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BioC 3.2: CHECK report for EBSeqHMM on moscato1

This page was generated on 2016-04-23 10:21:07 -0700 (Sat, 23 Apr 2016).

Package 304/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBSeqHMM 1.4.0
Ning Leng
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/EBSeqHMM
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ WARNINGS ] 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: EBSeqHMM
Version: 1.4.0
Command: rm -rf EBSeqHMM.buildbin-libdir EBSeqHMM.Rcheck && mkdir EBSeqHMM.buildbin-libdir EBSeqHMM.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EBSeqHMM.buildbin-libdir EBSeqHMM_1.4.0.tar.gz >EBSeqHMM.Rcheck\00install.out 2>&1 && cp EBSeqHMM.Rcheck\00install.out EBSeqHMM-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=EBSeqHMM.buildbin-libdir --install="check:EBSeqHMM-install.out" --force-multiarch --no-vignettes --timings EBSeqHMM_1.4.0.tar.gz
StartedAt: 2016-04-23 01:55:51 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:57:40 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 108.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: EBSeqHMM.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf EBSeqHMM.buildbin-libdir EBSeqHMM.Rcheck && mkdir EBSeqHMM.buildbin-libdir EBSeqHMM.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=EBSeqHMM.buildbin-libdir EBSeqHMM_1.4.0.tar.gz >EBSeqHMM.Rcheck\00install.out 2>&1 && cp EBSeqHMM.Rcheck\00install.out EBSeqHMM-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=EBSeqHMM.buildbin-libdir --install="check:EBSeqHMM-install.out" --force-multiarch --no-vignettes --timings EBSeqHMM_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/EBSeqHMM.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'EBSeqHMM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EBSeqHMM' 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 'EBSeqHMM' can be installed ... WARNING
Found the following significant warnings:
  Warning: package 'testthat' was built under R version 3.2.5
See 'D:/biocbld/bbs-3.2-bioc/meat/EBSeqHMM.Rcheck/00install.out' for details.
* 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 ... OK
* 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' ... [25s] OK
** running examples for arch 'x64' ... [28s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
GetAllPaths       5.90   0.00    5.89
EBSeqHMMTest      5.54   0.01    5.55
GetConfidentCalls 5.27   0.00    5.27
* 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
See
  'D:/biocbld/bbs-3.2-bioc/meat/EBSeqHMM.Rcheck/00check.log'
for details.


EBSeqHMM.Rcheck/00install.out:


install for i386

* installing *source* package 'EBSeqHMM' ...
** R
** data
** demo
** inst
** preparing package for lazy loading
Warning: package 'testthat' was built under R version 3.2.5
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'testthat' was built under R version 3.2.5

install for x64

* installing *source* package 'EBSeqHMM' ...
** testing if installed package can be loaded
Warning: package 'testthat' was built under R version 3.2.5
* MD5 sums
packaged installation of 'EBSeqHMM' as EBSeqHMM_1.4.0.zip
* DONE (EBSeqHMM)

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

nameusersystemelapsed
EBHMMNBMultiEM_2chain1.390.001.39
EBHMMNBfun0.080.010.09
EBHMMNBfunForMulti0.790.020.81
EBSeqHMM-package4.590.004.59
EBSeqHMMTest3.560.003.55
EBTest_ext0.220.000.22
GeneExampleData0.010.000.02
GetAllPaths3.780.013.79
GetConfidentCalls4.790.004.79
GetDECalls4.570.004.57
IsoExampleList000
LikefunNBHMM0.010.000.01
PlotExp0.020.000.02
beta.mom000
f0000

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

nameusersystemelapsed
EBHMMNBMultiEM_2chain1.250.001.25
EBHMMNBfun0.130.000.13
EBHMMNBfunForMulti0.750.000.75
EBSeqHMM-package4.110.004.12
EBSeqHMMTest5.540.015.55
EBTest_ext0.170.000.17
GeneExampleData0.000.020.02
GetAllPaths5.900.005.89
GetConfidentCalls5.270.005.27
GetDECalls4.50.04.5
IsoExampleList0.010.000.01
LikefunNBHMM0.020.000.02
PlotExp0.010.000.01
beta.mom000
f0000