Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.5: CHECK report for CINdex on tokay2

This page was generated on 2017-10-06 14:07:54 -0400 (Fri, 06 Oct 2017).

Package 222/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CINdex 1.4.0
Yuriy Gusev
Snapshot Date: 2017-10-05 23:41:59 -0400 (Thu, 05 Oct 2017)
URL: https://git.bioconductor.org/packages/CINdex
Last Commit: 4ed3640
Last Changed Date: 2017-04-24 15:45:44 -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 [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CINdex
Version: 1.4.0
Command: rm -rf CINdex.buildbin-libdir CINdex.Rcheck && mkdir CINdex.buildbin-libdir CINdex.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CINdex.buildbin-libdir CINdex_1.4.0.tar.gz >CINdex.Rcheck\00install.out 2>&1 && cp CINdex.Rcheck\00install.out CINdex-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CINdex.buildbin-libdir --install="check:CINdex-install.out" --force-multiarch --no-vignettes --timings CINdex_1.4.0.tar.gz
StartedAt: 2017-10-06 07:46:54 -0400 (Fri, 06 Oct 2017)
EndedAt: 2017-10-06 07:51:03 -0400 (Fri, 06 Oct 2017)
EllapsedTime: 249.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: CINdex.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CINdex.buildbin-libdir CINdex.Rcheck && mkdir CINdex.buildbin-libdir CINdex.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CINdex.buildbin-libdir CINdex_1.4.0.tar.gz >CINdex.Rcheck\00install.out 2>&1 && cp CINdex.Rcheck\00install.out CINdex-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CINdex.buildbin-libdir --install="check:CINdex-install.out" --force-multiarch --no-vignettes --timings CINdex_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CINdex.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 'CINdex/DESCRIPTION' ... OK
* this is package 'CINdex' 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 'CINdex' can be installed ... WARNING
Found the following significant warnings:
  Warning: package 'GenomicRanges' was built under R version 3.4.2
See 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CINdex.Rcheck/00install.out' for details.
* 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 15.55   0.53   16.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
run.cin.cyto 15.42   0.56   15.98
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-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
Warning: package 'GenomicRanges' was built under R version 3.4.2
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'GenomicRanges' was built under R version 3.4.2

install for x64

* installing *source* package 'CINdex' ...
** testing if installed package can be loaded
Warning: package 'GenomicRanges' was built under R version 3.4.2
* MD5 sums
packaged installation of 'CINdex' as CINdex_1.4.0.zip
* DONE (CINdex)

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

nameusersystemelapsed
comp.heatmap0.810.050.86
extract.genes.in.cyto.regions1.890.091.98
run.cin.chr0.480.030.51
run.cin.cyto15.55 0.5316.08
ttest.cyto.cin.heatmap0.700.010.71

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

nameusersystemelapsed
comp.heatmap1.090.051.14
extract.genes.in.cyto.regions2.020.112.13
run.cin.chr0.640.000.64
run.cin.cyto15.42 0.5615.98
ttest.cyto.cin.heatmap0.820.060.88