y]]), theta, col = col, xlab = xlab, ylab = ylab, chip = ""): unused argument (chip = "") nloglik: no visible binding for global variable '.fit.xx' nloglik: no visible binding for global variable '.fit.yy' nploglik: no visible binding for global variable '.fit.xx' nploglik: no visible binding for global variable '.fit.yy' nploglik: no visible binding for global variable '.fit.zz' s.check1: no visible global function definition for 'lod' s.marg: no visible binding for global variable 'x' shrinkplot: no visible global function definition for 's.fits' shrinkplot: no visible binding for global variable 'lims' Undefined global functions or variables: .fit.xx .fit.yy .fit.zz lims lod s.fits x * checking Rd files ... NOTE prepare_Rd: Simulation.pickgene.Rd:8: Dropping empty section \keyword prepare_Rd: Simulation.pickgene.Rd:5-6: Dropping empty section \usage prepare_Rd: Simulation.pickgene.Rd:7: Dropping empty section \details * 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * 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: 1 WARNING, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/pickgene.Rcheck/00check.log' for details.
pickgene.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/pickgene_1.56.0.tar.gz && rm -rf pickgene.buildbin-libdir && mkdir pickgene.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pickgene.buildbin-libdir pickgene_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL pickgene_1.56.0.zip && rm pickgene_1.56.0.tar.gz pickgene_1.56.0.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 33382 100 33382 0 0 407k 0 --:--:-- --:--:-- --:--:-- 440k install for i386 * installing *source* package 'pickgene' ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading Note: possible error in 'oddsplot(exp(data[[x]]), ': unused argument (chip = "") ** help *** installing help indices converting help for package 'pickgene' finding HTML links ... done Simulation.pickgene html em.ggb html model.pickgene html oddsplot html pickgene-internal html pickgene html robustscale 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 'pickgene' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'pickgene' as pickgene_1.56.0.zip * DONE (pickgene) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'pickgene' successfully unpacked and MD5 sums checked
pickgene.Rcheck/examples_i386/pickgene-Ex.timings
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pickgene.Rcheck/examples_x64/pickgene-Ex.timings
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