frma 1.28.0
Matthew N. McCall
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/frma | | Branch: RELEASE_3_5 | | Last Commit: ed8c459 | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf frma.buildbin-libdir frma.Rcheck && mkdir frma.buildbin-libdir frma.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=frma.buildbin-libdir frma_1.28.0.tar.gz >frma.Rcheck\00install.out 2>&1 && cp frma.Rcheck\00install.out frma-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=frma.buildbin-libdir --install="check:frma-install.out" --force-multiarch --no-vignettes --timings frma_1.28.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/frma.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'frma/DESCRIPTION' ... OK
* this is package 'frma' version '1.28.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'frma' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'Biobase'
A package should be listed in only one of these fields.
* 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
GNUSE: no visible binding for global variable 'median'
GNUSE: no visible binding for global variable 'quantile'
GNUSE: no visible global function definition for 'boxplot'
barcode: no visible global function definition for 'pnorm'
batchFit: no visible global function definition for 'median'
coerce<-,frmaExpressionSet-ExpressionSet: no visible global function
definition for 'slot<-'
coerce<-,frmaExpressionSet-ExpressionSet: no visible global function
definition for 'slot'
randomeffects<-,frmaExpressionSet: no visible global function
definition for 'validObject'
residuals<-,frmaExpressionSet: no visible global function definition
for 'validObject'
se.exprs<-,ExpressionSet: no visible global function definition for
'validObject'
se.exprs<-,frmaExpressionSet: no visible global function definition for
'validObject'
weights<-,frmaExpressionSet: no visible global function definition for
'validObject'
Undefined global functions or variables:
boxplot median pnorm quantile slot slot<- validObject
Consider adding
importFrom("graphics", "boxplot")
importFrom("methods", "slot", "slot<-", "validObject")
importFrom("stats", "median", "pnorm", "quantile")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GNUSE 13.64 0.25 16.28
barcode 9.58 0.11 9.83
frma 7.39 0.08 7.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GNUSE 18.79 0.19 19.01
barcode 12.49 0.50 13.00
frma 12.31 0.14 12.45
* 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 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/frma.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'frma' ...
** R
** inst
** preparing package for lazy loading
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'oligoClasses'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'oligoClasses'
install for x64
* installing *source* package 'frma' ...
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'oligoClasses'
* MD5 sums
packaged installation of 'frma' as frma_1.28.0.zip
* DONE (frma)