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BioC 3.5: CHECK report for COHCAP on tokay2

This page was generated on 2017-08-16 13:22:54 -0400 (Wed, 16 Aug 2017).

Package 262/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COHCAP 1.20.0
Charles Warden
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/COHCAP
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: COHCAP
Version: 1.20.0
Command: rm -rf COHCAP.buildbin-libdir COHCAP.Rcheck && mkdir COHCAP.buildbin-libdir COHCAP.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=COHCAP.buildbin-libdir COHCAP_1.20.0.tar.gz >COHCAP.Rcheck\00install.out 2>&1 && cp COHCAP.Rcheck\00install.out COHCAP-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=COHCAP.buildbin-libdir --install="check:COHCAP-install.out" --force-multiarch --no-vignettes --timings COHCAP_1.20.0.tar.gz
StartedAt: 2017-08-15 22:52:31 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:54:33 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 122.1 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 && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=COHCAP.buildbin-libdir COHCAP_1.20.0.tar.gz >COHCAP.Rcheck\00install.out 2>&1 && cp COHCAP.Rcheck\00install.out COHCAP-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=COHCAP.buildbin-libdir --install="check:COHCAP-install.out" --force-multiarch --no-vignettes --timings COHCAP_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/COHCAP.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 'COHCAP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'COHCAP' version '1.20.0'
* 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 'ref'
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'
Undefined global functions or variables:
  COHCAP.27k COHCAP.450k.HMM COHCAP.450k.UCSC na.rm ref
* 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
COHCAP.avg.by.island           4.49   0.09    7.89
COHCAP.integrate.avg.by.island 3.04   0.19    9.06
COHCAP.avg.by.site             2.70   0.03    5.88
COHCAP.denovo                  2.63   0.08    5.11
COHCAP.integrate.avg.by.site   2.55   0.11    6.69
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
COHCAP.avg.by.island           3.75   0.15    7.28
COHCAP.integrate.avg.by.island 3.00   0.16    8.43
COHCAP.integrate.avg.by.site   2.66   0.06    6.93
COHCAP.avg.by.site             2.58   0.10    5.77
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-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_1.20.0.zip
* DONE (COHCAP)

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

nameusersystemelapsed
COHCAP.BSSeq.preprocess0.030.000.15
COHCAP.annotate2.240.063.11
COHCAP.avg.by.island4.490.097.89
COHCAP.avg.by.site2.700.035.88
COHCAP.denovo2.630.085.11
COHCAP.integrate.avg.by.island3.040.199.06
COHCAP.integrate.avg.by.site2.550.116.69
COHCAP.qc1.360.062.09
COHCAP.site2.410.054.67

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

nameusersystemelapsed
COHCAP.BSSeq.preprocess0.000.020.13
COHCAP.annotate2.080.052.78
COHCAP.avg.by.island3.750.157.28
COHCAP.avg.by.site2.580.105.77
COHCAP.denovo2.290.044.90
COHCAP.integrate.avg.by.island3.000.168.43
COHCAP.integrate.avg.by.site2.660.066.93
COHCAP.qc1.640.022.30
COHCAP.site2.630.124.83