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BioC 3.3: CHECK report for CINdex on moscato2

This page was generated on 2016-10-13 12:55:09 -0700 (Thu, 13 Oct 2016).

Package 190/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CINdex 1.0.2
Yuriy Gusev
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/CINdex
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  ERROR  skipped 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  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: CINdex
Version: 1.0.2
Command: rm -rf CINdex.buildbin-libdir CINdex.Rcheck && mkdir CINdex.buildbin-libdir CINdex.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CINdex.buildbin-libdir CINdex_1.0.2.tar.gz >CINdex.Rcheck\00install.out 2>&1 && cp CINdex.Rcheck\00install.out CINdex-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=CINdex.buildbin-libdir --install="check:CINdex-install.out" --force-multiarch --no-vignettes --timings CINdex_1.0.2.tar.gz
StartedAt: 2016-10-13 02:07:38 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 02:13:15 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 336.5 seconds
RetCode: 0
Status:  OK  
CheckDir: CINdex.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CINdex.buildbin-libdir CINdex.Rcheck && mkdir CINdex.buildbin-libdir CINdex.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CINdex.buildbin-libdir CINdex_1.0.2.tar.gz >CINdex.Rcheck\00install.out 2>&1 && cp CINdex.Rcheck\00install.out CINdex-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=CINdex.buildbin-libdir --install="check:CINdex-install.out" --force-multiarch --no-vignettes --timings CINdex_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/CINdex.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CINdex/DESCRIPTION' ... OK
* this is package 'CINdex' version '1.0.2'
* 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 'CINdex' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data  17.7Mb
* 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
comp.heatmap: no visible binding for global variable 'dataMatrix'
process.probe.anno: no visible binding for global variable 'ID'
process.probe.anno: no visible binding for global variable 'midpoint'
process.reference.genome: no visible binding for global variable
  'chrom'
process.reference.genome: no visible binding for global variable 'name'
process.reference.genome: no visible binding for global variable
  'stain'
Undefined global functions or variables:
  ID chrom dataMatrix midpoint name stain
* 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
run.cin.cyto 21.56   0.28    21.9
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
run.cin.cyto 24.02   0.44   24.51
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'RunTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'RunTests.R'
 OK
* 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
  'E:/biocbld/bbs-3.3-bioc/meat/CINdex.Rcheck/00check.log'
for details.


CINdex.Rcheck/00install.out:


install for i386

* installing *source* package 'CINdex' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'CINdex' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CINdex' as CINdex_1.0.2.zip
* DONE (CINdex)

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

nameusersystemelapsed
comp.heatmap1.000.071.08
extract.genes.in.cyto.regions2.840.112.98
run.cin.chr0.640.010.66
run.cin.cyto21.56 0.2821.90
ttest.cyto.cin.heatmap0.850.021.18

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

nameusersystemelapsed
comp.heatmap1.610.031.80
extract.genes.in.cyto.regions3.210.163.38
run.cin.chr0.380.010.39
run.cin.cyto24.02 0.4424.51
ttest.cyto.cin.heatmap1.050.031.11