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BioC 3.2: CHECK report for CGHnormaliter on windows1.bioconductor.org

This page was generated on 2015-10-27 17:28:58 -0400 (Tue, 27 Oct 2015).

Package 156/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGHnormaliter 1.24.0
Bart P.P. van Houte
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CGHnormaliter
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CGHnormaliter
Version: 1.24.0
Command: rm -rf CGHnormaliter.buildbin-libdir CGHnormaliter.Rcheck && mkdir CGHnormaliter.buildbin-libdir CGHnormaliter.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CGHnormaliter.buildbin-libdir CGHnormaliter_1.24.0.tar.gz >CGHnormaliter.Rcheck\00install.out 2>&1 && cp CGHnormaliter.Rcheck\00install.out CGHnormaliter-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=CGHnormaliter.buildbin-libdir --install="check:CGHnormaliter-install.out" --force-multiarch --no-vignettes --timings CGHnormaliter_1.24.0.tar.gz
StartedAt: 2015-10-27 00:25:06 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 00:28:19 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 192.7 seconds
RetCode: 0
Status:  OK  
CheckDir: CGHnormaliter.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CGHnormaliter.buildbin-libdir CGHnormaliter.Rcheck && mkdir CGHnormaliter.buildbin-libdir CGHnormaliter.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CGHnormaliter.buildbin-libdir CGHnormaliter_1.24.0.tar.gz >CGHnormaliter.Rcheck\00install.out 2>&1 && cp CGHnormaliter.Rcheck\00install.out CGHnormaliter-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=CGHnormaliter.buildbin-libdir --install="check:CGHnormaliter-install.out" --force-multiarch --no-vignettes --timings CGHnormaliter_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/CGHnormaliter.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.24.0'
* 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
.readCghRaw: no visible global function definition for 'make_cghRaw'
.runCGHcall: no visible global function definition for 'ExpandCGHcall'
CGHnormaliter: no visible binding for global variable 'segment'
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'
* 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' ... [67s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
CGHnormaliter 65.87   0.05   66.04
** running examples for arch 'x64' ... [79s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
CGHnormaliter 77.73   0.05   77.78
* 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:/biocbld/bbs-3.2-bioc/meat/CGHnormaliter.Rcheck/00check.log'
for details.


CGHnormaliter.Rcheck/00install.out:


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_1.24.0.zip
* DONE (CGHnormaliter)

CGHnormaliter.Rcheck/examples_i386/CGHnormaliter-Ex.timings:

nameusersystemelapsed
CGHnormaliter65.87 0.0566.04
CGHnormaliter.write.table0.250.000.25

CGHnormaliter.Rcheck/examples_x64/CGHnormaliter-Ex.timings:

nameusersystemelapsed
CGHnormaliter77.73 0.0577.78
CGHnormaliter.write.table0.250.000.25