erma 0.1.23
VJ Carey
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/erma | | Last Changed Rev: 107571 / Revision: 107602 | | Last Changed Date: 2015-08-19 00:22:20 -0700 (Wed, 19 Aug 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf erma.buildbin-libdir erma.Rcheck && mkdir erma.buildbin-libdir erma.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=erma.buildbin-libdir erma_0.1.23.tar.gz >erma.Rcheck\00install.out 2>&1 && cp erma.Rcheck\00install.out erma-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=erma.buildbin-libdir --install="check:erma-install.out" --force-multiarch --no-vignettes --timings erma_0.1.23.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/erma.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'erma/DESCRIPTION' ... OK
* this is package 'erma' version '0.1.23'
* 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 'erma' can be installed ... OK
* checking installed package size ... NOTE
installed size is 199.6Mb
sub-directories of 1Mb or more:
bed_tabix 161.4Mb
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
* 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 ... WARNING
'library' or 'require' calls not declared from:
'GenomicRanges' 'ggplot2' 'shiny'
'library' or 'require' call to 'Homo.sapiens' which was already attached by Depends.
Please remove these calls from your code.
'library' or 'require' calls in package code:
'GenomicRanges' 'ggplot2' 'shiny'
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
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 ... WARNING
prepare_Rd: ErmaSet-class.Rd:10-12: Dropping empty section \description
checkRd: (5) ErmaSet-class.Rd:0-61: Must have a \description
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'ErmaSet-class.Rd':
'SummarizedExperiment0-class'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'map2range'
Undocumented data sets:
'farhSE'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'stateProfile':
stateProfile
Code: function(ermaset, symbol = "IL33", upstream = 2000, downstream
= 200, ctsize = 10, shortCellType = TRUE, tsswidth =
3)
Docs: function(ermaset, symbol = "IL33", upstream = 2000, downstream
= 200, ctsize = 10, shortCellType = TRUE)
Argument names in code not in docs:
tsswidth
stateProf
Code: function(ermaset, shortCellType = TRUE, ctsize = 10)
Docs: function(ermaset, ctsize = 10, shortCellType = TRUE)
Mismatches in argument names:
Position: 2 Code: shortCellType Docs: ctsize
Position: 3 Code: ctsize Docs: shortCellType
csProfile
Code: function(ermaset, symbol, upstream = 2000, downstream = 200,
useShiny = FALSE, ctsize = 10, shortCellType = TRUE,
tsswidth = 3)
Docs: function(ermaset, symbol, upstream = 2000, downstream = 200,
useShiny = FALSE, ctsize = 10, shortCellType = TRUE)
Argument names in code not in docs:
tsswidth
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'genemodel':
'map2range'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... [26s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
erma-package 8.44 0.22 8.83
** running examples for arch 'x64' ... [28s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
erma-package 8.21 0.22 8.43
* 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: 6 WARNINGs, 2 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/erma.Rcheck/00check.log'
for details.
install for i386
* 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
** 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
install for x64
* installing *source* package 'erma' ...
** 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
* MD5 sums
packaged installation of 'erma' as erma_0.1.23.zip
* DONE (erma)