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BioC 3.1: CHECK report for gwascat on moscato2

This page was generated on 2015-10-09 09:29:38 -0700 (Fri, 09 Oct 2015).

Package 451/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gwascat 1.12.0
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/gwascat
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: gwascat
Version: 1.12.0
Command: rm -rf gwascat.buildbin-libdir gwascat.Rcheck && mkdir gwascat.buildbin-libdir gwascat.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gwascat.buildbin-libdir gwascat_1.12.0.tar.gz >gwascat.Rcheck\00install.out 2>&1 && cp gwascat.Rcheck\00install.out gwascat-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=gwascat.buildbin-libdir --install="check:gwascat-install.out" --force-multiarch --no-vignettes --timings gwascat_1.12.0.tar.gz
StartedAt: 2015-10-09 02:46:37 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 02:54:22 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 464.7 seconds
RetCode: 0
Status:  OK  
CheckDir: gwascat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf gwascat.buildbin-libdir gwascat.Rcheck && mkdir gwascat.buildbin-libdir gwascat.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gwascat.buildbin-libdir gwascat_1.12.0.tar.gz >gwascat.Rcheck\00install.out 2>&1 && cp gwascat.Rcheck\00install.out gwascat-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=gwascat.buildbin-libdir --install="check:gwascat-install.out" --force-multiarch --no-vignettes --timings gwascat_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/gwascat.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 'gwascat/DESCRIPTION' ... OK
* this is package 'gwascat' version '1.12.0'
* 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 'gwascat' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 30.6Mb
  sub-directories of 1Mb or more:
    data     25.0Mb
    obo       1.3Mb
    olddata   2.2Mb
    tab       1.1Mb
* 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
* 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
'library' or 'require' calls in package code:
  'SNPlocs.Hsapiens.dbSNP.20120608' 'ggbio' 'graph'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'VariantAnnotation'
  All declared Imports should be used.
':::' call which should be '::': 'gQTLstats:::queryVCF'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bindcadd_snv: no visible global function definition for 'findOverlaps'
chklocs: no visible binding for global variable 'gwrngs19'
chklocs: no visible global function definition for 'getSNPlocs'
descendants: no visible global function definition for 'adj'
gwcex2gviz: no visible global function definition for 'exons'
ldtagr: no visible global function definition for 'rowRanges'
ldtagr: no visible global function definition for 'col.summary'
makeCurrentGwascat: no visible binding for global variable 'si.hs.38'
obo2graphNEL: no visible global function definition for
  'nodeDataDefaults<-'
obo2graphNEL: no visible global function definition for 'nodeData<-'
obo2graphNEL: no visible global function definition for 'nodes'
parentingDF: no visible global function definition for 'subGraph'
parentingDF: no visible global function definition for 'nodeData'
parentingDF: no visible global function definition for 'extractFromTo'
snpGenos: no visible global function definition for 'getSNPlocs'
traitsManh: no visible global function definition for 'autoplot'
traitsManh: no visible global function definition for 'aes'
traitsManh: no visible binding for global variable 'Pvalue_mlog'
variantProps: no visible binding for global variable 'gwrngs'
* 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' ... [36s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
riskyAlleleCount 12.34   0.06    12.4
** running examples for arch 'x64' ... [35s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
riskyAlleleCount 9.67   0.04    9.72
gwcex2gviz       5.60   0.15    5.75
* 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: 4 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/gwascat.Rcheck/00check.log'
for details.


gwascat.Rcheck/00install.out:


install for i386

* installing *source* package 'gwascat' ...
** R
** data
** 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 'gwascat' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'gwascat' as gwascat_1.12.0.zip
* DONE (gwascat)

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

nameusersystemelapsed
bindcadd_snv000
gwascat-package000
gwastagger1.980.022.00
gwaswloc-class000
gwcex2gviz4.460.084.54
gwdf_2012_02_02000
ldtagr1.490.041.89
locon60.030.000.03
makeCurrentGwascat0.000.020.02
riskyAlleleCount12.34 0.0612.40
topTraits0.520.000.51
traitsManh2.000.032.04

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

nameusersystemelapsed
bindcadd_snv000
gwascat-package000
gwastagger1.990.042.03
gwaswloc-class000
gwcex2gviz5.600.155.75
gwdf_2012_02_02000
ldtagr1.700.062.34
locon60.020.000.02
makeCurrentGwascat000
riskyAlleleCount9.670.049.72
topTraits0.270.000.26
traitsManh2.540.012.56