SCAN.UPC 2.19.1
Stephen R. Piccolo
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SCAN.UPC | | Last Changed Rev: 129937 / Revision: 131943 | | Last Changed Date: 2017-05-27 11:52:24 -0400 (Sat, 27 May 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf SCAN.UPC.buildbin-libdir SCAN.UPC.Rcheck && mkdir SCAN.UPC.buildbin-libdir SCAN.UPC.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SCAN.UPC.buildbin-libdir SCAN.UPC_2.19.1.tar.gz >SCAN.UPC.Rcheck\00install.out 2>&1 && cp SCAN.UPC.Rcheck\00install.out SCAN.UPC-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SCAN.UPC.buildbin-libdir --install="check:SCAN.UPC-install.out" --force-multiarch --no-vignettes --timings SCAN.UPC_2.19.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SCAN.UPC.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '2.19.1'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... 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-3.6-bioc/meat/SCAN.UPC.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'SCAN.UPC' ...
** R
** inst
** preparing 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
** 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)
================================================================================
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_2.19.1.zip
* DONE (SCAN.UPC)