Stephen R. Piccolo
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/SCAN.UPC |
| Branch: master |
| Last Commit: 529fbde |
| Last Changed Date: 2019-01-04 13:12:20 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:01:12 -0400 (Tue, 09 Apr 2019).
| Package 1432/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SCAN.UPC 2.25.1 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: SCAN.UPC |
| Version: 2.25.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SCAN.UPC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SCAN.UPC_2.25.1.tar.gz |
| StartedAt: 2019-04-09 05:45:52 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 05:50:20 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 267.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SCAN.UPC.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SCAN.UPC.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SCAN.UPC_2.25.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SCAN.UPC.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '2.25.1'
* 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
* 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-3.9-bioc/meat/SCAN.UPC.Rcheck/00check.log'
for details.
SCAN.UPC.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SCAN.UPC_2.25.1.tar.gz && rm -rf SCAN.UPC.buildbin-libdir && mkdir SCAN.UPC.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SCAN.UPC.buildbin-libdir SCAN.UPC_2.25.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SCAN.UPC_2.25.1.zip && rm SCAN.UPC_2.25.1.tar.gz SCAN.UPC_2.25.1.zip
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% 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 3516k 0 --:--:-- --:--:-- --:--:-- 3860k
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 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
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_2.25.1.zip
* DONE (SCAN.UPC)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SCAN.UPC' successfully unpacked and MD5 sums checked
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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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