leeBamViews 1.7.0
VJ Carey
| Snapshot Date: 2015-10-24 10:15:05 -0400 (Sat, 24 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/leeBamViews | | Last Changed Rev: 3462 / Revision: 3473 | | Last Changed Date: 2015-10-13 16:20:35 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings leeBamViews_1.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-data-experiment/meat/leeBamViews.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘leeBamViews/DESCRIPTION’ ... OK
* this is package ‘leeBamViews’ version ‘1.7.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘multicore’
* 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 ‘leeBamViews’ can be installed ... [11s/11s] OK
* checking installed package size ... NOTE
installed size is 11.3Mb
sub-directories of 1Mb or more:
bam 10.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
Artistic 2.0
Standardizable: TRUE
Standardized license specification:
Artistic-2.0
* 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 ... NOTE
Namespace in Imports field not imported from: ‘methods’
All declared Imports should be used.
Packages in Depends field not imported from:
‘BSgenome’ ‘Biobase’ ‘Rsamtools’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.tabulateReads: no visible global function definition for ‘bamRanges’
.tabulateReads: no visible global function definition for
‘elementMetadata’
.tabulateReads : alignByFirstRange: no visible global function
definition for ‘ScanBamParam’
.tabulateReads : alignByFirstRange: no visible global function
definition for ‘bamRanges’
.tabulateReads : alignByFirstRange: no visible global function
definition for ‘bamPaths’
.tabulateReads: no visible global function definition for ‘bamSamples’
.tabulateReads: no visible global function definition for ‘IRanges’
.tabulateReads: no visible global function definition for ‘GRanges’
.tabulateReads: no visible global function definition for ‘seqnames’
.tabulateReads: no visible global function definition for ‘values’
.tabulateReads: no visible global function definition for ‘values<-’
.tabulateReads: no visible global function definition for ‘DataFrame’
tabulateReads,BamViews-characterORNULL-missing-missing: no visible
binding for global variable ‘mclapply’
tabulateReads,BamViews-missing-missing-missing: no visible binding for
global variable ‘mclapply’
totalReadCounts,BamViews: no visible global function definition for
‘bamPaths’
totalReadCounts,BamViews: no visible binding for global variable
‘scanBam’
totalReadCounts,BamViews: no visible global function definition for
‘ScanBamParam’
Undefined global functions or variables:
DataFrame GRanges IRanges ScanBamParam bamPaths bamRanges bamSamples
elementMetadata mclapply scanBam seqnames values values<-
* 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 ... [16s/16s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
tabulateReads 6.388 0.056 6.468
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘lbvtest.R’ [10s/10s]
[10s/10s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘IRanges’
* 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 NOTEs
See
‘/home/biocbuild/bbs-3.3-data-experiment/meat/leeBamViews.Rcheck/00check.log’
for details.