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BioC 2.14: CHECK report for HCsnip on moscato2

This page was generated on 2014-10-08 08:55:24 -0700 (Wed, 08 Oct 2014).

Package 381/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HCsnip 1.4.0
Askar Obulkasim
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/HCsnip
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: HCsnip
Version: 1.4.0
Command: rm -rf HCsnip.buildbin-libdir && mkdir HCsnip.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HCsnip.buildbin-libdir HCsnip_1.4.0.tar.gz >HCsnip-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=HCsnip.buildbin-libdir --install="check:HCsnip-install.out" --force-multiarch --no-vignettes --timings HCsnip_1.4.0.tar.gz
StartedAt: 2014-10-08 02:04:24 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 02:12:40 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 495.8 seconds
RetCode: 0
Status:  OK  
CheckDir: HCsnip.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf HCsnip.buildbin-libdir && mkdir HCsnip.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HCsnip.buildbin-libdir HCsnip_1.4.0.tar.gz >HCsnip-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=HCsnip.buildbin-libdir --install="check:HCsnip-install.out" --force-multiarch --no-vignettes --timings HCsnip_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/HCsnip.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HCsnip/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HCsnip' version '1.4.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'survival' 'coin' 'fpc' 'clusterRepro' 'impute' 'randomForestSRC'
  'sm' 'sigaR' 'Biobase'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'HCsnip' 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 ... NOTE
Packages in Depends field not imported from:
  'Biobase' 'clusterRepro' 'coin' 'fpc' 'impute' 'randomForestSRC'
  'sigaR' 'sm' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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' ... [179s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
TwoHC_perm   113.16   0.14  113.32
TwoHC_assign  48.25   0.00   48.25
** running examples for arch 'x64' ... [188s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
TwoHC_perm   113.96   0.16  114.13
TwoHC_assign  55.16   0.04   55.21
* 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

NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/HCsnip.Rcheck/00check.log'
for details.

HCsnip.Rcheck/00install.out:


install for i386

* installing *source* package 'HCsnip' ...
** 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 'HCsnip' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HCsnip' as HCsnip_1.4.0.zip
* DONE (HCsnip)

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

nameusersystemelapsed
BullingerLeukemia0.060.020.07
EnvioPlot0.330.000.33
HCsnipper1.770.001.78
RSF_eval2.520.002.54
TcgaGBM0.110.010.13
TwoHC_assign48.25 0.0048.25
TwoHC_perm113.16 0.14113.32
cluster_pred1.820.021.84
measure1.880.001.87
perm_test2.370.032.40
surv_measure1.900.001.91

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

nameusersystemelapsed
BullingerLeukemia0.110.000.11
EnvioPlot0.420.000.42
HCsnipper1.980.021.99
RSF_eval2.760.022.80
TcgaGBM0.160.000.15
TwoHC_assign55.16 0.0455.21
TwoHC_perm113.96 0.16114.13
cluster_pred1.760.001.76
measure1.710.001.72
perm_test2.280.012.29
surv_measure1.70.01.7