Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:37:46 -0400 (Wed, 17 Oct 2018).
Package 42/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ampliQueso 1.18.0 Michal Okoniewski
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: ampliQueso |
Version: 1.18.0 |
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ampliQueso.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ampliQueso_1.18.0.tar.gz |
StartedAt: 2018-10-17 00:28:28 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 00:34:07 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 338.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ampliQueso.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ampliQueso.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ampliQueso_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ampliQueso.Rcheck' * using R version 3.5.1 Patched (2018-07-24 r75005) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ampliQueso/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ampliQueso' version '1.18.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'rnaSeqMap' 'knitr' 'rgl' 'ggplot2' 'gplots' 'parallel' 'doParallel' 'foreach' 'VariantAnnotation' 'genefilter' 'statmod' 'xtable' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 'ampliQueso' 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 ... 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 ... NOTE Namespace in Imports field not imported from: 'samr' All declared Imports should be used. Packages in Depends field not imported from: 'VariantAnnotation' 'doParallel' 'foreach' 'genefilter' 'ggplot2' 'gplots' 'knitr' 'parallel' 'rgl' 'statmod' 'xtable' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' call which should be '::': 'rnaSeqMap:::newSeqReads' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .callCamelTestReg: no visible global function definition for 'permp' .callSamPileup: no visible global function definition for 'hasArg' .callSamPileup: no visible global function definition for 'readVcf' .callSamPileup: no visible global function definition for 'seqnames' .callSamPileup: no visible global function definition for 'start' .callSamPileup: no visible global function definition for 'ranges' .callSamPileup: no visible global function definition for 'end' .callSamPileup: no visible global function definition for 'width' .callSamPileup: no visible global function definition for 'ref' .callSamPileup: no visible global function definition for 'strand' .callSamPileup: no visible global function definition for 'qual' .camelTest: no visible global function definition for 'read.table' .camelTest: no visible binding for global variable 'str' .camelTest: no visible global function definition for 'permp' .camelTestParReg: no visible global function definition for 'read.table' .camelTestParReg: no visible global function definition for 'makeCluster' .camelTestParReg: no visible global function definition for 'detectCores' .camelTestParReg: no visible global function definition for 'registerDoParallel' .camelTestParReg: no visible global function definition for '%dopar%' .camelTestParReg: no visible global function definition for 'foreach' .camelTestParReg: no visible global function definition for 'stopCluster' .compareCoveragesRegApply: no visible global function definition for 'read.table' .compareCoveragesRegParM: no visible global function definition for 'read.table' .compareCoveragesRegParM: no visible global function definition for 'makeCluster' .compareCoveragesRegParM: no visible global function definition for 'detectCores' .compareCoveragesRegParM: no visible global function definition for 'registerDoParallel' .compareCoveragesRegParM: no visible global function definition for '%dopar%' .compareCoveragesRegParM: no visible global function definition for 'foreach' .compareCoveragesRegParM: no visible global function definition for 'stopCluster' .compareCoveragesRegParR: no visible global function definition for 'read.table' .compareCoveragesRegParR: no visible global function definition for 'makeCluster' .compareCoveragesRegParR: no visible global function definition for 'detectCores' .compareCoveragesRegParR: no visible global function definition for 'registerDoParallel' .compareCoveragesRegParR: no visible global function definition for '%dopar%' .compareCoveragesRegParR: no visible global function definition for 'foreach' .compareCoveragesRegParR: no visible global function definition for 'stopCluster' .compareCoveragesRegSeq: no visible global function definition for 'read.table' .getSNP: no visible global function definition for 'read.table' .getSNP: no visible global function definition for 'hasArg' .getSNP: no visible global function definition for 'readVcf' .getSNP: no visible global function definition for 'seqnames' .getSNP: no visible global function definition for 'start' .getSNP: no visible global function definition for 'ranges' .getSNP: no visible global function definition for 'end' .getSNP: no visible global function definition for 'width' .getSNP: no visible global function definition for 'ref' .getSNP: no visible global function definition for 'strand' .getSNP: no visible global function definition for 'qual' .getSNPPar: no visible global function definition for 'makeCluster' .getSNPPar: no visible global function definition for 'detectCores' .getSNPPar: no visible global function definition for 'registerDoParallel' .getSNPPar: no visible global function definition for 'read.table' .getSNPPar: no visible global function definition for '%dopar%' .getSNPPar: no visible global function definition for 'foreach' .getSNPPar: no visible global function definition for 'stopCluster' .perm.samples: no visible global function definition for 'combn' compareCoverages: no visible global function definition for 'read.table' getCountTable: no visible global function definition for 'read.table' runAQReport: no visible global function definition for 'read.table' runAQReport: no visible global function definition for 'rowttests' runAQReport: no visible global function definition for 'p.adjust' runAQReport: no visible global function definition for '%do%' runAQReport: no visible global function definition for 'foreach' runAQReport: no visible global function definition for 'aggregate' runAQReport: no visible global function definition for 'knit' Undefined global functions or variables: %do% %dopar% aggregate combn detectCores end foreach hasArg knit makeCluster p.adjust permp qual ranges read.table readVcf ref registerDoParallel rowttests seqnames start stopCluster str strand width Consider adding importFrom("methods", "hasArg") importFrom("stats", "aggregate", "end", "p.adjust", "start") importFrom("utils", "combn", "read.table", "str") 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' ... WARNING Found the following significant warnings: Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/ampliQueso', resetting ** running examples for arch 'x64' ... WARNING Found the following significant warnings: Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/ampliQueso', resetting * 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: 2 WARNINGs, 4 NOTEs See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ampliQueso.Rcheck/00check.log' for details.
ampliQueso.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/ampliQueso_1.18.0.tar.gz && rm -rf ampliQueso.buildbin-libdir && mkdir ampliQueso.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ampliQueso.buildbin-libdir ampliQueso_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ampliQueso_1.18.0.zip && rm ampliQueso_1.18.0.tar.gz ampliQueso_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 2051k 100 2051k 0 0 25.3M 0 --:--:-- --:--:-- --:--:-- 27.8M install for i386 * installing *source* package 'ampliQueso' ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'ampliQueso' finding HTML links ... done camelSampleTable html camelTest html compareCoverages html compareCoveragesReg html getCountTable html getSNP html ndMax html ndMin html runAQReport html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'ampliQueso' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'ampliQueso' as ampliQueso_1.18.0.zip * DONE (ampliQueso) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library' package 'ampliQueso' successfully unpacked and MD5 sums checked In R CMD INSTALL
ampliQueso.Rcheck/examples_i386/ampliQueso-Ex.timings
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ampliQueso.Rcheck/examples_x64/ampliQueso-Ex.timings
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