Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:57:54 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE subSeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1756/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
subSeq 1.18.0 Andrew J. Bass
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | NA | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK |
Package: subSeq |
Version: 1.18.0 |
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:subSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings subSeq_1.18.0.tar.gz |
StartedAt: 2020-10-17 08:41:41 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 08:46:59 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 317.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: subSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:subSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings subSeq_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/subSeq.Rcheck' * using R version 4.0.3 (2020-10-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'subSeq/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'subSeq' version '1.18.0' * 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 'subSeq' 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 ... 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 DESeq2: no visible global function definition for 'selectMethod' ccc: no visible global function definition for 'cov' ccc: no visible global function definition for 'var' generateSubsampledMatrix : <anonymous>: no visible global function definition for 'rbinom' plot.summary.subsamples: no visible binding for global variable 'metric' plot.summary.subsamples: no visible binding for global variable 'value' plot.summary.subsamples: no visible binding for global variable 'significant' plot.summary.subsamples: no visible binding for global variable 'percent' plot.summary.subsamples: no visible binding for global variable 'method' plot.summary.subsamples: no visible binding for global variable 'depth' plot.summary.subsamples: no visible binding for global variable 'average.depth' plot.summary.subsamples: no visible binding for global variable 'average.value' subsample: no visible binding for global variable 'proportion' subsample: no visible binding for global variable 'replication' subsample: no visible binding for global variable '.' subsample: no visible binding for global variable 'pvalue' summary.subsamples: no visible binding for global variable 'count' summary.subsamples: no visible binding for global variable 'method' summary.subsamples: no visible binding for global variable 'depth' summary.subsamples: no visible binding for global variable 'pvalue' summary.subsamples: no visible binding for global variable 'proportion' summary.subsamples: no visible binding for global variable 'replication' summary.subsamples: no visible global function definition for 'p.adjust' summary.subsamples: no visible binding for global variable 'ID' summary.subsamples: no visible binding for global variable 'padj' summary.subsamples: no visible binding for global variable 'coefficient' summary.subsamples: no visible binding for global variable 'o.coefficient' summary.subsamples: no visible global function definition for 'cor' summary.subsamples: no visible binding for global variable 'valid' summary.subsamples: no visible binding for global variable 'o.lfdr' summary.subsamples: no visible binding for global variable 'o.padj' summary.subsamples: no visible binding for global variable 'significant' summary.subsamples: no visible binding for global variable 'estFDP' summary.subsamples: no visible binding for global variable 'rFDP' summary.subsamples: no visible binding for global variable 'metric' summary.subsamples: no visible binding for global variable 'value' summary.subsamples: no visible binding for global variable 'percent' voomLimma: no visible global function definition for 'model.matrix' Undefined global functions or variables: . ID average.depth average.value coefficient cor count cov depth estFDP method metric model.matrix o.coefficient o.lfdr o.padj p.adjust padj percent proportion pvalue rFDP rbinom replication selectMethod significant valid value var Consider adding importFrom("methods", "selectMethod") importFrom("stats", "cor", "cov", "model.matrix", "p.adjust", "rbinom", "var") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed generateSubsampledMatrix 39.70 1.27 40.97 subsample 36.96 0.05 37.00 getSeed 36.05 0.04 36.13 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed generateSubsampledMatrix 46.22 0.45 46.72 getSeed 39.30 0.07 39.36 subsample 31.71 0.03 31.75 * 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 NOTE See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/subSeq.Rcheck/00check.log' for details.
subSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/subSeq_1.18.0.tar.gz && rm -rf subSeq.buildbin-libdir && mkdir subSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=subSeq.buildbin-libdir subSeq_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL subSeq_1.18.0.zip && rm subSeq_1.18.0.tar.gz subSeq_1.18.0.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 2774k 100 2774k 0 0 21.0M 0 --:--:-- --:--:-- --:--:-- 22.2M install for i386 * installing *source* package 'subSeq' ... ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'subSeq' finding HTML links ... done combineSubsamples html generateSubsampledMatrix html getSeed html hammer html plot.subsamples html plot.summary.subsamples html ss html subsample html summary.subsamples 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 'subSeq' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'subSeq' as subSeq_1.18.0.zip * DONE (subSeq) * installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library' package 'subSeq' successfully unpacked and MD5 sums checked
subSeq.Rcheck/examples_i386/subSeq-Ex.timings
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subSeq.Rcheck/examples_x64/subSeq-Ex.timings
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