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BioC 3.0: CHECK report for COHCAP on moscato1

This page was generated on 2015-04-10 09:49:58 -0700 (Fri, 10 Apr 2015).

Package 188/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COHCAP 1.4.0
Charles Warden
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/COHCAP
Last Changed Rev: 98405 / Revision: 102249
Last Changed Date: 2015-01-16 11:24:50 -0800 (Fri, 16 Jan 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: COHCAP
Version: 1.4.0
Command: rm -rf COHCAP.buildbin-libdir COHCAP.Rcheck && mkdir COHCAP.buildbin-libdir COHCAP.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=COHCAP.buildbin-libdir COHCAP_1.4.0.tar.gz >COHCAP.Rcheck\00install.out 2>&1 && cp COHCAP.Rcheck\00install.out COHCAP-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=COHCAP.buildbin-libdir --install="check:COHCAP-install.out" --force-multiarch --no-vignettes --timings COHCAP_1.4.0.tar.gz
StartedAt: 2015-04-10 00:03:10 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:05:27 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 137.5 seconds
RetCode: 0
Status:  OK  
CheckDir: COHCAP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf COHCAP.buildbin-libdir COHCAP.Rcheck && mkdir COHCAP.buildbin-libdir COHCAP.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=COHCAP.buildbin-libdir COHCAP_1.4.0.tar.gz >COHCAP.Rcheck\00install.out 2>&1 && cp COHCAP.Rcheck\00install.out COHCAP-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=COHCAP.buildbin-libdir --install="check:COHCAP-install.out" --force-multiarch --no-vignettes --timings COHCAP_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/COHCAP.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'COHCAP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'COHCAP' version '1.4.0'
* 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 'COHCAP' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
COHCAP.annotate: no visible binding for global variable
  'COHCAP.450k.UCSC'
COHCAP.annotate: no visible binding for global variable
  'COHCAP.450k.HMM'
COHCAP.annotate: no visible binding for global variable 'COHCAP.27k'
COHCAP.avg.by.site: no visible binding for global variable
  'integrate.folder'
COHCAP.integrate.avg.by.island: no visible binding for global variable
  'na.rm'
cor.test.est: no visible binding for global variable 'na.rm'
cor.test.pvalue: no visible binding for global variable 'na.rm'
* 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' ... [58s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
COHCAP.annotate                2.61   0.06   10.54
COHCAP.site                    2.44   0.05    6.76
COHCAP.avg.by.island           2.38   0.09    8.51
COHCAP.integrate.avg.by.site   2.19   0.10    8.60
COHCAP.avg.by.site             2.09   0.08    7.61
COHCAP.integrate.avg.by.island 1.87   0.06   11.71
** running examples for arch 'x64' ... [47s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
COHCAP.integrate.avg.by.site   3.12   0.09    9.80
COHCAP.avg.by.island           2.48   0.09    7.80
COHCAP.integrate.avg.by.island 2.37   0.03   10.18
COHCAP.avg.by.site             2.29   0.02    8.43
* 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

NOTE: There was 1 note.
See
  'D:/biocbld/bbs-3.0-bioc/meat/COHCAP.Rcheck/00check.log'
for details.

COHCAP.Rcheck/00install.out:


install for i386

* installing *source* package 'COHCAP' ...
** R
** 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 'COHCAP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'COHCAP' as COHCAP_1.4.0.zip
* DONE (COHCAP)

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

nameusersystemelapsed
COHCAP.BSSeq.preprocess0.000.000.31
COHCAP.annotate 2.61 0.0610.54
COHCAP.avg.by.island2.380.098.51
COHCAP.avg.by.site2.090.087.61
COHCAP.integrate.avg.by.island 1.87 0.0611.71
COHCAP.integrate.avg.by.site2.190.108.60
COHCAP.qc1.710.013.15
COHCAP.site2.440.056.76

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

nameusersystemelapsed
COHCAP.BSSeq.preprocess0.000.000.09
COHCAP.annotate2.390.023.49
COHCAP.avg.by.island2.480.097.80
COHCAP.avg.by.site2.290.028.43
COHCAP.integrate.avg.by.island 2.37 0.0310.18
COHCAP.integrate.avg.by.site3.120.099.80
COHCAP.qc1.420.052.26
COHCAP.site2.410.084.98