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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SVAPLSseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings SVAPLSseq_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/SVAPLSseq.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SVAPLSseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SVAPLSseq' version '1.16.0'
* 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 'SVAPLSseq' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'SVAPLSseq' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/SVAPLSseq.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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'SVAPLSseq-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SVAPLSseq-package
> ### Title: SVAPLSseq: An R package to adjust for the hidden factors of
> ### variability in differential gene expression studies based on RNAseq
> ### data.
> ### Aliases: SVAPLSseq-package SVAPLSseq
> ### Keywords: models
>
> ### ** Examples
>
> ##Loading the Simulated Data
> data(sim.dat)
>
> ## Fitting a linear model with the surrogate variables and detecting the differentially expressed genes
> group = as.factor(c(rep(1, 10), rep(-1, 10)))
> sv <- svplsSurr(dat = sim.dat, group = group, surr.select = "automatic")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SVAPLSseq
--- call from context ---
svplsSurr(dat = sim.dat, group = group, surr.select = "automatic")
--- call from argument ---
if (class(dat) == "matrix") data = dat
--- R stacktrace ---
where 1: svplsSurr(dat = sim.dat, group = group, surr.select = "automatic")
--- value of length: 2 type: logical ---
[1] TRUE FALSE
--- function from context ---
function (dat, group, controls = NULL, phi = function(x) log(x +
const), const = 1, pls.method = "oscorespls", max.surrs = 3,
opt.surrs = 1, surr.select = c("automatic", "manual"), cutoff = 10^-7,
parallel = FALSE, num.cores = NULL, plot = FALSE)
{
if (class(dat) == "matrix")
data = dat
if (class(dat) == "SummarizedExperiment")
data = assay(dat)
if (class(dat) == "DGEList")
data = dat$counts
Y = phi(data)
if (parallel) {
e = unlist(mclapply(1:nrow(Y), function(u) lm(Y[u, ] ~
group)$resid, mc.cores = num.cores))
}
if (!parallel)
e = unlist(lapply(1:nrow(Y), function(u) lm(Y[u, ] ~
group)$resid))
E = matrix(e, nrow(Y), ncol(Y), byrow = TRUE)
if (!is.null(controls))
pls.fit = mvr(t(Y) ~ t(Y[controls, ]), ncomp = max.surrs,
method = pls.method)
if (is.null(controls))
pls.fit = mvr(t(E) ~ t(Y), ncomp = max.surrs, method = pls.method)
sc = scores(pls.fit)
surr.effect = paste("+", paste("sc[, ", paste(as.character(1:ncol(sc)),
"]", sep = ""), sep = "", collapse = "+"), sep = "")
if (surr.select == "automatic") {
if (!is.null(controls))
pvals = anova(lm(as.formula(paste("svd(Y[controls, ])$v[, 1] ~",
surr.effect, sep = " "))))[, 5]
if (is.null(controls))
pvals = anova(lm(as.formula(paste("svd(E)$v[, 1] ~",
surr.effect, sep = " "))))[, 5]
index = which(pvals < cutoff)
}
if (surr.select == "manual")
index = opt.surrs
if (length(index) == 0)
stop("No Significant Surrogate Variables")
if (length(index) > 0) {
surr = sc[, index]
if (length(index) == 1)
vars = var(surr)
if (length(index) > 1)
vars = apply(surr, 2, var)
prop.vars = vars/sum(vars)
if (plot == TRUE) {
surr.df = as.data.frame(surr[, 1:max.surrs])
colnames(surr.df) = paste("surr", as.character(1:max.surrs),
sep = "")
grp = factor(colnames(surr.df), levels = colnames(surr.df))
bp.df = data.frame(grp, prop.vars)
bp <- qplot(grp, data = bp.df, geom = "bar", weight = prop.vars) +
scale_x_discrete("Surrogate Variable") + scale_y_continuous("Explained Variance Proportion")
bp + theme(axis.text.x = element_text(angle = 0,
hjust = 1))
}
res = new("svplsSurr", surr = surr, prop.vars = prop.vars)
}
return(res)
}
<bytecode: 0x1b1c3520>
<environment: namespace:SVAPLSseq>
--- function search by body ---
Function svplsSurr in namespace SVAPLSseq has this body.
----------- END OF FAILURE REPORT --------------
Fatal error: the condition has length > 1
** running examples for arch 'x64' ... ERROR
Running examples in 'SVAPLSseq-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SVAPLSseq-package
> ### Title: SVAPLSseq: An R package to adjust for the hidden factors of
> ### variability in differential gene expression studies based on RNAseq
> ### data.
> ### Aliases: SVAPLSseq-package SVAPLSseq
> ### Keywords: models
>
> ### ** Examples
>
> ##Loading the Simulated Data
> data(sim.dat)
>
> ## Fitting a linear model with the surrogate variables and detecting the differentially expressed genes
> group = as.factor(c(rep(1, 10), rep(-1, 10)))
> sv <- svplsSurr(dat = sim.dat, group = group, surr.select = "automatic")
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
SVAPLSseq
--- call from context ---
svplsSurr(dat = sim.dat, group = group, surr.select = "automatic")
--- call from argument ---
if (class(dat) == "matrix") data = dat
--- R stacktrace ---
where 1: svplsSurr(dat = sim.dat, group = group, surr.select = "automatic")
--- value of length: 2 type: logical ---
[1] TRUE FALSE
--- function from context ---
function (dat, group, controls = NULL, phi = function(x) log(x +
const), const = 1, pls.method = "oscorespls", max.surrs = 3,
opt.surrs = 1, surr.select = c("automatic", "manual"), cutoff = 10^-7,
parallel = FALSE, num.cores = NULL, plot = FALSE)
{
if (class(dat) == "matrix")
data = dat
if (class(dat) == "SummarizedExperiment")
data = assay(dat)
if (class(dat) == "DGEList")
data = dat$counts
Y = phi(data)
if (parallel) {
e = unlist(mclapply(1:nrow(Y), function(u) lm(Y[u, ] ~
group)$resid, mc.cores = num.cores))
}
if (!parallel)
e = unlist(lapply(1:nrow(Y), function(u) lm(Y[u, ] ~
group)$resid))
E = matrix(e, nrow(Y), ncol(Y), byrow = TRUE)
if (!is.null(controls))
pls.fit = mvr(t(Y) ~ t(Y[controls, ]), ncomp = max.surrs,
method = pls.method)
if (is.null(controls))
pls.fit = mvr(t(E) ~ t(Y), ncomp = max.surrs, method = pls.method)
sc = scores(pls.fit)
surr.effect = paste("+", paste("sc[, ", paste(as.character(1:ncol(sc)),
"]", sep = ""), sep = "", collapse = "+"), sep = "")
if (surr.select == "automatic") {
if (!is.null(controls))
pvals = anova(lm(as.formula(paste("svd(Y[controls, ])$v[, 1] ~",
surr.effect, sep = " "))))[, 5]
if (is.null(controls))
pvals = anova(lm(as.formula(paste("svd(E)$v[, 1] ~",
surr.effect, sep = " "))))[, 5]
index = which(pvals < cutoff)
}
if (surr.select == "manual")
index = opt.surrs
if (length(index) == 0)
stop("No Significant Surrogate Variables")
if (length(index) > 0) {
surr = sc[, index]
if (length(index) == 1)
vars = var(surr)
if (length(index) > 1)
vars = apply(surr, 2, var)
prop.vars = vars/sum(vars)
if (plot == TRUE) {
surr.df = as.data.frame(surr[, 1:max.surrs])
colnames(surr.df) = paste("surr", as.character(1:max.surrs),
sep = "")
grp = factor(colnames(surr.df), levels = colnames(surr.df))
bp.df = data.frame(grp, prop.vars)
bp <- qplot(grp, data = bp.df, geom = "bar", weight = prop.vars) +
scale_x_discrete("Surrogate Variable") + scale_y_continuous("Explained Variance Proportion")
bp + theme(axis.text.x = element_text(angle = 0,
hjust = 1))
}
res = new("svplsSurr", surr = surr, prop.vars = prop.vars)
}
return(res)
}
<bytecode: 0x0000000015d79b90>
<environment: namespace:SVAPLSseq>
--- function search by body ---
Function svplsSurr in namespace SVAPLSseq 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: 2 ERRORs, 1 WARNING
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/SVAPLSseq.Rcheck/00check.log'
for details.