erma 0.2.0
VJ Carey
| 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/erma | | 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 | OK | OK | [ WARNINGS ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings erma_0.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/erma.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘erma/DESCRIPTION’ ... OK
* this is package ‘erma’ version ‘0.2.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘erma’ can be installed ... [16s/18s] WARNING
Found the following significant warnings:
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘erma’
See ‘/home/biocbuild/bbs-3.2-bioc/meat/erma.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 199.7Mb
sub-directories of 1Mb or more:
bed_tabix 161.3Mb
data 37.1Mb
* 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
* 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
geneTxRange: no visible global function definition for ‘select’
geneTxRange: no visible global function definition for ‘IRanges’
genemodel: no visible global function definition for ‘select’
genemodel: no visible global function definition for ‘IRanges’
genemodelOLD: no visible binding for global variable ‘exonsBy’
genemodelOLD: no visible global function definition for ‘select’
map2range: no visible global function definition for ‘select’
map2range: no visible global function definition for ‘IRanges’
stateProf: no visible global function definition for ‘keys’
stateProfOLD: no visible global function definition for ‘keys’
stateProfOLD : server: possible error in stateProfile(ermaset,
input$sym, ctsize = 12, width = input$scope): unused argument (width
= input$scope)
stateProfile: no visible binding for global variable ‘i’
stateProfile: no visible global function definition for ‘genome’
stateProfile: no visible global function definition for ‘seqlevels<-’
stateProfile: no visible global function definition for ‘seqlevels’
stateProfile : <anonymous>: no visible global function definition for
‘IRanges’
stateProfile: no visible binding for global variable ‘states_25’
stateProfile: no visible binding for global variable ‘short_celltype’
stateProfile: no visible binding for global variable ‘name’
subsetByRanges : <anonymous>: no visible global function definition for
‘genome’
subsetByRanges : <anonymous>: no visible global function definition for
‘seqlevels<-’
subsetByRanges : <anonymous>: no visible global function definition for
‘seqlevels’
* 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 ... [17s/17s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
erma-package 5.587 0.072 5.658
* 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: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/erma.Rcheck/00check.log’
for details.
* installing *source* package ‘erma’ ...
** R
** data
** inst
** preparing package for lazy loading
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘erma’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘erma’
* DONE (erma)