r3Cseq 1.16.0
Supat Thongjuea
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/r3Cseq | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf r3Cseq.buildbin-libdir r3Cseq.Rcheck && mkdir r3Cseq.buildbin-libdir r3Cseq.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=r3Cseq.buildbin-libdir r3Cseq_1.16.0.tar.gz >r3Cseq.Rcheck\00install.out 2>&1 && cp r3Cseq.Rcheck\00install.out r3Cseq-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=r3Cseq.buildbin-libdir --install="check:r3Cseq-install.out" --force-multiarch --no-vignettes --timings r3Cseq_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/r3Cseq.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'r3Cseq/DESCRIPTION' ... OK
* this is package 'r3Cseq' version '1.16.0'
* 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 'r3Cseq' 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
** 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
'library' or 'require' calls in package code:
'BSgenome.Hsapiens.UCSC.hg18.masked'
'BSgenome.Hsapiens.UCSC.hg19.masked'
'BSgenome.Mmusculus.UCSC.mm10.masked'
'BSgenome.Mmusculus.UCSC.mm9.masked'
'BSgenome.Rnorvegicus.UCSC.rn5.masked'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assign3CseqSigContact: no visible binding for global variable
'relative.position'
assign3CseqSigContact: no visible binding for global variable
'chromosome'
get3CseqRefGene: no visible binding for global variable 'hg18refGene'
get3CseqRefGene: no visible binding for global variable 'hg19refGene'
get3CseqRefGene: no visible binding for global variable 'mm9refGene'
get3CseqRefGene: no visible binding for global variable 'mm10refGene'
get3CseqRefGene: no visible binding for global variable 'rn5refGene'
getFragmentsPerWindow: no visible binding for global variable
'BSgenome.Hsapiens.UCSC.hg18.masked'
getFragmentsPerWindow: no visible binding for global variable
'BSgenome.Hsapiens.UCSC.hg19.masked'
getFragmentsPerWindow: no visible binding for global variable
'BSgenome.Mmusculus.UCSC.mm9.masked'
getFragmentsPerWindow: no visible binding for global variable
'BSgenome.Mmusculus.UCSC.mm10.masked'
getFragmentsPerWindow: no visible binding for global variable
'BSgenome.Rnorvegicus.UCSC.rn5.masked'
getPowerLawFittedCoeficient: no visible binding for global variable
'num'
getPowerLawFittedCoeficient: no visible binding for global variable
'nr_reads'
getViewpoint: no visible binding for global variable
'BSgenome.Hsapiens.UCSC.hg18.masked'
getViewpoint: no visible global function definition for 'DNAString'
getViewpoint: no visible binding for global variable
'BSgenome.Hsapiens.UCSC.hg19.masked'
getViewpoint: no visible binding for global variable
'BSgenome.Mmusculus.UCSC.mm9.masked'
getViewpoint: no visible binding for global variable
'BSgenome.Mmusculus.UCSC.mm10.masked'
getViewpoint: no visible binding for global variable
'BSgenome.Rnorvegicus.UCSC.rn5.masked'
makeInteractionMatrixNearCisPerWindow: no visible binding for global
variable 'BSgenome.Hsapiens.UCSC.hg19.masked'
makeInteractionMatrixNearCisPerWindow: no visible binding for global
variable 'BSgenome.Hsapiens.UCSC.hg18.masked'
makeInteractionMatrixNearCisPerWindow: no visible binding for global
variable 'BSgenome.Mmusculus.UCSC.mm9.masked'
makeInteractionMatrixNearCisPerWindow: no visible binding for global
variable 'BSgenome.Mmusculus.UCSC.mm10.masked'
makeInteractionMatrixNearCisPerWindow: no visible binding for global
variable 'BSgenome.Rnorvegicus.UCSC.rn5.masked'
plotInteractionsNearViewpoint: no visible binding for global variable
'BSgenome.Hsapiens.UCSC.hg18.masked'
plotInteractionsNearViewpoint: no visible binding for global variable
'BSgenome.Hsapiens.UCSC.hg19.masked'
plotInteractionsNearViewpoint: no visible binding for global variable
'BSgenome.Mmusculus.UCSC.mm9.masked'
plotInteractionsNearViewpoint: no visible binding for global variable
'BSgenome.Mmusculus.UCSC.mm10.masked'
plotInteractionsNearViewpoint: no visible binding for global variable
'BSgenome.Rnorvegicus.UCSC.rn5.masked'
plotInteractionsNearViewpoint: no visible binding for global variable
'chromosome'
plotInteractionsNearViewpoint: no visible binding for global variable
'exp_RPMs'
plotInteractionsNearViewpoint: no visible binding for global variable
'contr_RPMs'
plotInteractionsNearViewpoint: no visible binding for global variable
'log2fold'
plotInteractionsPerChromosome: no visible binding for global variable
'BSgenome.Hsapiens.UCSC.hg18.masked'
plotInteractionsPerChromosome: no visible binding for global variable
'BSgenome.Hsapiens.UCSC.hg19.masked'
plotInteractionsPerChromosome: no visible binding for global variable
'BSgenome.Mmusculus.UCSC.mm9.masked'
plotInteractionsPerChromosome: no visible binding for global variable
'BSgenome.Mmusculus.UCSC.mm10.masked'
plotInteractionsPerChromosome: no visible binding for global variable
'BSgenome.Rnorvegicus.UCSC.rn5.masked'
plotOverviewInteractions: no visible binding for global variable
'BSgenome.Hsapiens.UCSC.hg18.masked'
plotOverviewInteractions: no visible binding for global variable
'BSgenome.Hsapiens.UCSC.hg19.masked'
plotOverviewInteractions: no visible binding for global variable
'BSgenome.Mmusculus.UCSC.mm9.masked'
plotOverviewInteractions: no visible binding for global variable
'BSgenome.Mmusculus.UCSC.mm10.masked'
plotOverviewInteractions: no visible binding for global variable
'BSgenome.Rnorvegicus.UCSC.rn5.masked'
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
binding for global variable 'BSgenome.Hsapiens.UCSC.hg18.masked'
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
binding for global variable 'BSgenome.Hsapiens.UCSC.hg19.masked'
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
binding for global variable 'BSgenome.Mmusculus.UCSC.mm9.masked'
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
binding for global variable 'BSgenome.Mmusculus.UCSC.mm10.masked'
getEnzymeRestrictionPositionInSelectedGenome,repbaseEnzyme: no visible
binding for global variable 'BSgenome.Rnorvegicus.UCSC.rn5.masked'
getEnzymeRestrictionSequences,repbaseEnzyme-character: no visible
binding for global variable 'enzyme'
initialize,repbaseEnzyme : .local: no visible binding for global
variable 'enzyme.db'
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable 'BSgenome.Hsapiens.UCSC.hg18.masked'
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable 'BSgenome.Hsapiens.UCSC.hg19.masked'
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable 'BSgenome.Mmusculus.UCSC.mm9.masked'
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable 'BSgenome.Mmusculus.UCSC.mm10.masked'
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable 'BSgenome.Rnorvegicus.UCSC.rn5.masked'
plotDomainogramNearViewpoint,r3Cseq: no visible binding for global
variable 'chromosome'
* 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' ... [11s] OK
** running examples for arch 'x64' ... [11s] 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: 2 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/r3Cseq.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'r3Cseq' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "Biostrings" for requests: DNAString
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "Biostrings" for requests: DNAString
install for x64
* installing *source* package 'r3Cseq' ...
** testing if installed package can be loaded
No methods found in "Biostrings" for requests: DNAString
* MD5 sums
packaged installation of 'r3Cseq' as r3Cseq_1.16.0.zip
* DONE (r3Cseq)