erma 0.9.2
VJ Carey
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/erma | | Last Changed Rev: 130713 / Revision: 131943 | | Last Changed Date: 2017-06-27 13:05:27 -0400 (Tue, 27 Jun 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings erma_0.9.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/erma.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘0.9.2’
* 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 ... OK
* 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 ‘IRanges’
genemodelOLD: no visible binding for global variable ‘exonsBy’
map2range: no visible global function definition for ‘IRanges’
mapmeta: no visible global function definition for ‘read.csv’
stateProf: no visible global function definition for ‘keys’
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 global function definition for ‘data’
stateProfile: no visible binding for global variable ‘short_celltype’
stateProfile: no visible binding for global variable ‘states_25’
stateProfile: no visible binding for global variable ‘name’
statesByRange: no visible binding for global variable ‘mod’
statesByRange: no visible binding for global variable ‘upstream’
statesByRange: no visible binding for global variable ‘downstream’
statesByRange: no visible binding for global variable ‘i’
statesByRange: no visible global function definition for ‘genome’
statesByRange: no visible global function definition for ‘seqlevels<-’
statesByRange: no visible global function definition for ‘seqlevels’
statesByRange : <anonymous>: no visible global function definition for
‘IRanges’
statesByRange : <anonymous>: no visible binding for global variable
‘tss’
statesByRange: no visible global function definition for ‘data’
statesByRange: no visible binding for global variable ‘short_celltype’
statesByRange: no visible binding for global variable ‘states_25’
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’
Undefined global functions or variables:
IRanges data downstream exonsBy genome i keys mod name read.csv
select seqlevels seqlevels<- short_celltype states_25 tss upstream
Consider adding
importFrom("utils", "data", "read.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘subsetByRanges’
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':
stateProf
Code: function(ermaset, shortCellType = FALSE, ctsize = 10, iniSym =
"IL7R")
Docs: function(ermaset, shortCellType = TRUE, ctsize = 10, iniSym =
"IL7R")
Mismatches in argument default values:
Name: 'shortCellType' Code: FALSE Docs: TRUE
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'stateProfile'
‘iniSym’
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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
erma-package 8.664 0.364 9.247
* 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 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/erma.Rcheck/00check.log’
for details.
* installing *source* package ‘erma’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (erma)