Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:36:35 -0400 (Wed, 17 Oct 2018).
Package 1319/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
SCAN.UPC 2.22.0 Stephen R. Piccolo
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: SCAN.UPC |
Version: 2.22.0 |
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SCAN.UPC.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SCAN.UPC_2.22.0.tar.gz |
StartedAt: 2018-10-17 04:40:44 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 04:45:20 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 276.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SCAN.UPC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SCAN.UPC.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SCAN.UPC_2.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/SCAN.UPC.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 'SCAN.UPC/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'SCAN.UPC' version '2.22.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'Biobase' 'oligo' 'Biostrings' 'GEOquery' 'affy' 'affyio' 'foreach' 'sva' 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 'SCAN.UPC' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT * 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 BatchAdjust: no visible global function definition for 'varLabels' BatchAdjust: no visible global function definition for 'exprs<-' BatchAdjust: no visible global function definition for 'pData' BatchAdjustFromFile: no visible global function definition for 'sampleNames' BatchAdjustFromFile: no visible global function definition for 'pData' BatchAdjustFromFile: no visible global function definition for 'varLabels' BatchAdjustFromFile: no visible global function definition for 'pData<-' InstallBrainArrayPackage: no visible global function definition for 'download.file' InstallBrainArrayPackage: no visible global function definition for 'install.packages' ProcessGtfSubset: no visible global function definition for 'IRanges' RS_BC: no visible global function definition for 'median' RS_BC: no visible global function definition for 'dlnorm' RS_BC: no visible global function definition for 'rlnorm' UPC_Generic_ExpressionSet: no visible global function definition for 'pData' UPC_Generic_ExpressionSet: no visible global function definition for 'featureData' UPC_Generic_ExpressionSet: no visible global function definition for 'DNAStringSet' UPC_Generic_ExpressionSet: no visible global function definition for 'exprs<-' UPC_RNASeq: no visible global function definition for 'runif' UPC_RNASeq: no visible global function definition for 'sampleNames<-' UPC_RNASeq: no visible global function definition for 'featureNames<-' UPC_nb: no visible global function definition for 'dnbinom' UPC_nn: no visible global function definition for 'median' UPC_nn: no visible global function definition for 'var' UPC_nn: no visible global function definition for 'dnorm' UPC_nn: no visible global function definition for 'rnorm' UPC_nn_bayes: no visible global function definition for 'median' UPC_nn_bayes: no visible global function definition for 'var' assign_bin: no visible global function definition for 'rnorm' channelNormalize: no visible global function definition for 'var' downloadBeadChipFromGEO: no visible global function definition for 'untar' downloadFromGEO: no visible global function definition for 'untar' iglNormalize: no visible global function definition for 'loess' madNormalize: no visible global function definition for 'median' processCelFiles: no visible global function definition for '%dopar%' processCelFiles: no visible global function definition for 'sampleNames<-' processCelFiles: no visible global function definition for 'featureNames<-' processTwoColor: no visible global function definition for 'sampleNames<-' processTwoColor: no visible global function definition for 'featureNames<-' readAgilentData: no visible global function definition for 'read.delim' Undefined global functions or variables: %dopar% DNAStringSet IRanges dlnorm dnbinom dnorm download.file exprs<- featureData featureNames<- install.packages loess median pData pData<- read.delim rlnorm rnorm runif sampleNames sampleNames<- untar var varLabels Consider adding importFrom("stats", "dlnorm", "dnbinom", "dnorm", "loess", "median", "rlnorm", "rnorm", "runif", "var") importFrom("utils", "download.file", "install.packages", "read.delim", "untar") 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 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 NOTEs See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/SCAN.UPC.Rcheck/00check.log' for details.
SCAN.UPC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/SCAN.UPC_2.22.0.tar.gz && rm -rf SCAN.UPC.buildbin-libdir && mkdir SCAN.UPC.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SCAN.UPC.buildbin-libdir SCAN.UPC_2.22.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL SCAN.UPC_2.22.0.zip && rm SCAN.UPC_2.22.0.tar.gz SCAN.UPC_2.22.0.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 274k 100 274k 0 0 3850k 0 --:--:-- --:--:-- --:--:-- 4216k install for i386 * installing *source* package 'SCAN.UPC' ... ** R ** inst ** byte-compile and prepare package for lazy loading Parallel computing support for 'oligo/crlmm': Disabled - Load 'ff' - Load and register a 'foreach' adaptor Example - Using 'multicore' for 2 cores: library(doMC) registerDoMC(2) ================================================================================ ** help *** installing help indices converting help for package 'SCAN.UPC' finding HTML links ... done BatchAdjust html BatchAdjustFromFile html InstallBrainArrayPackage html ParseMetaFromGtfFile html SCAN html SCAN_TwoColor html UPC_Generic html UPC_Generic_ExpressionSet html UPC_RNASeq html UPC_RNASeq_Single html UPC_TwoColor html ** building package indices ** installing vignettes ** testing if installed package can be loaded Parallel computing support for 'oligo/crlmm': Disabled - Load 'ff' - Load and register a 'foreach' adaptor Example - Using 'multicore' for 2 cores: library(doMC) registerDoMC(2) ================================================================================ In R CMD INSTALL install for x64 * installing *source* package 'SCAN.UPC' ... ** testing if installed package can be loaded Parallel computing support for 'oligo/crlmm': Disabled - Load 'ff' - Load and register a 'foreach' adaptor Example - Using 'multicore' for 2 cores: library(doMC) registerDoMC(2) ================================================================================ * MD5 sums packaged installation of 'SCAN.UPC' as SCAN.UPC_2.22.0.zip * DONE (SCAN.UPC) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library' package 'SCAN.UPC' successfully unpacked and MD5 sums checked In R CMD INSTALL
SCAN.UPC.Rcheck/examples_i386/SCAN.UPC-Ex.timings
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SCAN.UPC.Rcheck/examples_x64/SCAN.UPC-Ex.timings
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