MergeMaid 2.60.0
Xiaogang Zhong
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/MergeMaid |
| Branch: RELEASE_3_11 |
| Last Commit: 3a02f39 |
| Last Changed Date: 2020-04-27 14:10:04 -0400 (Mon, 27 Apr 2020) |
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | ERROR | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MergeMaid.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MergeMaid_2.60.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MergeMaid.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MergeMaid/DESCRIPTION' ... OK
* this is package 'MergeMaid' version '2.60.0'
* 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 whether package 'MergeMaid' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'MergeMaid' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MergeMaid.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Packages in Depends field not imported from:
'MASS' 'methods' 'survival'
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
.dens.mergeExpressionSet: no visible global function definition for
'density'
.fdr.mergeCor: no visible global function definition for '.getnull'
.fdr.mergeCor: no visible global function definition for 'approxfun'
.fdr.mergeCor: no visible global function definition for 'density'
.fdr.mergeCor: no visible global function definition for 'integrate'
.ic.plot : norm: no visible global function definition for 'sd'
.ic.plot: no visible global function definition for 'cov'
.icor : norm: no visible global function definition for 'sd'
.icor: no visible global function definition for 'cov'
.intcor : norm: no visible global function definition for 'sd'
.intcor: no visible global function definition for 'new'
.integ.cal : sziicor: no visible global function definition for 'cor'
.mergemodel: no visible global function definition for 'lm'
.mergemodel: no visible binding for global variable 'na.omit'
.mergemodel: no visible global function definition for 'coxph'
.mergemodel: no visible global function definition for 'sd'
.mergemodel: no visible global function definition for 'glm'
.mergemodel: no visible binding for global variable 'binomial'
.model.outcome: no visible global function definition for 'new'
.nullicornorm : norm: no visible global function definition for 'sd'
.nullicornorm: no visible global function definition for 'cov'
.nullicornorm : getone: no visible global function definition for
'rnorm'
maxintcor: no visible global function definition for 'cov'
maxintcor: no visible global function definition for 'ginv'
mergeExprs: no visible global function definition for 'new'
mergeget: no visible global function definition for 'new'
subsetmES: no visible global function definition for 'new'
intersection,mergeExpressionSet: no visible global function definition
for 'new'
Undefined global functions or variables:
.getnull approxfun binomial cor cov coxph density ginv glm integrate
lm na.omit new rnorm sd
Consider adding
importFrom("methods", "new")
importFrom("stats", "approxfun", "binomial", "cor", "cov", "density",
"glm", "integrate", "lm", "na.omit", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'mergeExpressionSet,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'MergeMaid-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mergeCor
> ### Title: Class mergeCor, a class for storing data relevant to integrative
> ### correlation coefficients.
> ### Aliases: mergeCor-class mergeCor pairwise.cors integrative.cors
> ### pairwise.cors,mergeCor-method integrative.cors,mergeCor-method
> ### maxcors,mergeCor-method hist,mergeCor-method plot,list-method
> ### notes,mergeCor-method hist plot maxcors
> ### Keywords: classes
>
> ### ** Examples
>
> if(require(Biobase) & require(MASS)){
+ data(mergeData)
+ merged <- mergeExprs(sample1,sample2,sample3)
+ intcor3 <-intCor(merged,method="pearson")
+ plot(merged)
+ intcor2 <-intCor(merged[1:2],exact=FALSE)
+ plot(merged,pch=4,col=5)
+
+ pairwise.cors(intcor3)
+ integrative.cors(intcor3)
+ integrative.cors(intcor2)["Hs.12101"]
+ maxcors(intcor2)
+ }
----------- FAILURE REPORT --------------
--- failure: length > 1 in coercion to logical ---
--- srcref ---
:
--- package (from environment) ---
MergeMaid
--- call from context ---
.intcor(x = x, method = method, exact = exact, ...)
--- call from argument ---
method != "pearson" && !exact
--- R stacktrace ---
where 1: .intcor(x = x, method = method, exact = exact, ...)
where 2: intCor(merged[1:2], exact = FALSE)
where 3: intCor(merged[1:2], exact = FALSE)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (x, method = "pearson", exact = TRUE)
{
nn <- length(x)
if (nn <= 1)
stop("Number of studies in the mergeExpressionSet should not less than 2.")
if (method != "pearson" && !exact)
stop("When exact is FALSE, you can only use the method ''pearson''.")
if (method != "pearson" && method != "spearman" && exact)
stop("When exact is TRUE, you can only use the methods, ''pearson'' and ''spearman''.")
geneid <- rep(1, nrow(x@geneStudy))
for (i in 1:nn) {
geneid <- geneid * (x@geneStudy[, i])
}
geneuid <- geneNames(x)[geneid == 1]
nuid <- length(geneuid)
pcor <- alist(... = )
nnote <- rep(NA, nn)
for (i in 1:nn) {
matches1 <- match(geneuid, featureNames(exprs(x)[[i]]))
pcor[[i]] <- assayData(exprs(x)[[i]])[["exprs"]][matches1,
]
if (method == "spearman" && exact)
pcor[[i]] <- t(apply(pcor[[i]], 1, .intcor.order))
nnote[i] <- paste("study", i, sep = " ")
}
names(pcor) <- names(x)
np <- nn * (nn - 1)/2
ppair <- matrix(0, np, 2)
k <- 1
for (i in 1:(nn - 1)) {
for (j in (i + 1):nn) {
ppair[k, ] <- c(i, j)
k <- k + 1
}
}
norm = function(x) return((x - mean(x, na.rm = TRUE))/sd(x,
na.rm = TRUE))
icor <- matrix(NA, nuid, np)
canc <- rep(0, np)
for (i in 1:np) {
CC1 <- pcor[[ppair[i, 1]]]
CC2 <- pcor[[ppair[i, 2]]]
if (exact)
icor[, i] <- .integ.cal(CC1, CC2, method = method)
else icor[, i] <- .icor(CC1, CC2, method = method)
A = t(apply(CC1, 1, norm))
B = t(apply(CC2, 1, norm))
canc[i] <- maxintcor(A, B)
}
rownames(icor) <- geneuid
labels <- names(x)
if (is.null(labels))
labels = ""
result <- new("mergeCor", pairwise.cors = icor, notes = labels,
maxcors = canc)
return(result)
}
<bytecode: 0x06889970>
<environment: namespace:MergeMaid>
--- function search by body ---
Function .intcor in namespace MergeMaid has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: length > 1 in coercion to logical
** running examples for arch 'x64' ... ERROR
Running examples in 'MergeMaid-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mergeCor
> ### Title: Class mergeCor, a class for storing data relevant to integrative
> ### correlation coefficients.
> ### Aliases: mergeCor-class mergeCor pairwise.cors integrative.cors
> ### pairwise.cors,mergeCor-method integrative.cors,mergeCor-method
> ### maxcors,mergeCor-method hist,mergeCor-method plot,list-method
> ### notes,mergeCor-method hist plot maxcors
> ### Keywords: classes
>
> ### ** Examples
>
> if(require(Biobase) & require(MASS)){
+ data(mergeData)
+ merged <- mergeExprs(sample1,sample2,sample3)
+ intcor3 <-intCor(merged,method="pearson")
+ plot(merged)
+ intcor2 <-intCor(merged[1:2],exact=FALSE)
+ plot(merged,pch=4,col=5)
+
+ pairwise.cors(intcor3)
+ integrative.cors(intcor3)
+ integrative.cors(intcor2)["Hs.12101"]
+ maxcors(intcor2)
+ }
----------- FAILURE REPORT --------------
--- failure: length > 1 in coercion to logical ---
--- srcref ---
:
--- package (from environment) ---
MergeMaid
--- call from context ---
.intcor(x = x, method = method, exact = exact, ...)
--- call from argument ---
method != "pearson" && !exact
--- R stacktrace ---
where 1: .intcor(x = x, method = method, exact = exact, ...)
where 2: intCor(merged[1:2], exact = FALSE)
where 3: intCor(merged[1:2], exact = FALSE)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (x, method = "pearson", exact = TRUE)
{
nn <- length(x)
if (nn <= 1)
stop("Number of studies in the mergeExpressionSet should not less than 2.")
if (method != "pearson" && !exact)
stop("When exact is FALSE, you can only use the method ''pearson''.")
if (method != "pearson" && method != "spearman" && exact)
stop("When exact is TRUE, you can only use the methods, ''pearson'' and ''spearman''.")
geneid <- rep(1, nrow(x@geneStudy))
for (i in 1:nn) {
geneid <- geneid * (x@geneStudy[, i])
}
geneuid <- geneNames(x)[geneid == 1]
nuid <- length(geneuid)
pcor <- alist(... = )
nnote <- rep(NA, nn)
for (i in 1:nn) {
matches1 <- match(geneuid, featureNames(exprs(x)[[i]]))
pcor[[i]] <- assayData(exprs(x)[[i]])[["exprs"]][matches1,
]
if (method == "spearman" && exact)
pcor[[i]] <- t(apply(pcor[[i]], 1, .intcor.order))
nnote[i] <- paste("study", i, sep = " ")
}
names(pcor) <- names(x)
np <- nn * (nn - 1)/2
ppair <- matrix(0, np, 2)
k <- 1
for (i in 1:(nn - 1)) {
for (j in (i + 1):nn) {
ppair[k, ] <- c(i, j)
k <- k + 1
}
}
norm = function(x) return((x - mean(x, na.rm = TRUE))/sd(x,
na.rm = TRUE))
icor <- matrix(NA, nuid, np)
canc <- rep(0, np)
for (i in 1:np) {
CC1 <- pcor[[ppair[i, 1]]]
CC2 <- pcor[[ppair[i, 2]]]
if (exact)
icor[, i] <- .integ.cal(CC1, CC2, method = method)
else icor[, i] <- .icor(CC1, CC2, method = method)
A = t(apply(CC1, 1, norm))
B = t(apply(CC2, 1, norm))
canc[i] <- maxintcor(A, B)
}
rownames(icor) <- geneuid
labels <- names(x)
if (is.null(labels))
labels = ""
result <- new("mergeCor", pairwise.cors = icor, notes = labels,
maxcors = canc)
return(result)
}
<bytecode: 0x000000000c122068>
<environment: namespace:MergeMaid>
--- function search by body ---
Function .intcor in namespace MergeMaid has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: length > 1 in coercion to logical
* 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 ERRORs, 2 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/MergeMaid.Rcheck/00check.log'
for details.