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 3.2: CHECK report for FunciSNP on moscato1

This page was generated on 2015-08-11 13:10:50 -0700 (Tue, 11 Aug 2015).

Package 369/1062HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FunciSNP 1.11.0
Simon G. Coetzee
Snapshot Date: 2015-08-10 16:24:50 -0700 (Mon, 10 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/FunciSNP
Last Changed Rev: 102594 / Revision: 107311
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 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 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  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: FunciSNP
Version: 1.11.0
Command: rm -rf FunciSNP.buildbin-libdir FunciSNP.Rcheck && mkdir FunciSNP.buildbin-libdir FunciSNP.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=FunciSNP.buildbin-libdir FunciSNP_1.11.0.tar.gz >FunciSNP.Rcheck\00install.out 2>&1 && cp FunciSNP.Rcheck\00install.out FunciSNP-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=FunciSNP.buildbin-libdir --install="check:FunciSNP-install.out" --force-multiarch --no-vignettes --timings FunciSNP_1.11.0.tar.gz
StartedAt: 2015-08-11 05:01:11 -0700 (Tue, 11 Aug 2015)
EndedAt: 2015-08-11 05:09:27 -0700 (Tue, 11 Aug 2015)
EllapsedTime: 495.7 seconds
RetCode: 0
Status:  OK  
CheckDir: FunciSNP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf FunciSNP.buildbin-libdir FunciSNP.Rcheck && mkdir FunciSNP.buildbin-libdir FunciSNP.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=FunciSNP.buildbin-libdir FunciSNP_1.11.0.tar.gz >FunciSNP.Rcheck\00install.out 2>&1 && cp FunciSNP.Rcheck\00install.out FunciSNP-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=FunciSNP.buildbin-libdir --install="check:FunciSNP-install.out" --force-multiarch --no-vignettes --timings FunciSNP_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/FunciSNP.Rcheck'
* using R version 3.2.2 beta (2015-08-04 r68843)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FunciSNP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FunciSNP' version '1.11.0'
* 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 'FunciSNP' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'ggplot2'
A package should be listed in only one of these fields.
* 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
Namespaces in Imports field not imported from:
  'AnnotationDbi' 'GenomicRanges' 'org.Hs.eg.db'
  All declared Imports should be used.
':::' calls which should be '::':
  'Rsamtools:::close.TabixFile' 'Rsamtools:::isOpen'
  'Rsamtools:::open.TabixFile'
  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
AnnotateSummary: no visible global function definition for
  'GRangesList'
AnnotateSummary: no visible global function definition for
  'elementMetadata'
AnnotateSummary: no visible global function definition for 'GRanges'
AnnotateSummary: no visible global function definition for 'RangedData'
AnnotateSummary: no visible binding for global variable 'lincRNA'
AnnotateSummary: no visible binding for '<<-' assignment to 'txdb'
AnnotateSummary: no visible binding for global variable 'refseqgenes'
AnnotateSummary: no visible binding for global variable 'txdb'
CreateCorrelatedSNPs: no visible global function definition for
  'GRangesList'
FilterByFeatures: no visible global function definition for 'GRanges'
FilterByFeatures: no visible global function definition for
  'elementMetadata'
FilterByFeatures: no visible global function definition for
  'elementMetadata<-'
FilterByFeatures: no visible global function definition for
  'findOverlaps'
FilterByFeatures: no visible global function definition for 'queryHits'
FilterByFeatures: no visible global function definition for
  'GRangesList'
FilterByFeatures: no visible global function definition for
  'subjectHits'
FunciSNPbed: no visible global function definition for
  'package.version'
FunciSNPplot: no visible binding for global variable 'R.squared'
FunciSNPplot: no visible binding for global variable 'r.2'
FunciSNPplot: no visible binding for global variable
  'distance.from.tag'
FunciSNPplot: no visible binding for global variable 'variable'
FunciSNPplot: no visible binding for global variable 'sig'
FunciSNPplot: no visible binding for global variable 'value'
PullInVariants: no visible global function definition for 'GRanges'
SNPSummary: no visible global function definition for 'elementMetadata'
SNPSummary: no visible global function definition for
  'elementMetadata<-'
getFSNPs: no visible global function definition for 'package.version'
show,TagSNP: no visible global function definition for
  'elementMetadata'
* 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' ... [20s] OK
** running examples for arch 'x64' ... [26s] 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: 3 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/FunciSNP.Rcheck/00check.log'
for details.


FunciSNP.Rcheck/00install.out:


install for i386

* installing *source* package 'FunciSNP' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
No methods found in "matrixStats" for requests: makeGRangesFromDataFrame
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "matrixStats" for requests: makeGRangesFromDataFrame

install for x64

* installing *source* package 'FunciSNP' ...
** testing if installed package can be loaded
No methods found in "matrixStats" for requests: makeGRangesFromDataFrame
* MD5 sums
packaged installation of 'FunciSNP' as FunciSNP_1.11.0.zip
* DONE (FunciSNP)

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

nameusersystemelapsed
CorrelatedSNPs-class000
FunciSNP-package1.320.031.35
FunciSNPAnnotateSummary0.600.020.61
FunciSNPbed0.560.000.58
FunciSNPidsFromSummary000
FunciSNPplot1.510.031.54
FunciSNPsummaryOverlaps0.640.051.03
FunciSNPtable1.650.061.72
TSList-class000
TagSNP-class000
getFSNPs0.270.020.28

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

nameusersystemelapsed
CorrelatedSNPs-class000
FunciSNP-package1.650.031.69
FunciSNPAnnotateSummary0.880.052.90
FunciSNPbed0.730.051.28
FunciSNPidsFromSummary000
FunciSNPplot1.720.012.34
FunciSNPsummaryOverlaps0.690.020.70
FunciSNPtable2.310.082.39
TSList-class000
TagSNP-class000
getFSNPs0.210.030.23