CGHnormaliter 1.31.0
Bart P.P. van Houte
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CGHnormaliter | | Last Changed Rev: 129129 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 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 CGHnormaliter.buildbin-libdir CGHnormaliter.Rcheck && mkdir CGHnormaliter.buildbin-libdir CGHnormaliter.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CGHnormaliter.buildbin-libdir CGHnormaliter_1.31.0.tar.gz >CGHnormaliter.Rcheck\00install.out 2>&1 && cp CGHnormaliter.Rcheck\00install.out CGHnormaliter-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CGHnormaliter.buildbin-libdir --install="check:CGHnormaliter-install.out" --force-multiarch --no-vignettes --timings CGHnormaliter_1.31.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CGHnormaliter.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 'CGHnormaliter/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CGHnormaliter' version '1.31.0'
* 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 'CGHnormaliter' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'CGHbase' 'CGHcall'
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
** 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
.plotMA: no visible global function definition for 'pdf'
.plotMA: no visible global function definition for 'palette'
.plotMA: no visible global function definition for 'par'
.plotMA: no visible global function definition for 'plot'
.plotMA: no visible global function definition for 'title'
.plotMA: no visible global function definition for 'abline'
.plotMA: no visible global function definition for 'dev.off'
.readCghRaw: no visible global function definition for 'read.table'
.readCghRaw: no visible global function definition for 'make_cghRaw'
.runCGHcall: no visible global function definition for 'capture.output'
.runCGHcall: no visible global function definition for 'ExpandCGHcall'
CGHnormaliter: no visible binding for global variable 'segment'
CGHnormaliter: no visible global function definition for
'capture.output'
CGHnormaliter: no visible global function definition for 'normalize'
CGHnormaliter: no visible global function definition for
'postsegnormalize'
CGHnormaliter.write.table: no visible global function definition for
'segmented'
CGHnormaliter.write.table: no visible global function definition for
'calls'
Undefined global functions or variables:
ExpandCGHcall abline calls capture.output dev.off make_cghRaw
normalize palette par pdf plot postsegnormalize read.table segment
segmented title
Consider adding
importFrom("grDevices", "dev.off", "palette", "pdf")
importFrom("graphics", "abline", "par", "plot", "title")
importFrom("utils", "capture.output", "read.table")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
CGHnormaliter 47.28 0.04 47.5
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
CGHnormaliter 53.99 0.08 54.08
* 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-3.6-bioc/meat/CGHnormaliter.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'CGHnormaliter' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'CGHnormaliter' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CGHnormaliter' as CGHnormaliter_1.31.0.zip
* DONE (CGHnormaliter)