annmap 1.8.0
Chris Wirth
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/annmap | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| 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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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings annmap_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/annmap.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘annmap’ version ‘1.8.0’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘annmap’ can be installed ... [16s/16s] 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
* 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' call to ‘rjson’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.make.hash’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.load.and.parse: no visible global function definition for ‘fromJSON’
.xmcws.connect: no visible global function definition for ‘fromJSON’
convertBamToRle: no visible global function definition for ‘RangedData’
convertBamToRle: no visible global function definition for ‘IRanges’
convertBamToRle : <anonymous>: no visible global function definition
for ‘Rle’
geneToGeneRegionTrack : generate: no visible global function definition
for ‘GeneRegionTrack’
genomicPlot : <anonymous>: no visible global function definition for
‘IRanges’
ngsBridgePlot: no visible global function definition for ‘space’
ngsTracePlotter : local.draw: no visible global function definition for
‘runLength’
ngsTracePlotter : local.draw: no visible global function definition for
‘runValue’
ngsTraceScale : <anonymous>: no visible global function definition for
‘runValue’
seqnameMapping: no visible global function definition for ‘seqlevels<-’
seqnameMapping: no visible global function definition for ‘seqlevels’
transcriptCoordsToGenome : <anonymous>: no visible global function
definition for ‘IRanges’
transcriptToCodingRange : .fn: no visible global function definition
for ‘IRanges’
transcriptToTranslatedprobes : fn: no visible global function
definition for ‘IRanges’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'plot.ngs.Rd':
‘[IRanges]{Rle}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘doRUnit.R’ [16s/21s]
[16s/21s] 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
WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/annmap.Rcheck/00check.log’
for details.