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BioC 3.1: CHECK report for gQTLBase on moscato2

This page was generated on 2015-10-09 09:31:54 -0700 (Fri, 09 Oct 2015).

Package 432/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gQTLBase 1.0.0
VJ Carey
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/gQTLBase
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  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gQTLBase
Version: 1.0.0
Command: rm -rf gQTLBase.buildbin-libdir gQTLBase.Rcheck && mkdir gQTLBase.buildbin-libdir gQTLBase.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gQTLBase.buildbin-libdir gQTLBase_1.0.0.tar.gz >gQTLBase.Rcheck\00install.out 2>&1 && cp gQTLBase.Rcheck\00install.out gQTLBase-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=gQTLBase.buildbin-libdir --install="check:gQTLBase-install.out" --force-multiarch --no-vignettes --timings gQTLBase_1.0.0.tar.gz
StartedAt: 2015-10-09 02:33:36 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 02:47:54 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 857.8 seconds
RetCode: 0
Status:  OK  
CheckDir: gQTLBase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf gQTLBase.buildbin-libdir gQTLBase.Rcheck && mkdir gQTLBase.buildbin-libdir gQTLBase.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gQTLBase.buildbin-libdir gQTLBase_1.0.0.tar.gz >gQTLBase.Rcheck\00install.out 2>&1 && cp gQTLBase.Rcheck\00install.out gQTLBase-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=gQTLBase.buildbin-libdir --install="check:gQTLBase-install.out" --force-multiarch --no-vignettes --timings gQTLBase_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/gQTLBase.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 'gQTLBase/DESCRIPTION' ... OK
* this is package 'gQTLBase' version '1.0.0'
* 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 'gQTLBase' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DFstoreToFf: no visible binding for global variable 'x'
extractByProbes: no visible binding for global variable 'x'
extractByRanges: no visible binding for global variable 'x'
storeApply: no visible binding for global variable 'x'
storeToFf: no visible binding for global variable 'x'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [254s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
extractByProbes 88.94   1.14   90.11
ciseStore-class 42.45   0.35  104.81
storeApply      38.06   0.37   38.43
storeMapResults 12.67   0.25   14.57
** running examples for arch 'x64' ... [169s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
extractByProbes 76.83   0.56   77.41
ciseStore-class 35.41   0.43   35.83
storeApply      32.75   0.39   33.14
storeMapResults 15.91   0.29   16.94
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R' [154s]
 [155s] OK
** running tests for arch 'x64' ...
  Running 'test-all.R' [164s]
 [164s] 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

Status: 1 NOTE
See
  'E:/biocbld/bbs-3.1-bioc/meat/gQTLBase.Rcheck/00check.log'
for details.


gQTLBase.Rcheck/00install.out:


install for i386

* installing *source* package 'gQTLBase' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'gQTLBase' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'gQTLBase' as gQTLBase_1.0.0.zip
* DONE (gQTLBase)

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

nameusersystemelapsed
ciseStore-class 42.45 0.35104.81
extractByProbes88.94 1.1490.11
storeApply38.06 0.3738.43
storeMapResults12.67 0.2514.57
storeToFf1.170.031.20

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

nameusersystemelapsed
ciseStore-class35.41 0.4335.83
extractByProbes76.83 0.5677.41
storeApply32.75 0.3933.14
storeMapResults15.91 0.2916.94
storeToFf0.970.031.00