Back to the "Multiple platform build/check report" A  B  C  D  E  F [G] H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.4: CHECK report for gQTLBase on moscato1

This page was generated on 2016-09-21 03:46:37 -0700 (Wed, 21 Sep 2016).

Package 537/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gQTLBase 1.5.2
VJ Carey
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gQTLBase
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: 1.5.2
Command: rm -rf gQTLBase.buildbin-libdir gQTLBase.Rcheck && mkdir gQTLBase.buildbin-libdir gQTLBase.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gQTLBase.buildbin-libdir gQTLBase_1.5.2.tar.gz >gQTLBase.Rcheck\00install.out 2>&1 && cp gQTLBase.Rcheck\00install.out gQTLBase-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=gQTLBase.buildbin-libdir --install="check:gQTLBase-install.out" --force-multiarch --no-vignettes --timings gQTLBase_1.5.2.tar.gz
StartedAt: 2016-09-20 09:50:05 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:04:44 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 879.0 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gQTLBase.buildbin-libdir gQTLBase_1.5.2.tar.gz >gQTLBase.Rcheck\00install.out 2>&1 && cp gQTLBase.Rcheck\00install.out gQTLBase-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=gQTLBase.buildbin-libdir --install="check:gQTLBase-install.out" --force-multiarch --no-vignettes --timings gQTLBase_1.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/gQTLBase.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.5.2'
* 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
.describeStore: no visible global function definition for 'getJobInfo'
.extractByProbes: no visible binding for global variable 'x'
.extractByRanges: no visible global function definition for
  'subsetByOverlaps'
.extractByRanges: no visible binding for global variable 'x'
DFstoreToFf: no visible binding for global variable 'x'
cb2range: no visible global function definition for 'select'
cb2range: no visible global function definition for 'IRanges'
dendroReduce.bj: no visible global function definition for 'batchMap'
dendroReduce.fe: no visible binding for global variable 'i'
describeStore.old: no visible global function definition for 'hist'
ffapp2: no visible global function definition for 'as.ff'
ffapp2: no visible global function definition for 'appendLevels'
ffapp2: no visible global function definition for 'as.which'
mergeGWhits: no visible global function definition for 'genome'
storeApply: no visible binding for global variable 'x'
storeApply2: no visible binding for global variable 'x'
storeToFf: no visible binding for global variable 'x'
show,storeDescription: no visible global function definition for
  'median'
Undefined global functions or variables:
  IRanges appendLevels as.ff as.which batchMap genome getJobInfo hist i
  median select subsetByOverlaps x
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "median")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: ufeatByTiling.Rd:50-52: Dropping empty section \seealso
* 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' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
storeApply      30.35   0.33  145.77
mergeCIstates    6.65   0.13   12.32
extractByProbes  6.20   0.07   35.72
ciseStore-class  0.50   0.00    7.10
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
storeApply      29.74   0.28   30.01
extractByProbes  8.62   0.11    8.73
mergeCIstates    7.05   0.23    7.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.R'
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'BiocParallel'
* 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
  'D:/biocbld/bbs-3.4-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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'gQTLBase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gQTLBase' as gQTLBase_1.5.2.zip
* DONE (gQTLBase)

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

nameusersystemelapsed
ciseStore-class0.50.07.1
describeStore000
extractByProbes 6.20 0.0735.72
mergeCIstates 6.65 0.1312.32
storeApply 30.35 0.33145.77
storeMapResults000
storeToFf0.720.010.75
ufeatByTiling000

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

nameusersystemelapsed
ciseStore-class1.170.031.20
describeStore000
extractByProbes8.620.118.73
mergeCIstates7.050.237.39
storeApply29.74 0.2830.01
storeMapResults000
storeToFf0.720.020.91
ufeatByTiling000