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 | |  |
| 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 | |
##############################################################################
##############################################################################
###
### 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.
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)