Stephen R. Piccolo
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/SCAN.UPC |
| Branch: RELEASE_3_9 |
| Last Commit: a91b021 |
| Last Changed Date: 2019-05-02 11:53:38 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:50:37 -0400 (Wed, 16 Oct 2019).
| Package 1460/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SCAN.UPC 2.26.0 Stephen R. Piccolo
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: SCAN.UPC |
| Version: 2.26.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SCAN.UPC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SCAN.UPC_2.26.0.tar.gz |
| StartedAt: 2019-10-16 06:34:21 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:39:48 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 326.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SCAN.UPC.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SCAN.UPC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SCAN.UPC_2.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SCAN.UPC.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SCAN.UPC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SCAN.UPC’ version ‘2.26.0’
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
‘/Users/biocbuild/bbs-3.9-bioc/meat/SCAN.UPC.Rcheck/00check.log’
for details.
SCAN.UPC.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SCAN.UPC
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘SCAN.UPC’ ...
** using staged installation
** 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
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
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)
================================================================================
** testing if installed package can be loaded from final location
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)
================================================================================
** testing if installed package keeps a record of temporary installation path
* DONE (SCAN.UPC)
SCAN.UPC.Rcheck/SCAN.UPC-Ex.timings
| name | user | system | elapsed | |
| InstallBrainArrayPackage | 0 | 0 | 0 | |
| ParseMetaFromGtfFile | 0.000 | 0.000 | 0.001 | |
| SCAN | 0.000 | 0.000 | 0.001 | |
| SCAN_TwoColor | 0.000 | 0.000 | 0.001 | |
| UPC_Generic_ExpressionSet | 0.000 | 0.001 | 0.001 | |
| UPC_RNASeq | 0 | 0 | 0 | |
| UPC_TwoColor | 0.000 | 0.001 | 0.001 | |