CHECK report for rHVDM on merida1
This page was generated on 2020-04-15 12:35:04 -0400 (Wed, 15 Apr 2020).
rHVDM 1.52.0
Martino Barenco
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/rHVDM |
| Branch: RELEASE_3_10 |
| Last Commit: 75b8a95 |
| Last Changed Date: 2019-10-29 13:07:47 -0400 (Tue, 29 Oct 2019) |
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | ERROR | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] | OK | |
Summary
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rHVDM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rHVDM_1.52.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/rHVDM.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rHVDM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rHVDM’ version ‘1.52.0’
* 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 ‘rHVDM’ can be installed ... WARNING
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
Warning: Package 'rHVDM' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.10-bioc/meat/rHVDM.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
data 5.1Mb
* 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 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
.bin.ut: no visible global function definition for ‘quantile’
.binb.ut: no visible global function definition for ‘quantile’
.geneoutput: no visible global function definition for ‘png’
.geneoutput: no visible global function definition for ‘par’
.geneoutput: no visible global function definition for ‘plot’
.geneoutput: no visible global function definition for ‘arrows’
.geneoutput: no visible global function definition for ‘lines’
.geneoutput: no visible global function definition for ‘dev.off’
.greport: no visible global function definition for ‘runif’
.parameteroutput: no visible global function definition for ‘png’
.parameteroutput: no visible global function definition for ‘par’
.parameteroutput: no visible global function definition for ‘arrows’
.parameteroutput: no visible global function definition for ‘dev.off’
.parameteroutput: no visible global function definition for ‘plot’
.parameteroutput: no visible global function definition for ‘lines’
.parameteroutput: no visible global function definition for ‘cov2cor’
.parameteroutputg: no visible global function definition for ‘png’
.parameteroutputg: no visible global function definition for ‘par’
.parameteroutputg: no visible global function definition for ‘arrows’
.parameteroutputg: no visible global function definition for ‘dev.off’
.parameteroutputg: no visible global function definition for ‘cov2cor’
.parameteroutputg.nl: no visible global function definition for ‘png’
.parameteroutputg.nl: no visible global function definition for ‘par’
.parameteroutputg.nl: no visible global function definition for
‘arrows’
.parameteroutputg.nl: no visible global function definition for
‘dev.off’
.parameteroutputg.nl: no visible global function definition for
‘cov2cor’
.scoreoutput: no visible global function definition for ‘qchisq’
.scoreoutput: no visible global function definition for ‘png’
.scoreoutput: no visible global function definition for ‘par’
.scoreoutput: no visible global function definition for ‘plot’
.scoreoutput: no visible global function definition for ‘dchisq’
.scoreoutput: no visible global function definition for ‘points’
.scoreoutput: no visible global function definition for ‘qnorm’
.scoreoutput: no visible global function definition for ‘lines’
.scoreoutput: no visible global function definition for ‘dev.off’
.scorout: no visible global function definition for ‘pchisq’
.screenoutput: no visible global function definition for ‘png’
.screenoutput: no visible global function definition for ‘plot’
.screenoutput: no visible global function definition for ‘lines’
.screenoutput: no visible global function definition for ‘dev.off’
.sreport: no visible global function definition for ‘runif’
.treport: no visible global function definition for ‘runif’
Undefined global functions or variables:
arrows cov2cor dchisq dev.off lines par pchisq plot png points qchisq
qnorm quantile runif
Consider adding
importFrom("grDevices", "dev.off", "png")
importFrom("graphics", "arrows", "lines", "par", "plot", "points")
importFrom("stats", "cov2cor", "dchisq", "pchisq", "qchisq", "qnorm",
"quantile", "runif")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘rHVDM-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estimerrors
> ### Title: computes the standard deviation of the measurement error using
> ### pre-calculated tables specific to the plattform or user-defined table
> ### Aliases: estimerrors
> ### Keywords: IO ts
>
> ### ** Examples
>
> data(HVDMexample)
> fiveGybis<-estimerrors(eset=fiveGyMAS5,plattid="affy_HGU133A",refchips=leastnoisychips)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
rHVDM
--- call from context ---
.computeinderrtable(X = X, errtable = errtable, refchips = refs)
--- call from argument ---
if (refchips == 0) {
wei <- rep(0, m)
}
--- R stacktrace ---
where 1: .computeinderrtable(X = X, errtable = errtable, refchips = refs)
where 2: .computerrs(eset = eset, errtable = errtable, refs = refchips)
where 3: estimerrors(eset = fiveGyMAS5, plattid = "affy_HGU133A", refchips = leastnoisychips)
--- value of length: 3 type: logical ---
[1] FALSE FALSE FALSE
--- function from context ---
function (X, errtable, refchips)
{
N <- dim(X)[2]
if (missing(refchips)) {
refchips <- c(1:N)
}
m <- dim(errtable)[1]
res <- matrix(rep(0, m * N), m, N)
dimnames(res)[[2]] <- dimnames(X)[[2]]
coeffmul <- rep(1/N, N)
aver <- as.vector(X %*% coeffmul)
difsq <- (X - aver)^2
bnds <- c(-20, errtable[, 1])
for (i in c(1:(m - 1))) {
bnds[i + 1] <- errtable[i, 1]/2 + errtable[i + 1, 1]/2
}
bnds[m + 1] <- log(max(aver) + 1)
if (refchips == 0) {
wei <- rep(0, m)
}
for (i in c(1:m)) {
keep <- ((log(aver) > bnds[i]) & (log(aver) <= bnds[i +
1]))
ngenes <- sum(keep * 1)
coe <- rep(1/ngenes, ngenes)
res[i, ] <- as.vector(t(difsq[keep, ]) %*% coe)
if (refchips == 0) {
wei[i] <- ngenes
}
}
if (refchips == 0) {
refchips <- .retlessnoisy(X = res, weight = wei, N = 3)
print(refchips)
}
nref <- length(refchips)
coe <- rep(1/nref, nref)
avrefchi <- res[, refchips] %*% coe
ratio <- as.vector(errtable[, 2]/avrefchi)
res <- cbind(errtable[, 1], res * ratio)
dimnames(res)[[2]][1] <- "avg"
res
}
<bytecode: 0x7fde2e54a618>
<environment: namespace:rHVDM>
--- function search by body ---
Function .computeinderrtable in namespace rHVDM has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
* 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: 1 ERROR, 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/rHVDM.Rcheck/00check.log’
for details.
Installation output
rHVDM.Rcheck/00install.out
Tests output
Example timings
rHVDM.Rcheck/rHVDM-Ex.timings