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BioC 2.13: CHECK report for HCsnip on moscato1

This page was generated on 2014-04-05 09:51:16 -0700 (Sat, 05 Apr 2014).

Package 340/750HostnameOS / ArchBUILDCHECKBUILD BIN
HCsnip 1.2.0
Askar Obulkasim
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/HCsnip
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: HCsnip
Version: 1.2.0
Command: rm -rf HCsnip.buildbin-libdir && mkdir HCsnip.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HCsnip.buildbin-libdir HCsnip_1.2.0.tar.gz >HCsnip-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=HCsnip.buildbin-libdir --install="check:HCsnip-install.out" --force-multiarch --no-vignettes --timings HCsnip_1.2.0.tar.gz && mv HCsnip.buildbin-libdir/* HCsnip.Rcheck/ && rmdir HCsnip.buildbin-libdir
StartedAt: 2014-04-05 04:31:52 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:41:59 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 607.8 seconds
RetCode: 0
Status:  OK  
CheckDir: HCsnip.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/HCsnip.Rcheck'
* using R version 3.0.3 (2014-03-06)
* 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 '1.2.0'
* 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 '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
* 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 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'HCsnip.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [247s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
TwoHC_perm   141.63   0.27  141.96
TwoHC_assign  83.96   0.00   84.01
** running examples for arch 'x64' ... [241s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
TwoHC_perm   135.54   0.44  136.01
TwoHC_assign  80.98   0.01   81.06
* 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
  'D:/biocbld/bbs-2.13-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_1.2.0.zip
* DONE (HCsnip)

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

nameusersystemelapsed
BullingerLeukemia0.080.000.08
EnvioPlot0.490.000.49
HCsnipper1.990.022.01
RSF_eval3.260.013.46
TcgaGBM0.270.000.26
TwoHC_assign83.96 0.0084.01
TwoHC_perm141.63 0.27141.96
cluster_pred2.060.022.08
measure2.180.002.18
perm_test2.870.002.87
surv_measure2.130.012.14

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

nameusersystemelapsed
BullingerLeukemia0.230.020.25
EnvioPlot0.600.000.59
HCsnipper2.080.012.09
RSF_eval3.620.023.96
TcgaGBM0.180.000.19
TwoHC_assign80.98 0.0181.06
TwoHC_perm135.54 0.44136.01
cluster_pred2.960.022.98
measure3.140.003.14
perm_test2.930.042.98
surv_measure1.90.01.9