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BioC 3.1: CHECK report for SPEM on moscato2

This page was generated on 2015-10-09 09:30:16 -0700 (Fri, 09 Oct 2015).

Package 932/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPEM 1.8.0
Xinyi YANG
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/SPEM
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SPEM
Version: 1.8.0
Command: rm -rf SPEM.buildbin-libdir SPEM.Rcheck && mkdir SPEM.buildbin-libdir SPEM.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SPEM.buildbin-libdir SPEM_1.8.0.tar.gz >SPEM.Rcheck\00install.out 2>&1 && cp SPEM.Rcheck\00install.out SPEM-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=SPEM.buildbin-libdir --install="check:SPEM-install.out" --force-multiarch --no-vignettes --timings SPEM_1.8.0.tar.gz
StartedAt: 2015-10-09 06:27:07 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 06:28:56 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 108.5 seconds
RetCode: 0
Status:  OK  
CheckDir: SPEM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SPEM.buildbin-libdir SPEM.Rcheck && mkdir SPEM.buildbin-libdir SPEM.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SPEM.buildbin-libdir SPEM_1.8.0.tar.gz >SPEM.Rcheck\00install.out 2>&1 && cp SPEM.Rcheck\00install.out SPEM-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=SPEM.buildbin-libdir --install="check:SPEM-install.out" --force-multiarch --no-vignettes --timings SPEM_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/SPEM.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SPEM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SPEM' version '1.8.0'
* 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 'SPEM' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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' 'Rsolnp' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
opt_parameter: no visible global function definition for 'solnp'
SPEM,ExpressionSet: no visible global function definition for 'exprs'
SPEM,ExpressionSet: no visible global function definition for 'pData'
row_optimize,ExpressionSet: no visible global function definition for
  'exprs'
s_diff,ExpressionSet: no visible global function definition for 'exprs'
s_diff,ExpressionSet: no visible global function definition for 'pData'
* 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' ... [21s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
row_optimize 19.34   0.02   19.37
** running examples for arch 'x64' ... [45s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
row_optimize 42.96      0   42.96
* 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: 3 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/SPEM.Rcheck/00check.log'
for details.


SPEM.Rcheck/00install.out:


install for i386

* installing *source* package 'SPEM' ...
** 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 'SPEM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SPEM' as SPEM_1.8.0.zip
* DONE (SPEM)

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

nameusersystemelapsed
SPEM0.240.000.23
row_optimize19.34 0.0219.37
s_diff0.160.000.16
sos000

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

nameusersystemelapsed
SPEM0.390.000.39
row_optimize42.96 0.0042.96
s_diff0.200.000.21
sos0.020.000.01