focalCall 1.3.0
Oscar Krijgsman
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/focalCall | | Last Changed Rev: 102594 / Revision: 107696 | | Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | 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-3.2-bioc/R/bin/R CMD check --no-vignettes --timings focalCall_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/focalCall.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘focalCall/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘focalCall’ version ‘1.3.0’
* 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 ‘focalCall’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.match_CNV2CGH: no visible global function definition for ‘bpstart’
.match_CNV2CGH: no visible global function definition for ‘chromosomes’
.match_CNV2CGH: no visible global function definition for ‘bpend’
FreqPlot: no visible global function definition for ‘chromosomes’
FreqPlotfocal: no visible global function definition for ‘chromosomes’
FreqPlotfocal: no visible global function definition for
‘assayDataElement’
FreqPlotfocal: no visible global function definition for ‘fData’
focalCall: no visible global function definition for ‘calls’
focalCall: no visible global function definition for ‘featureNames’
focalCall: no visible global function definition for ‘segmented’
focalCall: no visible global function definition for ‘chromosomes’
focalCall: no visible global function definition for ‘bpstart’
focalCall: no visible global function definition for
‘assayDataElement<-’
focalCall: no visible global function definition for ‘assayDataElement’
focalCall: no visible global function definition for ‘bpend’
focalCall: no visible global function definition for ‘fData’
focalCall: no visible global function definition for ‘fData<-’
igvFiles: no visible global function definition for ‘calls’
igvFiles: no visible global function definition for ‘chromosomes’
igvFiles: no visible global function definition for ‘bpstart’
igvFiles: no visible global function definition for ‘bpend’
igvFiles: no visible global function definition for ‘featureNames’
igvFiles: no visible global function definition for ‘segmented’
igvFiles: no visible global function definition for ‘assayDataElement’
singleSample: no visible global function definition for ‘calls’
singleSample: no visible global function definition for ‘featureNames’
singleSample: no visible global function definition for ‘fData’
singleSample: no visible global function definition for ‘fData<-’
singleSample: no visible global function definition for
‘assayDataElement<-’
singleSample: no visible global function definition for ‘segmented’
singleSample: no visible global function definition for ‘chromosomes’
singleSample: no visible global function definition for ‘bpend’
singleSample: no visible global function definition for ‘bpstart’
singleSample: no visible global function definition for
‘assayDataElement’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
focalCall 5.033 0.019 5.082
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [1s/1s]
[1s/1s] 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
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/focalCall.Rcheck/00check.log’
for details.