sigaR 1.15.0
Wessel N. van Wieringen
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sigaR | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | 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 sigaR_1.15.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/sigaR.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 ‘sigaR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sigaR’ version ‘1.15.0’
* 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 ‘sigaR’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘mvtnorm’ ‘penalized’
A package should be listed in only one of these fields.
* 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
summary,entTest: warning in round(object@statistic, d = 3): partial
argument match of 'd' to 'digits'
summary,entTest: warning in round(object@p.value, d = 3): partial
argument match of 'd' to 'digits'
summary,miTest: warning in round(object@statistic, d = 3): partial
argument match of 'd' to 'digits'
summary,miTest: warning in round(object@p.value, d = 3): partial
argument match of 'd' to 'digits'
summary,rcmFit: warning in round(object@betas, d = 3): partial argument
match of 'd' to 'digits'
summary,rcmFit: warning in round(object@tau2s, d = 3): partial argument
match of 'd' to 'digits'
summary,rcmFit: warning in round(object@av.sigma2s, d = 3): partial
argument match of 'd' to 'digits'
summary,rcmFit: warning in round(object@rho, d = 3): partial argument
match of 'd' to 'digits'
summary,rcmFit: warning in round(object@shrinkage, d = 3): partial
argument match of 'd' to 'digits'
summary,rcmFit: warning in round(object@loglik, d = 3): partial
argument match of 'd' to 'digits'
summary,rcmTest: warning in round(object@betas, d = 3): partial
argument match of 'd' to 'digits'
summary,rcmTest: warning in round(object@tau2s, d = 3): partial
argument match of 'd' to 'digits'
summary,rcmTest: warning in round(object@av.sigma2s, d = 3): partial
argument match of 'd' to 'digits'
summary,rcmTest: warning in round(object@rho, d = 3): partial argument
match of 'd' to 'digits'
summary,rcmTest: warning in round(object@shrinkage, d = 3): partial
argument match of 'd' to 'digits'
summary,rcmTest: warning in round(object@loglik, d = 3): partial
argument match of 'd' to 'digits'
summary,rcmTest: warning in round(object@statistic, d = 3): partial
argument match of 'd' to 'digits'
summary,rcmTest: warning in round(object@p.value, d = 3): partial
argument match of 'd' to 'digits'
.pi0est: no visible global function definition for ‘convest’
ExpressionSet2weightedSubset: no visible binding for global variable
‘sigaR’
RCMestimation : RCMmlH2: multiple local function definitions for
‘tau.estimator’ with different formal arguments
RCMtest: no visible binding for global variable ‘sigaR’
RCMtest: no visible binding for global variable ‘quadprog’
RCMtest: no visible binding for global variable ‘MASS’
cghCall2maximumSubset: no visible binding for global variable ‘sigaR’
cghCall2order: no visible global function definition for ‘probdloss’
cghCall2order: no visible global function definition for ‘probdloss<-’
cghCall2subset: no visible global function definition for ‘probdloss’
cghCall2weightedSubset: no visible global function definition for
‘probdloss’
cghCall2weightedSubset: no visible binding for global variable ‘sigaR’
cghSeg2weightedSubset: no visible binding for global variable ‘sigaR’
entropyTest: no visible binding for global variable ‘sigaR’
entropyTest: no visible binding for global variable ‘corpcor’
matchAnn2Ann: no visible binding for global variable ‘sigaR’
matchCGHcall2ExpressionSet: no visible binding for global variable
‘sigaR’
merge2cghCalls: no visible global function definition for ‘probdloss’
mutInfTest: no visible binding for global variable ‘sigaR’
mutInfTest: no visible binding for global variable ‘corpcor’
Undefined global functions or variables:
MASS convest corpcor probdloss probdloss<- quadprog sigaR
* 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 ... [133s/133s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mutInfTest 102.006 3.886 106.005
cisEffectTune 11.090 0.000 11.097
* 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-3.3-bioc/meat/sigaR.Rcheck/00check.log’
for details.