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BioC 3.0: CHECK report for BaseSpaceR on moscato1

This page was generated on 2015-03-31 09:49:26 -0700 (Tue, 31 Mar 2015).

Package 68/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BaseSpaceR 1.10.0
Adrian Alexa
Snapshot Date: 2015-03-30 16:20:12 -0700 (Mon, 30 Mar 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/BaseSpaceR
Last Changed Rev: 95439 / Revision: 101626
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: BaseSpaceR
Version: 1.10.0
Command: rm -rf BaseSpaceR.buildbin-libdir BaseSpaceR.Rcheck && mkdir BaseSpaceR.buildbin-libdir BaseSpaceR.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BaseSpaceR.buildbin-libdir BaseSpaceR_1.10.0.tar.gz >BaseSpaceR.Rcheck\00install.out 2>&1 && cp BaseSpaceR.Rcheck\00install.out BaseSpaceR-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=BaseSpaceR.buildbin-libdir --install="check:BaseSpaceR-install.out" --force-multiarch --no-vignettes --timings BaseSpaceR_1.10.0.tar.gz
StartedAt: 2015-03-30 22:50:16 -0700 (Mon, 30 Mar 2015)
EndedAt: 2015-03-30 22:51:47 -0700 (Mon, 30 Mar 2015)
EllapsedTime: 91.1 seconds
RetCode: 0
Status:  OK  
CheckDir: BaseSpaceR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BaseSpaceR.buildbin-libdir BaseSpaceR.Rcheck && mkdir BaseSpaceR.buildbin-libdir BaseSpaceR.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BaseSpaceR.buildbin-libdir BaseSpaceR_1.10.0.tar.gz >BaseSpaceR.Rcheck\00install.out 2>&1 && cp BaseSpaceR.Rcheck\00install.out BaseSpaceR-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=BaseSpaceR.buildbin-libdir --install="check:BaseSpaceR-install.out" --force-multiarch --no-vignettes --timings BaseSpaceR_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/BaseSpaceR.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BaseSpaceR/DESCRIPTION' ... OK
* this is package 'BaseSpaceR' version '1.10.0'
* 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 'BaseSpaceR' 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
'library' or 'require' call to 'Rsamtools' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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 ... NOTE
asBamFile: no visible global function definition for 'BamFile'
* 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' ... [19s] OK
** running examples for arch 'x64' ... [16s] 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/BaseSpaceR.Rcheck/00check.log'
for details.

BaseSpaceR.Rcheck/00install.out:


install for i386

* installing *source* package 'BaseSpaceR' ...
** 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 'BaseSpaceR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BaseSpaceR' as BaseSpaceR_1.10.0.zip
* DONE (BaseSpaceR)

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

nameusersystemelapsed
AppAuth-class0.280.054.84
AppResults-class000
AppSessionAuth000
AppSessions-class000
Coverage0.010.000.02
Error000
Files-class0.130.001.57
FilesExtra0.120.011.31
Genomes-class0.170.002.26
Projects-class0.130.001.48
Response-class000
Runs-class0.210.001.72
Samples-class0.500.023.46
ServiceURI-class000
Users-class0.130.000.74
Variants0.150.000.81
data-aAuth0.060.000.34

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

nameusersystemelapsed
AppAuth-class0.310.061.97
AppResults-class000
AppSessionAuth000
AppSessions-class0.020.000.01
Coverage000
Error000
Files-class0.070.000.92
FilesExtra0.110.000.87
Genomes-class0.110.001.64
Projects-class0.090.001.79
Response-class000
Runs-class0.190.002.34
Samples-class0.260.003.29
ServiceURI-class000
Users-class0.130.000.86
Variants0.090.000.86
data-aAuth0.050.000.44