Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:33:16 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the riboSeqR package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1529/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
riboSeqR 1.24.0 (landing page) Thomas J. Hardcastle
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: riboSeqR |
Version: 1.24.0 |
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:riboSeqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings riboSeqR_1.24.0.tar.gz |
StartedAt: 2021-05-06 06:13:18 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 06:16:12 -0400 (Thu, 06 May 2021) |
EllapsedTime: 174.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: riboSeqR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:riboSeqR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings riboSeqR_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/riboSeqR.Rcheck' * using R version 4.0.5 (2021-03-31) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'riboSeqR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'riboSeqR' 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 'riboSeqR' 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 .readAlignments : <anonymous>: no visible global function definition for 'read.delim' filterHits : <anonymous> : <anonymous>: no visible global function definition for 'chisq.test' frameCounting : getHits: no visible global function definition for 'queryHits' frameCounting : getHits: no visible global function definition for 'subjectHits' lengthDist: no visible global function definition for 'modifyList' lengthDist: no visible global function definition for 'rainbow' lengthDist: no visible binding for global variable 'lines' plotCDS: no visible global function definition for 'dev.list' plotCDS: no visible global function definition for 'par' plotCDS : <anonymous> : <anonymous> : makeMatz: no visible binding for global variable 'weighted.mean' plotCDS : <anonymous> : <anonymous>: no visible global function definition for 'barplot' plotCDS : <anonymous> : <anonymous>: no visible global function definition for 'rainbow' plotCDS : <anonymous> : <anonymous>: no visible global function definition for 'axis' plotFS: no visible global function definition for 'barplot' plotFS: no visible global function definition for 'rainbow' plotTranscript: no visible global function definition for 'dev.list' plotTranscript: no visible global function definition for 'par' plotTranscript: no visible global function definition for 'barplot' plotTranscript: no visible global function definition for 'axis' plotTranscript: no visible global function definition for 'rect' plotTranscript: no visible global function definition for 'text' plotTranscript: no visible global function definition for 'rgb' plotTranscript: no visible global function definition for 'segments' rnaCounts : <anonymous>: no visible global function definition for 'subjectHits' Undefined global functions or variables: axis barplot chisq.test dev.list lines modifyList par queryHits rainbow read.delim rect rgb segments subjectHits text weighted.mean Consider adding importFrom("grDevices", "dev.list", "rainbow", "rgb") importFrom("graphics", "axis", "barplot", "lines", "par", "rect", "segments", "text") importFrom("stats", "chisq.test", "weighted.mean") importFrom("utils", "modifyList", "read.delim") to your NAMESPACE file. * 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... Running 'runTests.R' 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 NOTE See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/riboSeqR.Rcheck/00check.log' for details.
riboSeqR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/riboSeqR_1.24.0.tar.gz && rm -rf riboSeqR.buildbin-libdir && mkdir riboSeqR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=riboSeqR.buildbin-libdir riboSeqR_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL riboSeqR_1.24.0.zip && rm riboSeqR_1.24.0.tar.gz riboSeqR_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 3546k 100 3546k 0 0 34.1M 0 --:--:-- --:--:-- --:--:-- 34.6M install for i386 * installing *source* package 'riboSeqR' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'riboSeqR' finding HTML links ... done filterHits html findCDS html frameCounting html frameShift html lengthDist html libScales html logoContext html plotCDS html plotTranscript html readRibodata html riboCoding-class html riboData-class html riboSeqR-package html rnaCounts html sliceCounts 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 'riboSeqR' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'riboSeqR' as riboSeqR_1.24.0.zip * DONE (riboSeqR) * installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library' package 'riboSeqR' successfully unpacked and MD5 sums checked
riboSeqR.Rcheck/tests_i386/runTests.Rout R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("riboSeqR") Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows RUNIT TEST PROTOCOL -- Thu May 06 06:16:02 2021 *********************************************** Number of test functions: 0 Number of errors: 0 Number of failures: 0 1 Test Suite : riboSeqR RUnit Tests - 0 test functions, 0 errors, 0 failures Number of test functions: 0 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 4.00 0.23 4.23 |
riboSeqR.Rcheck/tests_x64/runTests.Rout R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("riboSeqR") Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows RUNIT TEST PROTOCOL -- Thu May 06 06:16:08 2021 *********************************************** Number of test functions: 0 Number of errors: 0 Number of failures: 0 1 Test Suite : riboSeqR RUnit Tests - 0 test functions, 0 errors, 0 failures Number of test functions: 0 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 5.67 0.14 5.79 |
riboSeqR.Rcheck/examples_i386/riboSeqR-Ex.timings
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riboSeqR.Rcheck/examples_x64/riboSeqR-Ex.timings
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